Publications 2020

@article{morales_genotypic_2020,
	title = {Genotypic and phenotypic characterization of a large, diverse population of maize near-isogenic lines},
	volume = {103},
	copyright = {© 2020 Society for Experimental Biology and John Wiley \& Sons Ltd},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.14787},
	doi = {10.1111/tpj.14787},
	abstract = {Genome-wide association (GWA) studies can identify quantitative trait loci (QTL) putatively underlying traits of interest, and nested association mapping (NAM) can further assess allelic series. Near-isogenic lines (NILs) can be used to characterize, dissect and validate QTL, but the development of NILs is costly. Previous studies have utilized limited numbers of NILs and introgression donors. We characterized a panel of 1270 maize NILs derived from crosses between 18 diverse inbred lines and the recurrent inbred parent B73, referred to as the nested NILs (nNILs). The nNILs were phenotyped for flowering time, height and resistance to three foliar diseases, and genotyped with genotyping-by-sequencing. Across traits, broad-sense heritability (0.4–0.8) was relatively high. The 896 genotyped nNILs contain 2638 introgressions, which span the entire genome with substantial overlap within and among allele donors. GWA with the whole panel identified 29 QTL for height and disease resistance with allelic variation across donors. To date, this is the largest and most diverse publicly available panel of maize NILs to be phenotypically and genotypically characterized. The nNILs are a valuable resource for the maize community, providing an extensive collection of introgressions from the founders of the maize NAM population in a B73 background combined with data on six agronomically important traits and from genotyping-by-sequencing. We demonstrate that the nNILs can be used for QTL mapping and allelic testing. The majority of nNILs had four or fewer introgressions, and could readily be used for future fine mapping studies.},
	language = {en},
	number = {3},
	urldate = {2024-03-22},
	journal = {The Plant Journal},
	author = {Morales, Laura and Repka, A. C. and Swarts, Kelly L. and Stafstrom, William C. and He, Yijian and Sermons, Shannon M. and Yang, Qin and Lopez-Zuniga, Luis O. and Rucker, Elizabeth and Thomason, Wade E. and Nelson, Rebecca J. and Balint-Kurti, Peter J.},
	year = {2020},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.14787},
	keywords = {Zea mays, allelic analysis, disease resistance, flowering time, genetics, genome-wide association, genotyping-by-sequencing, maize, near-isogenic lines, plant height, quantitative trait loci},
	pages = {1246--1255},
}

Genome-wide association (GWA) studies can identify quantitative trait loci (QTL) putatively underlying traits of interest, and nested association mapping (NAM) can further assess allelic series. Near-isogenic lines (NILs) can be used to characterize, dissect and validate QTL, but the development of NILs is costly. Previous studies have utilized limited numbers of NILs and introgression donors. We characterized a panel of 1270 maize NILs derived from crosses between 18 diverse inbred lines and the recurrent inbred parent B73, referred to as the nested NILs (nNILs). The nNILs were phenotyped for flowering time, height and resistance to three foliar diseases, and genotyped with genotyping-by-sequencing. Across traits, broad-sense heritability (0.4–0.8) was relatively high. The 896 genotyped nNILs contain 2638 introgressions, which span the entire genome with substantial overlap within and among allele donors. GWA with the whole panel identified 29 QTL for height and disease resistance with allelic variation across donors. To date, this is the largest and most diverse publicly available panel of maize NILs to be phenotypically and genotypically characterized. The nNILs are a valuable resource for the maize community, providing an extensive collection of introgressions from the founders of the maize NAM population in a B73 background combined with data on six agronomically important traits and from genotyping-by-sequencing. We demonstrate that the nNILs can be used for QTL mapping and allelic testing. The majority of nNILs had four or fewer introgressions, and could readily be used for future fine mapping studies.

@article{zhou_co-incidence_2020,
	title = {Co-incidence of {Damage} and {Microbial} {Patterns} {Controls} {Localized} {Immune} {Responses} in {Roots}},
	volume = {180},
	issn = {00928674},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S009286742030060X},
	doi = {10.1016/j.cell.2020.01.013},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Cell},
	author = {Zhou, Feng and Emonet, Aurélia and Dénervaud Tendon, Valérie and Marhavý, Peter and Wu, Dousheng and Lahaye, Thomas and Geldner, Niko},
	month = feb,
	year = {2020},
	pages = {440--453.e18},
}

@article{wang_monomer_2020,
	title = {Monomer {Structural} {Stability} of a {Tau} {Class} {Glutathione} {Transferase} ({PtGSTU1}) from \textit{{Pinus} tabulaeformis}},
	volume = {33},
	issn = {1001-1498},
	url = {http://www.lykxyj.com/en/article/doi/10.13275/j.cnki.lykxyj.2020.02.001},
	doi = {10.13275/j.cnki.lykxyj.2020.02.001},
	number = {2},
	urldate = {2023-04-27},
	journal = {林业科学研究},
	author = {Wang, Xiao-Xia and Yang, Hai-Ling and Mao, Jian-Feng and Wang, Xiao-Ru},
	month = mar,
	year = {2020},
	note = {Publisher: 林业科学研究},
	pages = {1--8},
}

@article{sun_genetic_2020,
	title = {Genetic {Variation} {Related} to {High} {Elevation} {Adaptation} {Revealed} by {Common} {Garden} {Experiments} in {Pinus} yunnanensis},
	volume = {10},
	issn = {1664-8021},
	url = {https://www.frontiersin.org/articles/10.3389/fgene.2019.01405},
	doi = {10.3389/fgene.2019.01405},
	abstract = {Local adaptation, adaptation to specialized niches and environmental clines have been extensively reported for forest trees. Investigation of the adaptive genetic variation is crucial for forest resource management and breeding, especially in the context of global climate change. Here, we utilized a Pinus yunnanensis common garden experiments established at high and low elevation sites to assess the differences in growth and survival among populations and between the two common garden sites. The studied traits showed significant variation between the two test sites and among populations, suggesting adaptive divergence. To detect genetic variation related to environment, we captured 103,608 high quality SNPs based on RNA sequencing, and used them to assess the genetic diversity and population structure. We identified 321 outlier SNPs from 131 genes showing significant divergence in allelic frequency between survival populations of two sites. Functional categories associated with adaptation to high elevation were found to be related to flavonoid biosynthesis, response to UV, DNA repair, response to reactive oxygen species, and membrane lipid metabolic process. Further investigation of the outlier genes showed overrepresentation of the flavonoid biosynthesis pathway, suggesting that this pathway may play a key role in P. yunnanensis adaptation to high elevation environments. The outlier genes identified, and their variants, provide a basic reference for advanced investigations.},
	urldate = {2023-04-27},
	journal = {Frontiers in Genetics},
	author = {Sun, Yan-Qiang and Zhao, Wei and Xu, Chao-Qun and Xu, Yulan and El-Kassaby, Yousry A. and De La Torre, Amanda R. and Mao, Jian-Feng},
	year = {2020},
}

Local adaptation, adaptation to specialized niches and environmental clines have been extensively reported for forest trees. Investigation of the adaptive genetic variation is crucial for forest resource management and breeding, especially in the context of global climate change. Here, we utilized a Pinus yunnanensis common garden experiments established at high and low elevation sites to assess the differences in growth and survival among populations and between the two common garden sites. The studied traits showed significant variation between the two test sites and among populations, suggesting adaptive divergence. To detect genetic variation related to environment, we captured 103,608 high quality SNPs based on RNA sequencing, and used them to assess the genetic diversity and population structure. We identified 321 outlier SNPs from 131 genes showing significant divergence in allelic frequency between survival populations of two sites. Functional categories associated with adaptation to high elevation were found to be related to flavonoid biosynthesis, response to UV, DNA repair, response to reactive oxygen species, and membrane lipid metabolic process. Further investigation of the outlier genes showed overrepresentation of the flavonoid biosynthesis pathway, suggesting that this pathway may play a key role in P. yunnanensis adaptation to high elevation environments. The outlier genes identified, and their variants, provide a basic reference for advanced investigations.

@article{jiao_development_2020,
	title = {Development of a {Large} {Gene}-{Associated} {SSR} {Marker} {Set} and in-{Depth} {Genetic} {Characterization} in {Scarlet} {Sage}},
	volume = {11},
	issn = {1664-8021},
	url = {https://www.frontiersin.org/articles/10.3389/fgene.2020.00504},
	doi = {10.3389/fgene.2020.00504},
	abstract = {Salvia splendens, scarlet or tropical sage, is a tender perennial herbaceous flowering plant popularly grown in public and private gardens all over the world. In this study, we developed a set of simple sequence repeats (SSRs) from genome-wide sequences to assess the genetic diversity and population structure among 112 cultivars. We obtained 364,379 SSRs by mining scarlet sage’s recently published whole genome sequence; 14,545 gene-associated SSR loci were identified in 2 kb gene flanking regions. Among the 768 gene-associated SSR primer sets we screened, 576 loci successfully amplified in DNA pools of 3–4 different cultivars, of which 271 remained polymorphic when tested across eight individual plants. We searched for the related gene functions attributable to these gene-associated SSRs using diverse databases, resulting in 259 Non-redundant matching sequences, 205 individual Gene Ontology (GO) terms, 236 assigned to eukaryotic orthologous groups, and 67 KEGG-annotated (Kyoto Encyclopedia of Genes and Genomes) sequences. We finally selected 41 polymorphic SSR loci to infer genetic diversity and population structure among 112 S. splendens accessions. Based on the developed gene-associated SSRs, clustering analyses consistently revealed two distinct genetic groups within the core collection of S. splendens cultivars. This work developed and characterized an exhaustive set of genome-wide gene-associated SSR markers for scarlet sage. These SSRs can provide species identification, genetic diversity and population structure information for S. splendens, and will therefore be important tools for the management and protection of S. splendens germplasm.},
	urldate = {2023-04-27},
	journal = {Frontiers in Genetics},
	author = {Jiao, Si-Qian and Dong, Ai-Xiang and Shi, Tian-Le and Liu, Hui and Porth, Ilga and Xin, Hai-Bo and Mao, Jian-Feng},
	year = {2020},
}

Salvia splendens, scarlet or tropical sage, is a tender perennial herbaceous flowering plant popularly grown in public and private gardens all over the world. In this study, we developed a set of simple sequence repeats (SSRs) from genome-wide sequences to assess the genetic diversity and population structure among 112 cultivars. We obtained 364,379 SSRs by mining scarlet sage’s recently published whole genome sequence; 14,545 gene-associated SSR loci were identified in 2 kb gene flanking regions. Among the 768 gene-associated SSR primer sets we screened, 576 loci successfully amplified in DNA pools of 3–4 different cultivars, of which 271 remained polymorphic when tested across eight individual plants. We searched for the related gene functions attributable to these gene-associated SSRs using diverse databases, resulting in 259 Non-redundant matching sequences, 205 individual Gene Ontology (GO) terms, 236 assigned to eukaryotic orthologous groups, and 67 KEGG-annotated (Kyoto Encyclopedia of Genes and Genomes) sequences. We finally selected 41 polymorphic SSR loci to infer genetic diversity and population structure among 112 S. splendens accessions. Based on the developed gene-associated SSRs, clustering analyses consistently revealed two distinct genetic groups within the core collection of S. splendens cultivars. This work developed and characterized an exhaustive set of genome-wide gene-associated SSR markers for scarlet sage. These SSRs can provide species identification, genetic diversity and population structure information for S. splendens, and will therefore be important tools for the management and protection of S. splendens germplasm.

@incollection{yan_terpene_2020,
	address = {Cham},
	series = {Compendium of {Plant} {Genomes}},
	title = {The {Terpene} {Synthase} {Gene} {Family} in {Norway} {Spruce}},
	isbn = {978-3-030-21001-4},
	url = {https://doi.org/10.1007/978-3-030-21001-4_11},
	abstract = {Terpenes (isoprenes) represent a diverse group of chemical compounds that plants produce during normal development (e.g., phytohormones), and mostly as secondary metabolites with important roles in defense responses against diverse environmental stressors, either abiotic or biotic in nature. Studies with an aspect on conifer-derived terpenes have highlighted some of the underlying metabolic and molecular mechanisms in the implicated defense processes. Terpene synthases (TPSs), being the core enzymes for terpenes’ functional diversity, therefore, gained attention as the key elements for molecular terpene studies. Norway spruce (Picea abies) is arguably Europe’s native conifer with the most substantial economic and ecological value given its vast geographic distribution throughout the continent as an indigenous species and, introduced, as an important plantation species outside its natural range. In this study, we aimed at retrieving TPS genes from the genomes of Norway spruce and, in addition, of representative land plant lineages in order to resolve their phylogenetic relationship. We show that the majority of TPS genes from gymnosperms are distributed within the TPS-d subfamily. As expected, the “DDXXD” and the “RXR” motifs are highly conserved for TPS in general, and the structural characteristics of closely related TPS genes are highly similar. Concrete subfamily membership along with shared structural molecular properties was the main driver of gene expression variation among Norway spruce TPSs, indicating important functional divergence. In this study, the two key factors within TPS gene structure that were related to differential TPS gene expression were found to be motif composition and intron size. Our study is valuable for further in-depth functional evaluation of these additionally uncovered spruce TPSs and will support future efforts in metabolic engineering involving terpenes.},
	language = {en},
	urldate = {2023-04-27},
	booktitle = {The {Spruce} {Genome}},
	publisher = {Springer International Publishing},
	author = {Yan, Xue-Mei and Zhou, Shan-Shan and Porth, Ilga M. and Mao, Jian-Feng},
	editor = {Porth, Ilga M. and De la Torre, Amanda R.},
	year = {2020},
	doi = {10.1007/978-3-030-21001-4_11},
	keywords = {Conserved motif, Functional divergence, Gene expression, Gene structure, Picea abies, Terpene synthase},
	pages = {177--192},
}

Terpenes (isoprenes) represent a diverse group of chemical compounds that plants produce during normal development (e.g., phytohormones), and mostly as secondary metabolites with important roles in defense responses against diverse environmental stressors, either abiotic or biotic in nature. Studies with an aspect on conifer-derived terpenes have highlighted some of the underlying metabolic and molecular mechanisms in the implicated defense processes. Terpene synthases (TPSs), being the core enzymes for terpenes’ functional diversity, therefore, gained attention as the key elements for molecular terpene studies. Norway spruce (Picea abies) is arguably Europe’s native conifer with the most substantial economic and ecological value given its vast geographic distribution throughout the continent as an indigenous species and, introduced, as an important plantation species outside its natural range. In this study, we aimed at retrieving TPS genes from the genomes of Norway spruce and, in addition, of representative land plant lineages in order to resolve their phylogenetic relationship. We show that the majority of TPS genes from gymnosperms are distributed within the TPS-d subfamily. As expected, the “DDXXD” and the “RXR” motifs are highly conserved for TPS in general, and the structural characteristics of closely related TPS genes are highly similar. Concrete subfamily membership along with shared structural molecular properties was the main driver of gene expression variation among Norway spruce TPSs, indicating important functional divergence. In this study, the two key factors within TPS gene structure that were related to differential TPS gene expression were found to be motif composition and intron size. Our study is valuable for further in-depth functional evaluation of these additionally uncovered spruce TPSs and will support future efforts in metabolic engineering involving terpenes.

@article{zhao_effects_2020,
	title = {Effects of landscapes and range expansion on population structure and local adaptation},
	volume = {228},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.16619},
	doi = {10.1111/nph.16619},
	abstract = {Understanding the origin and distribution of genetic diversity across landscapes is critical for predicting the future of organisms in changing climates. This study investigated how adaptive and demographic forces have shaped diversity and population structure in Pinus densata, a keystone species on Qinghai-Tibetan Plateau (QTP). We examined the distribution of genomic diversity across the range of P. densata using exome capture sequencing. We applied spatially explicit tests to dissect the impacts of allele surfing, geographic isolation and environmental gradients on population differentiation and forecasted how this genetic legacy may limit the persistence of P. densata in future climates. We found that allele surfing from range expansion could explain the distribution of 39\% of the c. 48 000 genotyped single nucleotide polymorphisms (SNPs). Uncorrected, these allele frequency clines severely confounded inferences of selection. After controlling for demographic processes, isolation-by-environment explained 9.2–19.5\% of the genetic structure, with c. 4.0\% of loci being affected by selection. Allele surfing and genotype–environment associations resulted in genomic mismatch under projected climate scenarios. We illustrate that significant local adaptation, when coupled with reduced diversity as a result of demographic history, constrains potential evolutionary response to climate change. The strong signal of genomic vulnerability in P. densata may be representative for other QTP endemics.},
	language = {en},
	number = {1},
	urldate = {2023-04-27},
	journal = {New Phytologist},
	author = {Zhao, Wei and Sun, Yan-Qiang and Pan, Jin and Sullivan, Alexis R. and Arnold, Michael L. and Mao, Jian-Feng and Wang, Xiao-Ru},
	year = {2020},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.16619},
	keywords = {Pinus densata, Qinghai-Tibetan Plateau, allele frequency cline, exome sequences, genomic mismatch, local adaptation, nucleotide diversity},
	pages = {330--343},
}

Understanding the origin and distribution of genetic diversity across landscapes is critical for predicting the future of organisms in changing climates. This study investigated how adaptive and demographic forces have shaped diversity and population structure in Pinus densata, a keystone species on Qinghai-Tibetan Plateau (QTP). We examined the distribution of genomic diversity across the range of P. densata using exome capture sequencing. We applied spatially explicit tests to dissect the impacts of allele surfing, geographic isolation and environmental gradients on population differentiation and forecasted how this genetic legacy may limit the persistence of P. densata in future climates. We found that allele surfing from range expansion could explain the distribution of 39% of the c. 48 000 genotyped single nucleotide polymorphisms (SNPs). Uncorrected, these allele frequency clines severely confounded inferences of selection. After controlling for demographic processes, isolation-by-environment explained 9.2–19.5% of the genetic structure, with c. 4.0% of loci being affected by selection. Allele surfing and genotype–environment associations resulted in genomic mismatch under projected climate scenarios. We illustrate that significant local adaptation, when coupled with reduced diversity as a result of demographic history, constrains potential evolutionary response to climate change. The strong signal of genomic vulnerability in P. densata may be representative for other QTP endemics.

@article{ma_acer_2020,
	title = {The {Acer} truncatum genome provides insights into nervonic acid biosynthesis},
	volume = {104},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.14954},
	doi = {10.1111/tpj.14954},
	abstract = {Acer truncatum (purpleblow maple) is a woody tree species that produces seeds with high levels of valuable fatty acids (especially nervonic acid). However, the lack of a complete genome sequence has limited both basic and applied research on A. truncatum. We describe a high-quality draft genome assembly comprising 633.28 Mb (contig N50 = 773.17 kb; scaffold N50 = 46.36 Mb) with at least 28 438 predicted genes. The genome underwent an ancient triplication, similar to the core eudicots, but there have been no recent whole-genome duplication events. Acer yangbiense and A. truncatum are estimated to have diverged about 9.4 million years ago. A combined genomic, transcriptomic, metabonomic, and cell ultrastructural analysis provided new insights into the biosynthesis of very long-chain monounsaturated fatty acids. In addition, three KCS genes were found that may contribute to regulating nervonic acid biosynthesis. The KCS paralogous gene family expanded to 28 members, with 10 genes clustered together and distributed in the 0.27-Mb region of pseudochromosome 4. Our chromosome-scale genomic characterization may facilitate the discovery of agronomically important genes and stimulate functional genetic research on A. truncatum. Furthermore, the data presented also offer important foundations from which to study the molecular mechanisms influencing the production of nervonic acids.},
	language = {en},
	number = {3},
	urldate = {2023-04-27},
	journal = {The Plant Journal},
	author = {Ma, Qiuyue and Sun, Tianlin and Li, Shushun and Wen, Jing and Zhu, Lu and Yin, Tongming and Yan, Kunyuan and Xu, Xiao and Li, Shuxian and Mao, Jianfeng and Wang, Ya-nan and Jin, Shuangxia and Zhao, Xing and Li, Qianzhong},
	year = {2020},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.14954},
	keywords = {Acer truncatum, KCS, de novo assembly, nervonic acid, very long-chain monounsaturated fatty acid},
	pages = {662--678},
}

Acer truncatum (purpleblow maple) is a woody tree species that produces seeds with high levels of valuable fatty acids (especially nervonic acid). However, the lack of a complete genome sequence has limited both basic and applied research on A. truncatum. We describe a high-quality draft genome assembly comprising 633.28 Mb (contig N50 = 773.17 kb; scaffold N50 = 46.36 Mb) with at least 28 438 predicted genes. The genome underwent an ancient triplication, similar to the core eudicots, but there have been no recent whole-genome duplication events. Acer yangbiense and A. truncatum are estimated to have diverged about 9.4 million years ago. A combined genomic, transcriptomic, metabonomic, and cell ultrastructural analysis provided new insights into the biosynthesis of very long-chain monounsaturated fatty acids. In addition, three KCS genes were found that may contribute to regulating nervonic acid biosynthesis. The KCS paralogous gene family expanded to 28 members, with 10 genes clustered together and distributed in the 0.27-Mb region of pseudochromosome 4. Our chromosome-scale genomic characterization may facilitate the discovery of agronomically important genes and stimulate functional genetic research on A. truncatum. Furthermore, the data presented also offer important foundations from which to study the molecular mechanisms influencing the production of nervonic acids.

@article{luo_complete_2020,
	title = {The complete mitochondrial genome of an endangered tree: {Malania} oleifera},
	volume = {5},
	issn = {null},
	shorttitle = {The complete mitochondrial genome of an endangered tree},
	url = {https://doi.org/10.1080/23802359.2020.1841583},
	doi = {10.1080/23802359.2020.1841583},
	abstract = {Malania oleifera is an endangered species found in restricted areas in Karst areas in Southwestern China and is also with significant economic and ecological values. Here, complete mitochondrial genome of M. oleifera was characterized, which is the first for the Olacaceae family. The mitogenome is 527,575 bp in length with a GC content of 45.65\%, including one pseudogene, and 38 protein-coding, 32 tRNA, three rRNA genes. Eleven genes have two copies in the mitogenome, and 3 genes are trans-spliced. Phylogenetic tree found that M. oleifera is making a sister branch to that of species from Rosids and Asterids.},
	number = {4},
	urldate = {2023-04-27},
	journal = {Mitochondrial DNA Part B},
	author = {Luo, Hang and Xu, Jie and Jiao, Si-Qian and Zhang, Ren-Gang and Mao, Jian-Feng},
	month = oct,
	year = {2020},
	pmid = {33426292},
	note = {Publisher: Taylor \& Francis
\_eprint: https://doi.org/10.1080/23802359.2020.1841583},
	keywords = {Malania oleifera, endangered species, mitochondrial genome},
	pages = {3829--3830},
}

Malania oleifera is an endangered species found in restricted areas in Karst areas in Southwestern China and is also with significant economic and ecological values. Here, complete mitochondrial genome of M. oleifera was characterized, which is the first for the Olacaceae family. The mitogenome is 527,575 bp in length with a GC content of 45.65%, including one pseudogene, and 38 protein-coding, 32 tRNA, three rRNA genes. Eleven genes have two copies in the mitogenome, and 3 genes are trans-spliced. Phylogenetic tree found that M. oleifera is making a sister branch to that of species from Rosids and Asterids.

@article{liu_tetracentron_2020,
	title = {The {Tetracentron} genome provides insight into the early evolution of eudicots and the formation of vessel elements},
	volume = {21},
	issn = {1474-760X},
	url = {https://doi.org/10.1186/s13059-020-02198-7},
	doi = {10.1186/s13059-020-02198-7},
	abstract = {Tetracentron sinense is an endemic and endangered deciduous tree. It belongs to the Trochodendrales, one of four early diverging lineages of eudicots known for having vesselless secondary wood. Sequencing and resequencing of the T. sinense genome will help us understand eudicot evolution, the genetic basis of tracheary element development, and the genetic diversity of this relict species.},
	number = {1},
	urldate = {2023-04-27},
	journal = {Genome Biology},
	author = {Liu, Ping-Li and Zhang, Xi and Mao, Jian-Feng and Hong, Yan-Ming and Zhang, Ren-Gang and E, Yilan and Nie, Shuai and Jia, Kaihua and Jiang, Chen-Kun and He, Jian and Shen, Weiwei and He, Qizouhong and Zheng, Wenqing and Abbas, Samar and Jewaria, Pawan Kumar and Tian, Xuechan and Liu, Chang-jun and Jiang, Xiaomei and Yin, Yafang and Liu, Bo and Wang, Li and Jin, Biao and Ma, Yongpeng and Qiu, Zongbo and Baluška, František and Šamaj, Jozef and He, Xinqiang and Niu, Shihui and Xie, Jianbo and Xie, Lei and Xu, Huimin and Kong, Hongzhi and Ge, Song and Dixon, Richard A. and Jiao, Yuannian and Lin, Jinxing},
	month = dec,
	year = {2020},
	keywords = {Genetic diversity, Phylogenomic, Resequencing, Tetracentron sinense, VND7, Vessel, Whole genome duplication},
	pages = {291},
}

Tetracentron sinense is an endemic and endangered deciduous tree. It belongs to the Trochodendrales, one of four early diverging lineages of eudicots known for having vesselless secondary wood. Sequencing and resequencing of the T. sinense genome will help us understand eudicot evolution, the genetic basis of tracheary element development, and the genetic diversity of this relict species.

@article{jia_landscape_2020,
	title = {Landscape genomics predicts climate change-related genetic offset for the widespread {Platycladus} orientalis ({Cupressaceae})},
	volume = {13},
	issn = {1752-4571},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/eva.12891},
	doi = {10.1111/eva.12891},
	abstract = {Understanding and quantifying populations' adaptive genetic variation and their response to climate change are critical to reforestation's seed source selection, forest management decisions, and gene conservation. Landscape genomics combined with geographic and environmental information provide an opportunity to interrogate forest populations' genome-wide variation for understanding the extent to which evolutionary forces shape past and contemporary populations' genetic structure, and identify those populations that may be most at risk under future climate change. Here, we used genotyping by sequencing to generate over 11,000 high-quality variants from Platycladus orientalis range-wide collection to evaluate its diversity and to predict genetic offset under future climate scenarios. Platycladus orientalis is a widespread conifer in China with significant ecological, timber, and medicinal values. We found population structure and evidences of isolation by environment, indicative of adaptation to local conditions. Gradient forest modeling identified temperature-related variables as the most important environmental factors influencing genetic variation and predicted areas with higher risk under future climate change. This study provides an important reference for forest resource management and conservation for P. orientalis.},
	language = {en},
	number = {4},
	urldate = {2023-04-27},
	journal = {Evolutionary Applications},
	author = {Jia, Kai-Hua and Zhao, Wei and Maier, Paul Andrew and Hu, Xian-Ge and Jin, Yuqing and Zhou, Shan-Shan and Jiao, Si-Qian and El-Kassaby, Yousry A and Wang, Tongli and Wang, Xiao-Ru and Mao, Jian-Feng},
	year = {2020},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/eva.12891},
	keywords = {Platycladus orientalis, adaptation, climate change, genetic offset, genotyping by sequencing, population structure},
	pages = {665--676},
}

Understanding and quantifying populations' adaptive genetic variation and their response to climate change are critical to reforestation's seed source selection, forest management decisions, and gene conservation. Landscape genomics combined with geographic and environmental information provide an opportunity to interrogate forest populations' genome-wide variation for understanding the extent to which evolutionary forces shape past and contemporary populations' genetic structure, and identify those populations that may be most at risk under future climate change. Here, we used genotyping by sequencing to generate over 11,000 high-quality variants from Platycladus orientalis range-wide collection to evaluate its diversity and to predict genetic offset under future climate scenarios. Platycladus orientalis is a widespread conifer in China with significant ecological, timber, and medicinal values. We found population structure and evidences of isolation by environment, indicative of adaptation to local conditions. Gradient forest modeling identified temperature-related variables as the most important environmental factors influencing genetic variation and predicted areas with higher risk under future climate change. This study provides an important reference for forest resource management and conservation for P. orientalis.

@article{hu_transcriptome-wide_2020,
	title = {Transcriptome-wide identification and profiling of {miRNAs} in a stress-tolerant conifer {Sabina} chinensis},
	volume = {45},
	issn = {0973-7138},
	url = {https://doi.org/10.1007/s12038-020-0002-4},
	doi = {10.1007/s12038-020-0002-4},
	abstract = {miRNAs are important regulatory components involving in many biological processes, including plant development, vegetative and reproductive growth, and stress response. However, identification and characterization of miRNAs still remain limited for conifer species. In this study, with deep sequencing, we obtained 1,314,450 unique reads with 18–30 nt length from a stress-tolerant conifer, Sabina chinensis. We identified 37 conserved and 103 novel miRNAs, their unique characteristics were further analyzed, and 10 randomly selected were validated by qRT-PCR. Through miRNA target predictions and annotations, we found miRNA may have several targets as well a target could be regulated by several miRNAs, and a total of 2,397 mRNAs were predicted to be targets of the 140 miRNAs. These targets included not only important transcription factors such as auxin response factors, but also indispensable non-transcriptional factor proteins. Pathway-based analysis showed that S. chinensis miRNAs are involved in 172 metabolic pathways, of which 3 were discovered in adaptation-related pathways, indicating their possible relevance to the species’ stress-tolerance characteristics. This study is expected to lay the foundation for exploring the regulative roles of miRNAs in development, growth, and response to environmental stresses of S. chinensis.},
	language = {en},
	number = {1},
	urldate = {2023-04-27},
	journal = {Journal of Biosciences},
	author = {Hu, Xian-Ge and Zhou, Shan-Shan and Yang, Ying and Liu, Hui and Anil, Shrestha and Wang, Qing and Zhao, Wei and Gao, Qiong and El-Kassaby, Yousry A. and Wang, Tongli and Li, Yue and Mao, Jian-Feng},
	month = feb,
	year = {2020},
	keywords = {Sabina chinensis, miRNA, miRNA target, pathway},
	pages = {41},
}

miRNAs are important regulatory components involving in many biological processes, including plant development, vegetative and reproductive growth, and stress response. However, identification and characterization of miRNAs still remain limited for conifer species. In this study, with deep sequencing, we obtained 1,314,450 unique reads with 18–30 nt length from a stress-tolerant conifer, Sabina chinensis. We identified 37 conserved and 103 novel miRNAs, their unique characteristics were further analyzed, and 10 randomly selected were validated by qRT-PCR. Through miRNA target predictions and annotations, we found miRNA may have several targets as well a target could be regulated by several miRNAs, and a total of 2,397 mRNAs were predicted to be targets of the 140 miRNAs. These targets included not only important transcription factors such as auxin response factors, but also indispensable non-transcriptional factor proteins. Pathway-based analysis showed that S. chinensis miRNAs are involved in 172 metabolic pathways, of which 3 were discovered in adaptation-related pathways, indicating their possible relevance to the species’ stress-tolerance characteristics. This study is expected to lay the foundation for exploring the regulative roles of miRNAs in development, growth, and response to environmental stresses of S. chinensis.

@article{melida_arabinoxylan-oligosaccharides_2020,
	title = {Arabinoxylan-{Oligosaccharides} {Act} as {Damage} {Associated} {Molecular} {Patterns} in {Plants} {Regulating} {Disease} {Resistance}},
	volume = {11},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2020.01210},
	doi = {10.3389/fpls.2020.01210},
	abstract = {Immune responses in plants can be triggered by damage/microbe-associated molecular patterns (DAMPs/MAMPs) upon recognition by plant pattern recognition receptors (PRRs). DAMPs are signaling molecules synthesized by plants or released from host cellular structures (e.g., plant cell walls) upon pathogen infection or wounding. Despite the hypothesized important role of plant cell wall-derived DAMPs in plant-pathogen interactions, a very limited number of these DAMPs are well characterized. Recent work demonstrated that pectin-enriched cell wall fractions extracted from the cell wall mutant impaired in Arabidopsis Response Regulator 6 (arr6), that showed altered disease resistance to several pathogens, triggered more intense immune responses than those activated by similar cell wall fractions from wild-type plants. It was hypothesized that arr6 cell wall fractions could be differentially enriched in DAMPs. In this work, we describe the characterization of the previous immune-active fractions of arr6 showing the highest triggering capacities upon further fractionation by chromatographic means. These analyses pointed to a role of pentose-based oligosaccharides triggering plant immune responses. The characterization of several pentose-based oligosaccharide structures revealed that β-1,4-xylooligosaccharides of specific degrees of polymerization and carrying arabinose decorations are sensed as DAMPs by plants. Moreover, the pentasaccharide 33-α-L-arabinofuranosyl-xylotetraose (XA3XX) was found as a highly active DAMP structure triggering strong immune responses in Arabidopsis thaliana and enhancing crop disease resistance.},
	urldate = {2023-03-10},
	journal = {Frontiers in Plant Science},
	author = {Mélida, Hugo and Bacete, Laura and Ruprecht, Colin and Rebaque, Diego and del Hierro, Irene and López, Gemma and Brunner, Frédéric and Pfrengle, Fabian and Molina, Antonio},
	year = {2020},
}

Immune responses in plants can be triggered by damage/microbe-associated molecular patterns (DAMPs/MAMPs) upon recognition by plant pattern recognition receptors (PRRs). DAMPs are signaling molecules synthesized by plants or released from host cellular structures (e.g., plant cell walls) upon pathogen infection or wounding. Despite the hypothesized important role of plant cell wall-derived DAMPs in plant-pathogen interactions, a very limited number of these DAMPs are well characterized. Recent work demonstrated that pectin-enriched cell wall fractions extracted from the cell wall mutant impaired in Arabidopsis Response Regulator 6 (arr6), that showed altered disease resistance to several pathogens, triggered more intense immune responses than those activated by similar cell wall fractions from wild-type plants. It was hypothesized that arr6 cell wall fractions could be differentially enriched in DAMPs. In this work, we describe the characterization of the previous immune-active fractions of arr6 showing the highest triggering capacities upon further fractionation by chromatographic means. These analyses pointed to a role of pentose-based oligosaccharides triggering plant immune responses. The characterization of several pentose-based oligosaccharide structures revealed that β-1,4-xylooligosaccharides of specific degrees of polymerization and carrying arabinose decorations are sensed as DAMPs by plants. Moreover, the pentasaccharide 33-α-L-arabinofuranosyl-xylotetraose (XA3XX) was found as a highly active DAMP structure triggering strong immune responses in Arabidopsis thaliana and enhancing crop disease resistance.

@article{bacete_role_2020,
	title = {The {Role} of {Mechanoperception} in {Plant} {Cell} {Wall} {Integrity} {Maintenance}},
	volume = {9},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2223-7747},
	url = {https://www.mdpi.com/2223-7747/9/5/574},
	doi = {10.3390/plants9050574},
	abstract = {The plant cell walls surrounding all plant cells are highly dynamic structures, which change their composition and organization in response to chemical and physical stimuli originating both in the environment and in plants themselves. They are intricately involved in all interactions between plants and their environment while also providing adaptive structural support during plant growth and development. A key mechanism contributing to these adaptive changes is the cell wall integrity (CWI) maintenance mechanism. It monitors and maintains the functional integrity of cell walls by initiating adaptive changes in cellular and cell wall metabolism. Despite its importance, both our understanding of its mode of action and knowledge regarding the molecular components that form it are limited. Intriguingly, the available evidence implicates mechanosensing in the mechanism. Here, we provide an overview of the knowledge available regarding the molecular mechanisms involved in and discuss how mechanoperception and signal transduction may contribute to plant CWI maintenance.},
	language = {en},
	number = {5},
	urldate = {2023-03-10},
	journal = {Plants},
	author = {Bacete, Laura and Hamann, Thorsten},
	month = may,
	year = {2020},
	note = {Number: 5
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {cell wall, cell wall integrity, mechanoperception, mechanosensing, plant defense, plant environment interaction},
	pages = {574},
}

The plant cell walls surrounding all plant cells are highly dynamic structures, which change their composition and organization in response to chemical and physical stimuli originating both in the environment and in plants themselves. They are intricately involved in all interactions between plants and their environment while also providing adaptive structural support during plant growth and development. A key mechanism contributing to these adaptive changes is the cell wall integrity (CWI) maintenance mechanism. It monitors and maintains the functional integrity of cell walls by initiating adaptive changes in cellular and cell wall metabolism. Despite its importance, both our understanding of its mode of action and knowledge regarding the molecular components that form it are limited. Intriguingly, the available evidence implicates mechanosensing in the mechanism. Here, we provide an overview of the knowledge available regarding the molecular mechanisms involved in and discuss how mechanoperception and signal transduction may contribute to plant CWI maintenance.

@article{bacete_arabidopsis_2020,
	title = {Arabidopsis {Response} {Regulator} 6 ({ARR6}) {Modulates} {Plant} {Cell}-{Wall} {Composition} and {Disease} {Resistance}},
	volume = {33},
	issn = {0894-0282},
	url = {https://apsjournals.apsnet.org/doi/10.1094/MPMI-12-19-0341-R},
	doi = {10.1094/MPMI-12-19-0341-R},
	abstract = {The cytokinin signaling pathway, which is mediated by Arabidopsis response regulator (ARR) proteins, has been involved in the modulation of some disease-resistance responses. Here, we describe novel functions of ARR6 in the control of plant disease-resistance and cell-wall composition. Plants impaired in ARR6 function (arr6) were more resistant and susceptible, respectively, to the necrotrophic fungus Plectosphaerella cucumerina and to the vascular bacterium Ralstonia solanacearum, whereas Arabidopsis plants that overexpress ARR6 showed the opposite phenotypes, which further support a role of ARR6 in the modulation of disease-resistance responses against these pathogens. Transcriptomics and metabolomics analyses revealed that, in arr6 plants, canonical disease-resistance pathways, like those activated by defensive phytohormones, were not altered, whereas immune responses triggered by microbe-associated molecular patterns were slightly enhanced. Cell-wall composition of arr6 plants was found to be severely altered compared with that of wild-type plants. Remarkably, pectin-enriched cell-wall fractions extracted from arr6 walls triggered more intense immune responses than those activated by similar wall fractions from wild-type plants, suggesting that arr6 pectin fraction is enriched in wall-related damage-associated molecular patterns, which trigger immune responses. This work supports a novel function of ARR6 in the control of cell-wall composition and disease resistance and reinforces the role of the plant cell wall in the modulation of specific immune responses.},
	number = {5},
	urldate = {2023-03-10},
	journal = {Molecular Plant-Microbe Interactions®},
	author = {Bacete, Laura and Mélida, Hugo and López, Gemma and Dabos, Patrick and Tremousaygue, Dominique and Denancé, Nicolas and Miedes, Eva and Bulone, Vincent and Goffner, Deborah and Molina, Antonio},
	month = may,
	year = {2020},
	note = {Publisher: Scientific Societies},
	keywords = {Arabidopsis response regulators (ARR), Plectosphaerella cucumerina, Ralstonia solanacearum, cell wall, cytokinin, damage-associated molecular patterns (DAMPs), disease resistance, immunity},
	pages = {767--780},
}

The cytokinin signaling pathway, which is mediated by Arabidopsis response regulator (ARR) proteins, has been involved in the modulation of some disease-resistance responses. Here, we describe novel functions of ARR6 in the control of plant disease-resistance and cell-wall composition. Plants impaired in ARR6 function (arr6) were more resistant and susceptible, respectively, to the necrotrophic fungus Plectosphaerella cucumerina and to the vascular bacterium Ralstonia solanacearum, whereas Arabidopsis plants that overexpress ARR6 showed the opposite phenotypes, which further support a role of ARR6 in the modulation of disease-resistance responses against these pathogens. Transcriptomics and metabolomics analyses revealed that, in arr6 plants, canonical disease-resistance pathways, like those activated by defensive phytohormones, were not altered, whereas immune responses triggered by microbe-associated molecular patterns were slightly enhanced. Cell-wall composition of arr6 plants was found to be severely altered compared with that of wild-type plants. Remarkably, pectin-enriched cell-wall fractions extracted from arr6 walls triggered more intense immune responses than those activated by similar wall fractions from wild-type plants, suggesting that arr6 pectin fraction is enriched in wall-related damage-associated molecular patterns, which trigger immune responses. This work supports a novel function of ARR6 in the control of cell-wall composition and disease resistance and reinforces the role of the plant cell wall in the modulation of specific immune responses.

@article{bacete_plant_2020,
	title = {Plant {Biology}: {Plants} {Turn} {Down} the {Volume} to {Respond} to {Cell} {Swelling}},
	volume = {30},
	issn = {0960-9822},
	shorttitle = {Plant {Biology}},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982220307806},
	doi = {10.1016/j.cub.2020.06.001},
	abstract = {Turgor manipulation to induce plant cell swelling is one of the classic experiments undertaken in biology courses in schools and at universities. However, only now do we start to understand the molecular mechanisms responsible for detecting plant cell swelling.},
	language = {en},
	number = {14},
	urldate = {2023-03-10},
	journal = {Current Biology},
	author = {Bacete, Laura and Hamann, Thorsten},
	month = jul,
	year = {2020},
	pages = {R804--R806},
}

Turgor manipulation to induce plant cell swelling is one of the classic experiments undertaken in biology courses in schools and at universities. However, only now do we start to understand the molecular mechanisms responsible for detecting plant cell swelling.

@article{hong_heterologous_2020,
	title = {Heterologous {microProtein} expression identifies {LITTLE} {NINJA}, a dominant regulator of jasmonic acid signaling},
	volume = {117},
	url = {https://www.pnas.org/doi/full/10.1073/pnas.2005198117},
	doi = {10.1073/pnas.2005198117},
	abstract = {MicroProteins are small, often single-domain proteins that are sequence-related to larger, often multidomain proteins. Here, we used a combination of comparative genomics and heterologous synthetic misexpression to isolate functional cereal microProtein regulators. Our approach identified LITTLE NINJA (LNJ), a microProtein that acts as a modulator of jasmonic acid (JA) signaling. Ectopic expression of LNJ in Arabidopsis resulted in stunted plants that resembled the decuple JAZ (jazD) mutant. In fact, comparing the transcriptomes of transgenic LNJ overexpressor plants and jazD revealed a large overlap of deregulated genes, suggesting that ectopic LNJ expression altered JA signaling. Transgenic Brachypodium plants with elevated LNJ expression levels showed deregulation of JA signaling as well and displayed reduced growth and enhanced production of side shoots (tiller). This tillering effect was transferable between grass species, and overexpression of LNJ in barley and rice caused similar traits. We used a clustered regularly interspaced short palindromic repeats (CRISPR) approach and created a LNJ-like protein in Arabidopsis by deleting parts of the coding sentence of the AFP2 gene that encodes a NINJA-domain protein. These afp2-crispr mutants were also stunted in size and resembled jazD. Thus, similar genome-engineering approaches can be exploited as a future tool to create LNJ proteins and produce cereals with altered architectures.},
	number = {42},
	urldate = {2022-11-30},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Hong, Shin-Young and Sun, Bin and Straub, Daniel and Blaakmeer, Anko and Mineri, Lorenzo and Koch, Jonas and Brinch-Pedersen, Henrik and Holme, Inger B. and Burow, Meike and Lyngs Jørgensen, Hans Jørgen and Albà, M. Mar and Wenkel, Stephan},
	month = oct,
	year = {2020},
	pages = {26197--26205},
}

MicroProteins are small, often single-domain proteins that are sequence-related to larger, often multidomain proteins. Here, we used a combination of comparative genomics and heterologous synthetic misexpression to isolate functional cereal microProtein regulators. Our approach identified LITTLE NINJA (LNJ), a microProtein that acts as a modulator of jasmonic acid (JA) signaling. Ectopic expression of LNJ in Arabidopsis resulted in stunted plants that resembled the decuple JAZ (jazD) mutant. In fact, comparing the transcriptomes of transgenic LNJ overexpressor plants and jazD revealed a large overlap of deregulated genes, suggesting that ectopic LNJ expression altered JA signaling. Transgenic Brachypodium plants with elevated LNJ expression levels showed deregulation of JA signaling as well and displayed reduced growth and enhanced production of side shoots (tiller). This tillering effect was transferable between grass species, and overexpression of LNJ in barley and rice caused similar traits. We used a clustered regularly interspaced short palindromic repeats (CRISPR) approach and created a LNJ-like protein in Arabidopsis by deleting parts of the coding sentence of the AFP2 gene that encodes a NINJA-domain protein. These afp2-crispr mutants were also stunted in size and resembled jazD. Thus, similar genome-engineering approaches can be exploited as a future tool to create LNJ proteins and produce cereals with altered architectures.

@article{dehaan_roadmap_2020,
	title = {Roadmap for {Accelerated} {Domestication} of an {Emerging} {Perennial} {Grain} {Crop}},
	volume = {25},
	issn = {1360-1385},
	url = {https://www.cell.com/trends/plant-science/abstract/S1360-1385(20)30053-4},
	doi = {10.1016/j.tplants.2020.02.004},
	language = {English},
	number = {6},
	urldate = {2022-11-30},
	journal = {Trends in Plant Science},
	author = {DeHaan, Lee and Larson, Steve and López-Marqués, Rosa L. and Wenkel, Stephan and Gao, Caixia and Palmgren, Michael},
	month = jun,
	year = {2020},
	keywords = {accelerated domestication, genome editing, perennial grain crops},
	pages = {525--537},
}

@article{botterweg-paredes_light_2020,
	title = {Light affects tissue patterning of the hypocotyl in the shade-avoidance response},
	volume = {16},
	issn = {1553-7404},
	url = {https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1008678},
	doi = {10.1371/journal.pgen.1008678},
	abstract = {Plants have evolved strategies to avoid shade and optimize the capture of sunlight. While some species are tolerant to shade, plants such as Arabidopsis thaliana are shade-intolerant and induce elongation of their hypocotyl to outcompete neighboring plants. We report the identification of a developmental module acting downstream of shade perception controlling vascular patterning. We show that Arabidopsis plants react to shade by increasing the number and types of water-conducting tracheary elements in the vascular cylinder to maintain vascular density constant. Mutations in genes affecting vascular patterning impair the production of additional xylem and also show defects in the shade-induced hypocotyl elongation response. Comparative analysis of the shade-induced transcriptomes revealed differences between wild type and vascular patterning mutants and it appears that the latter mutants fail to induce sets of genes encoding biosynthetic and cell wall modifying enzymes. Our results thus set the stage for a deeper understanding of how growth and patterning are coordinated in a dynamic environment.},
	language = {en},
	number = {3},
	urldate = {2022-11-30},
	journal = {PLOS Genetics},
	author = {Botterweg-Paredes, Esther and Blaakmeer, Anko and Hong, Shin-Young and Sun, Bin and Mineri, Lorenzo and Kruusvee, Valdeko and Xie, Yakun and Straub, Daniel and Ménard, Delphine and Pesquet, Edouard and Wenkel, Stephan},
	month = mar,
	year = {2020},
	keywords = {Arabidopsis thaliana, Auxins, Gene expression, Genetically modified plants, Hypocotyl, Seedlings, Transcription factors, White light},
	pages = {e1008678},
}

Plants have evolved strategies to avoid shade and optimize the capture of sunlight. While some species are tolerant to shade, plants such as Arabidopsis thaliana are shade-intolerant and induce elongation of their hypocotyl to outcompete neighboring plants. We report the identification of a developmental module acting downstream of shade perception controlling vascular patterning. We show that Arabidopsis plants react to shade by increasing the number and types of water-conducting tracheary elements in the vascular cylinder to maintain vascular density constant. Mutations in genes affecting vascular patterning impair the production of additional xylem and also show defects in the shade-induced hypocotyl elongation response. Comparative analysis of the shade-induced transcriptomes revealed differences between wild type and vascular patterning mutants and it appears that the latter mutants fail to induce sets of genes encoding biosynthetic and cell wall modifying enzymes. Our results thus set the stage for a deeper understanding of how growth and patterning are coordinated in a dynamic environment.

@article{eguen_control_2020,
	title = {Control of flowering in rice through synthetic {microProteins}},
	volume = {62},
	issn = {1744-7909},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jipb.12865},
	doi = {10.1111/jipb.12865},
	abstract = {Photoperiod-dependent flowering in rice is regulated by HEADING DATE 1 (Hd1), which acts as both an activator and repressor of flowering in a daylength-dependent manner. To investigate the use of microProteins as a tool to modify rice sensitivity to the photoperiod, we designed a synthetic Hd1 microProtein (Hd1miP) capable of interacting with Hd1 protein, and overexpressed it in rice. Transgenic OX-Hd1miP plants flowered significantly earlier than wild type plants when grown in non-inductive long day conditions. Our results show the potential of microProteins to serve as powerful tools for modulating crop traits and unraveling protein function.},
	language = {en},
	number = {6},
	urldate = {2022-11-30},
	journal = {Journal of Integrative Plant Biology},
	author = {Eguen, Tenai and Ariza, Jorge Gomez and Brambilla, Vittoria and Sun, Bin and Bhati, Kaushal Kumar and Fornara, Fabio and Wenkel, Stephan},
	year = {2020},
	pages = {730--736},
}

Photoperiod-dependent flowering in rice is regulated by HEADING DATE 1 (Hd1), which acts as both an activator and repressor of flowering in a daylength-dependent manner. To investigate the use of microProteins as a tool to modify rice sensitivity to the photoperiod, we designed a synthetic Hd1 microProtein (Hd1miP) capable of interacting with Hd1 protein, and overexpressed it in rice. Transgenic OX-Hd1miP plants flowered significantly earlier than wild type plants when grown in non-inductive long day conditions. Our results show the potential of microProteins to serve as powerful tools for modulating crop traits and unraveling protein function.

@article{choi_light_2020,
	series = {Photobiology},
	title = {Light {Triggers} the {miRNA}-{Biogenetic} {Inconsistency} for {De}-etiolated {Seedling} {Survivability} in {Arabidopsis} thaliana},
	volume = {13},
	issn = {1674-2052},
	url = {https://www.sciencedirect.com/science/article/pii/S1674205219303375},
	doi = {10.1016/j.molp.2019.10.011},
	abstract = {The shift of dark-grown seedlings into light causes enormous transcriptome changes followed by a dramatic developmental transition. Here, we show that microRNA (miRNA) biogenesis also undergoes regulatory changes during de-etiolation. Etiolated seedlings maintain low levels of primary miRNAs (pri-miRNAs) and miRNA processing core proteins, such as Dicer-like 1, SERRATE, and HYPONASTIC LEAVES 1, whereas during de-etiolation both pri-miRNAs and the processing components accumulate to high levels. However, the levels of most miRNAs do not notably increase in response to light. To reconcile this inconsistency, we demonstrated that an unknown suppressor decreases miRNA-processing activity and light-induced SMALL RNA DEGRADING NUCLEASE 1 shortens the half-life of several miRNAs in de-etiolated seedlings. Taken together, these data suggest a novel mechanism, miRNA-biogenetic inconsistency, which accounts for the intricacy of miRNA biogenesis during de-etiolation. This mechanism is essential for the survival of de-etiolated seedlings after long-term skotomorphogenesis and their optimal adaptation to ever-changing light conditions.},
	language = {en},
	number = {3},
	urldate = {2022-11-30},
	journal = {Molecular Plant},
	author = {Choi, Suk Won and Ryu, Moon Young and Viczián, András and Jung, Hyun Ju and Kim, Gu Min and Arce, Agustin L. and Achkar, Natalia P. and Manavella, Pablo and Dolde, Ulla and Wenkel, Stephan and Molnár, Attila and Nagy, Ferenc and Cho, Seok Keun and Yang, Seong Wook},
	month = mar,
	year = {2020},
	keywords = {Light signaling, miRNA biogenesis},
	pages = {431--445},
}

The shift of dark-grown seedlings into light causes enormous transcriptome changes followed by a dramatic developmental transition. Here, we show that microRNA (miRNA) biogenesis also undergoes regulatory changes during de-etiolation. Etiolated seedlings maintain low levels of primary miRNAs (pri-miRNAs) and miRNA processing core proteins, such as Dicer-like 1, SERRATE, and HYPONASTIC LEAVES 1, whereas during de-etiolation both pri-miRNAs and the processing components accumulate to high levels. However, the levels of most miRNAs do not notably increase in response to light. To reconcile this inconsistency, we demonstrated that an unknown suppressor decreases miRNA-processing activity and light-induced SMALL RNA DEGRADING NUCLEASE 1 shortens the half-life of several miRNAs in de-etiolated seedlings. Taken together, these data suggest a novel mechanism, miRNA-biogenetic inconsistency, which accounts for the intricacy of miRNA biogenesis during de-etiolation. This mechanism is essential for the survival of de-etiolated seedlings after long-term skotomorphogenesis and their optimal adaptation to ever-changing light conditions.

@article{hong_multi-level_2020,
	title = {Multi-level analysis of the interactions between {REVOLUTA} and {MORE} {AXILLARY} {BRANCHES} 2 in controlling plant development reveals parallel, independent and antagonistic functions},
	volume = {147},
	issn = {0950-1991},
	url = {https://doi.org/10.1242/dev.183681},
	doi = {10.1242/dev.183681},
	abstract = {Class III homeodomain leucine zipper (HD-ZIPIII) transcription factors play fundamental roles in controlling plant development. The known HD-ZIPIII target genes encode proteins involved in the production and dissipation of the auxin signal, HD-ZIPII transcription factors and components that feedback to regulate HD-ZIPIII expression or protein activity. Here, we have investigated the regulatory hierarchies of the control of MORE AXILLARY BRANCHES2 (MAX2) by the HD-ZIPIII protein REVOLUTA (REV). We found that REV can interact with the promoter of MAX2. In agreement, rev10D gain-of-function mutants had increased levels of MAX2 expression, while rev loss-of-function mutants showed lower levels of MAX2 in some tissues. Like REV, MAX2 plays known roles in the control of plant architecture, photobiology and senescence, which prompted us to initiate a multi-level analysis of growth phenotypes of hd-zipIII, max2 and respective higher order mutants thereof. Our data suggest a complex relationship of synergistic and antagonistic activities between REV and MAX2; these interactions appear to depend on the developmental context and do not all involve the direct regulation of MAX2 by REV.},
	number = {10},
	urldate = {2022-11-30},
	journal = {Development},
	author = {Hong, Shin-Young and Botterweg-Paredes, Esther and Doll, Jasmin and Eguen, Tenai and Blaakmeer, Anko and Matton, Sanne and Xie, Yakun and Skjøth Lunding, Bjørg and Zentgraf, Ulrike and Guan, Chunmei and Jiao, Yuling and Wenkel, Stephan},
	month = may,
	year = {2020},
	pages = {dev183681},
}

Class III homeodomain leucine zipper (HD-ZIPIII) transcription factors play fundamental roles in controlling plant development. The known HD-ZIPIII target genes encode proteins involved in the production and dissipation of the auxin signal, HD-ZIPII transcription factors and components that feedback to regulate HD-ZIPIII expression or protein activity. Here, we have investigated the regulatory hierarchies of the control of MORE AXILLARY BRANCHES2 (MAX2) by the HD-ZIPIII protein REVOLUTA (REV). We found that REV can interact with the promoter of MAX2. In agreement, rev10D gain-of-function mutants had increased levels of MAX2 expression, while rev loss-of-function mutants showed lower levels of MAX2 in some tissues. Like REV, MAX2 plays known roles in the control of plant architecture, photobiology and senescence, which prompted us to initiate a multi-level analysis of growth phenotypes of hd-zipIII, max2 and respective higher order mutants thereof. Our data suggest a complex relationship of synergistic and antagonistic activities between REV and MAX2; these interactions appear to depend on the developmental context and do not all involve the direct regulation of MAX2 by REV.

@article{bhati_global_2020,
	title = {Global {Analysis} of {Cereal} {microProteins} {Suggests} {Diverse} {Roles} in {Crop} {Development} and {Environmental} {Adaptation}},
	volume = {10},
	issn = {2160-1836},
	url = {https://doi.org/10.1534/g3.120.400794},
	doi = {10.1534/g3.120.400794},
	abstract = {MicroProteins are a class of small single-domain proteins that post-translationally regulate larger multidomain proteins from which they evolved or which they relate to. They disrupt the normal function of their targets by forming microProtein-target heterodimers through compatible protein-protein interaction (PPI) domains. Recent studies confirm the significance of microProteins in the fine-tuning of plant developmental processes such as shoot apical meristem maintenance and flowering time regulation. While there are a number of well-characterized microProteins in Arabidopsis thaliana, studies from more complex plant genomes are still missing. We have previously developed miPFinder, a software for identifying microProteins from annotated genomes. Here we present an improved version where we have updated the algorithm to increase its accuracy and speed, and used it to analyze five cereal crop genomes – wheat, rice, barley, maize and sorghum. We found 20,064 potential microProteins from a total of 258,029 proteins in these five organisms, of which approximately 2000 are high-confidence, i.e., likely to function as actual microProteins. Gene ontology analysis of these 2000 microProtein candidates revealed their roles in stress, light and growth responses, hormone signaling and transcriptional regulation. Using a recently developed rice gene co-expression database, we analyzed 347 potential rice microProteins that are also conserved in other cereal crops and found over 50 of these rice microProteins to be co-regulated with their identified interaction partners. Overall, our study reveals a rich source of biotechnologically interesting small proteins that regulate fundamental plant processes such a growth and stress response that could be utilized in crop bioengineering.},
	number = {10},
	urldate = {2022-11-30},
	journal = {G3 Genes{\textbar}Genomes{\textbar}Genetics},
	author = {Bhati, Kaushal Kumar and Kruusvee, Valdeko and Straub, Daniel and Chandran, Anil Kumar Nalini and Jung, Ki-Hong and Wenkel, Stephan},
	month = oct,
	year = {2020},
	pages = {3709--3717},
}

MicroProteins are a class of small single-domain proteins that post-translationally regulate larger multidomain proteins from which they evolved or which they relate to. They disrupt the normal function of their targets by forming microProtein-target heterodimers through compatible protein-protein interaction (PPI) domains. Recent studies confirm the significance of microProteins in the fine-tuning of plant developmental processes such as shoot apical meristem maintenance and flowering time regulation. While there are a number of well-characterized microProteins in Arabidopsis thaliana, studies from more complex plant genomes are still missing. We have previously developed miPFinder, a software for identifying microProteins from annotated genomes. Here we present an improved version where we have updated the algorithm to increase its accuracy and speed, and used it to analyze five cereal crop genomes – wheat, rice, barley, maize and sorghum. We found 20,064 potential microProteins from a total of 258,029 proteins in these five organisms, of which approximately 2000 are high-confidence, i.e., likely to function as actual microProteins. Gene ontology analysis of these 2000 microProtein candidates revealed their roles in stress, light and growth responses, hormone signaling and transcriptional regulation. Using a recently developed rice gene co-expression database, we analyzed 347 potential rice microProteins that are also conserved in other cereal crops and found over 50 of these rice microProteins to be co-regulated with their identified interaction partners. Overall, our study reveals a rich source of biotechnologically interesting small proteins that regulate fundamental plant processes such a growth and stress response that could be utilized in crop bioengineering.

@article{amstutz_atypical_2020,
	title = {An atypical short-chain dehydrogenase–reductase functions in the relaxation of photoprotective {qH} in {Arabidopsis}},
	volume = {6},
	issn = {2055-0278},
	url = {http://www.nature.com/articles/s41477-020-0591-9},
	doi = {10.1038/s41477-020-0591-9},
	abstract = {Photosynthetic organisms experience wide fluctuations in light intensity and regulate light harvesting accordingly to prevent damage from excess energy. The antenna quenching component qH is a sustained form of energy dissipation that protects the photosynthetic apparatus under stress conditions. This photoprotective mechanism requires the plastid lipocalin LCNP and is prevented by SUPPRESSOR OF QUENCHING1 (SOQ1) under non-stress conditions. However, the molecular mechanism of qH relaxation has yet to be resolved. Here, we isolated and characterized RELAXATION OF QH1 (ROQH1), an atypical short-chain dehydrogenase–reductase that functions as a qH-relaxation factor in Arabidopsis. The ROQH1 gene belongs to the GreenCut2 inventory specific to photosynthetic organisms, and the ROQH1 protein localizes to the chloroplast stroma lamellae membrane. After a cold and high-light treatment, qH does not relax in roqh1 mutants and qH does not occur in leaves overexpressing ROQH1. When the soq1 and roqh1 mutations are combined, qH can neither be prevented nor relaxed and soq1 roqh1 displays constitutive qH and light-limited growth. We propose that LCNP and ROQH1 perform dosage-dependent, antagonistic functions to protect the photosynthetic apparatus and maintain light-harvesting efficiency in plants.},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Nature Plants},
	author = {Amstutz, Cynthia L. and Fristedt, Rikard and Schultink, Alex and Merchant, Sabeeha S. and Niyogi, Krishna K. and Malnoë, Alizée},
	month = feb,
	year = {2020},
	pages = {154--166},
}

Photosynthetic organisms experience wide fluctuations in light intensity and regulate light harvesting accordingly to prevent damage from excess energy. The antenna quenching component qH is a sustained form of energy dissipation that protects the photosynthetic apparatus under stress conditions. This photoprotective mechanism requires the plastid lipocalin LCNP and is prevented by SUPPRESSOR OF QUENCHING1 (SOQ1) under non-stress conditions. However, the molecular mechanism of qH relaxation has yet to be resolved. Here, we isolated and characterized RELAXATION OF QH1 (ROQH1), an atypical short-chain dehydrogenase–reductase that functions as a qH-relaxation factor in Arabidopsis. The ROQH1 gene belongs to the GreenCut2 inventory specific to photosynthetic organisms, and the ROQH1 protein localizes to the chloroplast stroma lamellae membrane. After a cold and high-light treatment, qH does not relax in roqh1 mutants and qH does not occur in leaves overexpressing ROQH1. When the soq1 and roqh1 mutations are combined, qH can neither be prevented nor relaxed and soq1 roqh1 displays constitutive qH and light-limited growth. We propose that LCNP and ROQH1 perform dosage-dependent, antagonistic functions to protect the photosynthetic apparatus and maintain light-harvesting efficiency in plants.

@article{hoermayer_wounding-induced_2020,
	title = {Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots},
	volume = {117},
	url = {https://www.pnas.org/doi/full/10.1073/pnas.2003346117},
	doi = {10.1073/pnas.2003346117},
	number = {26},
	urldate = {2022-05-16},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Hoermayer, Lukas and Montesinos, Juan Carlos and Marhava, Petra and Benková, Eva and Yoshida, Saiko and Friml, Jiří},
	month = jun,
	year = {2020},
	note = {Publisher: Proceedings of the National Academy of Sciences},
	pages = {15322--15331},
}

@article{graeff_local_2020,
	title = {Local and {Systemic} {Effects} of {Brassinosteroid} {Perception} in {Developing} {Phloem}},
	volume = {30},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982220302025},
	doi = {10.1016/j.cub.2020.02.029},
	abstract = {The plant vasculature is an essential adaptation to terrestrial growth. Its phloem component permits efficient transfer of photosynthates between source and sink organs but also transports signals that systemically coordinate physiology and development. Here, we provide evidence that developing phloem orchestrates cellular behavior of adjacent tissues in the growth apices of plants, the meristems. Arabidopsis thaliana plants that lack the three receptor kinases BRASSINOSTEROID INSENSITIVE 1 (BRI1), BRI1-LIKE 1 (BRL1), and BRL3 (“bri3” mutants) can no longer sense brassinosteroid phytohormones and display severe dwarfism as well as patterning and differentiation defects, including disturbed phloem development. We found that, despite the ubiquitous expression of brassinosteroid receptors in growing plant tissues, exclusive expression of the BRI1 receptor in developing phloem is sufficient to systemically correct cellular growth and patterning defects that underlie the bri3 phenotype. Although this effect is brassinosteroid-dependent, it cannot be reproduced with dominant versions of known downstream effectors of BRI1 signaling and therefore possibly involves a non-canonical signaling output. Interestingly, the rescue of bri3 by phloem-specific BRI1 expression is associated with antagonism toward phloem-specific CLAVATA3/EMBRYO SURROUNDING REGION-RELATED 45 (CLE45) peptide signaling in roots. Hyperactive CLE45 signaling causes phloem sieve element differentiation defects, and consistently, knockout of CLE45 perception in bri3 background restores proper phloem development. However, bri3 dwarfism is retained in such lines. Our results thus reveal local and systemic effects of brassinosteroid perception in the phloem: whereas it locally antagonizes CLE45 signaling to permit phloem differentiation, it systemically instructs plant organ formation via a phloem-derived, non-cell-autonomous signal.},
	language = {en},
	number = {9},
	urldate = {2022-05-02},
	journal = {Current Biology},
	author = {Graeff, Moritz and Rana, Surbhi and Marhava, Petra and Moret, Bernard and Hardtke, Christian S.},
	month = may,
	year = {2020},
	keywords = {BAM3, BRI1, CLE45, brassinosteroids, organizer, phloem},
	pages = {1626--1638.e3},
}

The plant vasculature is an essential adaptation to terrestrial growth. Its phloem component permits efficient transfer of photosynthates between source and sink organs but also transports signals that systemically coordinate physiology and development. Here, we provide evidence that developing phloem orchestrates cellular behavior of adjacent tissues in the growth apices of plants, the meristems. Arabidopsis thaliana plants that lack the three receptor kinases BRASSINOSTEROID INSENSITIVE 1 (BRI1), BRI1-LIKE 1 (BRL1), and BRL3 (“bri3” mutants) can no longer sense brassinosteroid phytohormones and display severe dwarfism as well as patterning and differentiation defects, including disturbed phloem development. We found that, despite the ubiquitous expression of brassinosteroid receptors in growing plant tissues, exclusive expression of the BRI1 receptor in developing phloem is sufficient to systemically correct cellular growth and patterning defects that underlie the bri3 phenotype. Although this effect is brassinosteroid-dependent, it cannot be reproduced with dominant versions of known downstream effectors of BRI1 signaling and therefore possibly involves a non-canonical signaling output. Interestingly, the rescue of bri3 by phloem-specific BRI1 expression is associated with antagonism toward phloem-specific CLAVATA3/EMBRYO SURROUNDING REGION-RELATED 45 (CLE45) peptide signaling in roots. Hyperactive CLE45 signaling causes phloem sieve element differentiation defects, and consistently, knockout of CLE45 perception in bri3 background restores proper phloem development. However, bri3 dwarfism is retained in such lines. Our results thus reveal local and systemic effects of brassinosteroid perception in the phloem: whereas it locally antagonizes CLE45 signaling to permit phloem differentiation, it systemically instructs plant organ formation via a phloem-derived, non-cell-autonomous signal.

@article{zhang_arabidopsis_2020,
	title = {Arabidopsis {Flippases} {Cooperate} with {ARF} {GTPase} {Exchange} {Factors} to {Regulate} the {Trafficking} and {Polarity} of {PIN} {Auxin} {Transporters}[{OPEN}]},
	volume = {32},
	issn = {1040-4651},
	url = {https://doi.org/10.1105/tpc.19.00869},
	doi = {10.1105/tpc.19.00869},
	abstract = {Cell polarity is a fundamental feature of all multicellular organisms. PIN auxin transporters are important cell polarity markers that play crucial roles in a plethora of developmental processes in plants. Here, to identify components involved in cell polarity establishment and maintenance in plants, we performed a forward genetic screening of PIN2:PIN1-HA;pin2 Arabidopsis (Arabidopsis thaliana) plants, which ectopically express predominantly basally localized PIN1 in root epidermal cells, leading to agravitropic root growth. We identified the regulator of PIN polarity 12 (repp12) mutation, which restored gravitropic root growth and caused a switch in PIN1-HA polarity from the basal to apical side of root epidermal cells. Next Generation Sequencing and complementation experiments established the causative mutation of repp12 as a single amino acid exchange in Aminophospholipid ATPase3 (ALA3), a phospholipid flippase predicted to function in vesicle formation. repp12 and ala3 T-DNA mutants show defects in many auxin-regulated processes, asymmetric auxin distribution, and PIN trafficking. Analysis of quintuple and sextuple mutants confirmed the crucial roles of ALA proteins in regulating plant development as well as PIN trafficking and polarity. Genetic and physical interaction studies revealed that ALA3 functions together with the ADP ribosylation factor GTPase exchange factors GNOM and BIG3 in regulating PIN polarity, trafficking, and auxin-mediated development.},
	number = {5},
	urldate = {2022-05-02},
	journal = {The Plant Cell},
	author = {Zhang, Xixi and Adamowski, Maciek and Marhava, Petra and Tan, Shutang and Zhang, Yuzhou and Rodriguez, Lesia and Zwiewka, Marta and Pukyšová, Vendula and Sánchez, Adrià Sans and Raxwal, Vivek Kumar and Hardtke, Christian S. and Nodzyński, Tomasz and Friml, Jiří},
	month = may,
	year = {2020},
	pages = {1644--1664},
}

Cell polarity is a fundamental feature of all multicellular organisms. PIN auxin transporters are important cell polarity markers that play crucial roles in a plethora of developmental processes in plants. Here, to identify components involved in cell polarity establishment and maintenance in plants, we performed a forward genetic screening of PIN2:PIN1-HA;pin2 Arabidopsis (Arabidopsis thaliana) plants, which ectopically express predominantly basally localized PIN1 in root epidermal cells, leading to agravitropic root growth. We identified the regulator of PIN polarity 12 (repp12) mutation, which restored gravitropic root growth and caused a switch in PIN1-HA polarity from the basal to apical side of root epidermal cells. Next Generation Sequencing and complementation experiments established the causative mutation of repp12 as a single amino acid exchange in Aminophospholipid ATPase3 (ALA3), a phospholipid flippase predicted to function in vesicle formation. repp12 and ala3 T-DNA mutants show defects in many auxin-regulated processes, asymmetric auxin distribution, and PIN trafficking. Analysis of quintuple and sextuple mutants confirmed the crucial roles of ALA proteins in regulating plant development as well as PIN trafficking and polarity. Genetic and physical interaction studies revealed that ALA3 functions together with the ADP ribosylation factor GTPase exchange factors GNOM and BIG3 in regulating PIN polarity, trafficking, and auxin-mediated development.

@article{marhava_plasma_2020,
	title = {Plasma {Membrane} {Domain} {Patterning} and {Self}-{Reinforcing} {Polarity} in {Arabidopsis}},
	volume = {52},
	issn = {1534-5807},
	url = {https://www.sciencedirect.com/science/article/pii/S1534580719309840},
	doi = {10.1016/j.devcel.2019.11.015},
	abstract = {Cell polarity is a key feature in the development of multicellular organisms. For instance, asymmetrically localized plasma-membrane-integral PIN-FORMED (PIN) proteins direct transcellular fluxes of the phytohormone auxin that govern plant development. Fine-tuned auxin flux is important for root protophloem sieve element differentiation and requires the interacting plasma-membrane-associated BREVIS RADIX (BRX) and PROTEIN KINASE ASSOCIATED WITH BRX (PAX) proteins. We observed “donut-like” polar PIN localization in developing sieve elements that depends on complementary, “muffin-like” polar localization of BRX and PAX. Plasma membrane association and polarity of PAX, and indirectly BRX, largely depends on phosphatidylinositol-4,5-bisphosphate. Consistently, mutants in phosphatidylinositol-4-phosphate 5-kinases (PIP5Ks) display protophloem differentiation defects similar to brx mutants. The same PIP5Ks are in complex with BRX and display “muffin-like” polar localization. Our data suggest that the BRX-PAX module recruits PIP5Ks to reinforce PAX polarity and thereby the polarity of all three proteins, which is required to maintain a local PIN minimum.},
	language = {en},
	number = {2},
	urldate = {2022-05-02},
	journal = {Developmental Cell},
	author = {Marhava, Petra and Aliaga Fandino, Ana Cecilia and Koh, Samuel W. H. and Jelínková, Adriana and Kolb, Martina and Janacek, Dorina P. and Breda, Alice S. and Cattaneo, Pietro and Hammes, Ulrich Z. and Petrášek, Jan and Hardtke, Christian S.},
	month = jan,
	year = {2020},
	keywords = {DRP1A, PIP5K1, PIP5K2, endocytosis, phloem, polar auxin transport, polarity, protophloem, root},
	pages = {223--235.e5},
}

Cell polarity is a key feature in the development of multicellular organisms. For instance, asymmetrically localized plasma-membrane-integral PIN-FORMED (PIN) proteins direct transcellular fluxes of the phytohormone auxin that govern plant development. Fine-tuned auxin flux is important for root protophloem sieve element differentiation and requires the interacting plasma-membrane-associated BREVIS RADIX (BRX) and PROTEIN KINASE ASSOCIATED WITH BRX (PAX) proteins. We observed “donut-like” polar PIN localization in developing sieve elements that depends on complementary, “muffin-like” polar localization of BRX and PAX. Plasma membrane association and polarity of PAX, and indirectly BRX, largely depends on phosphatidylinositol-4,5-bisphosphate. Consistently, mutants in phosphatidylinositol-4-phosphate 5-kinases (PIP5Ks) display protophloem differentiation defects similar to brx mutants. The same PIP5Ks are in complex with BRX and display “muffin-like” polar localization. Our data suggest that the BRX-PAX module recruits PIP5Ks to reinforce PAX polarity and thereby the polarity of all three proteins, which is required to maintain a local PIN minimum.

@article{moret_local_2020,
	title = {Local auxin competition explains fragmented differentiation patterns},
	volume = {11},
	copyright = {2020 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-020-16803-7},
	doi = {10.1038/s41467-020-16803-7},
	abstract = {Trajectories of cellular ontogeny are tightly controlled and often involve feedback-regulated molecular antagonism. For example, sieve element differentiation along developing protophloem cell files of Arabidopsis roots requires two antagonistic regulators of auxin efflux. Paradoxically, loss-of-function in either regulator triggers similar, seemingly stochastic differentiation failures of individual sieve element precursors. Here we show that these patterning defects are distinct and non-random. They can be explained by auxin-dependent bistability that emerges from competition for auxin between neighboring cells. This bistability depends on the presence of an auxin influx facilitator, and can be triggered by either flux enhancement or repression. Our results uncover a hitherto overlooked aspect of auxin uptake, and highlight the contributions of local auxin influx, efflux and biosynthesis to protophloem formation. Moreover, the combined experimental-modeling approach suggests that without auxin efflux homeostasis, auxin influx interferes with coordinated differentiation.},
	language = {en},
	number = {1},
	urldate = {2022-05-02},
	journal = {Nature Communications},
	author = {Moret, Bernard and Marhava, Petra and Aliaga Fandino, Ana Cecilia and Hardtke, Christian S. and ten Tusscher, Kirsten H. W.},
	month = jun,
	year = {2020},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Auxin, Patterning},
	pages = {2965},
}

Trajectories of cellular ontogeny are tightly controlled and often involve feedback-regulated molecular antagonism. For example, sieve element differentiation along developing protophloem cell files of Arabidopsis roots requires two antagonistic regulators of auxin efflux. Paradoxically, loss-of-function in either regulator triggers similar, seemingly stochastic differentiation failures of individual sieve element precursors. Here we show that these patterning defects are distinct and non-random. They can be explained by auxin-dependent bistability that emerges from competition for auxin between neighboring cells. This bistability depends on the presence of an auxin influx facilitator, and can be triggered by either flux enhancement or repression. Our results uncover a hitherto overlooked aspect of auxin uptake, and highlight the contributions of local auxin influx, efflux and biosynthesis to protophloem formation. Moreover, the combined experimental-modeling approach suggests that without auxin efflux homeostasis, auxin influx interferes with coordinated differentiation.

@article{parry_current_2020,
	title = {Current status of the multinational {Arabidopsis} community},
	volume = {4},
	issn = {2475-4455},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/pld3.248},
	doi = {10/gpn668},
	abstract = {The multinational Arabidopsis research community is highly collaborative and over the past thirty years these activities have been documented by the Multinational Arabidopsis Steering Committee (MASC). Here, we (a) highlight recent research advances made with the reference plant Arabidopsis thaliana; (b) provide summaries from recent reports submitted by MASC subcommittees, projects and resources associated with MASC and from MASC country representatives; and (c) initiate a call for ideas and foci for the “fourth decadal roadmap,” which will advise and coordinate the global activities of the Arabidopsis research community.},
	language = {en},
	number = {7},
	urldate = {2022-03-14},
	journal = {Plant Direct},
	author = {Parry, Geraint and Provart, Nicholas J. and Brady, Siobhan M. and Uzilday, Baris and Committee, The Multinational Arabidopsis Steering},
	year = {2020},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/pld3.248},
	keywords = {Arabidopsis thaliana, Research Network, collaboration, roadmap},
	pages = {e00248},
}

The multinational Arabidopsis research community is highly collaborative and over the past thirty years these activities have been documented by the Multinational Arabidopsis Steering Committee (MASC). Here, we (a) highlight recent research advances made with the reference plant Arabidopsis thaliana; (b) provide summaries from recent reports submitted by MASC subcommittees, projects and resources associated with MASC and from MASC country representatives; and (c) initiate a call for ideas and foci for the “fourth decadal roadmap,” which will advise and coordinate the global activities of the Arabidopsis research community.

@article{abreu_metabolite_2020,
	title = {A metabolite roadmap of the wood‐forming tissue in {Populus} tremula},
	volume = {228},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.16799},
	doi = {10.1111/nph.16799},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Abreu, Ilka N. and Johansson, Annika I. and Sokołowska, Katarzyna and Niittylä, Totte and Sundberg, Björn and Hvidsten, Torgeir R. and Street, Nathaniel R. and Moritz, Thomas},
	month = dec,
	year = {2020},
	pages = {1559--1572},
}

@article{wang_evidence_2020,
	title = {Evidence for widespread selection in shaping the genomic landscape during speciation of {Populus}},
	volume = {29},
	issn = {0962-1083, 1365-294X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.15388},
	doi = {10.1111/mec.15388},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Molecular Ecology},
	author = {Wang, Jing and Street, Nathaniel R. and Park, Eung‐Jun and Liu, Jianquan and Ingvarsson, Pär K.},
	month = mar,
	year = {2020},
	pages = {1120--1136},
}

@article{mahler_leaf_2020,
	title = {Leaf shape in {Populus} tremula is a complex, omnigenic trait},
	volume = {10},
	issn = {2045-7758, 2045-7758},
	url = {https://onlinelibrary.wiley.com/doi/10.1002/ece3.6691},
	doi = {10.1002/ece3.6691},
	language = {en},
	number = {21},
	urldate = {2021-06-07},
	journal = {Ecology and Evolution},
	author = {Mähler, Niklas and Schiffthaler, Bastian and Robinson, Kathryn M. and Terebieniec, Barbara K. and Vučak, Matej and Mannapperuma, Chanaka and Bailey, Mark E. S. and Jansson, Stefan and Hvidsten, Torgeir R. and Street, Nathaniel R.},
	month = nov,
	year = {2020},
	pages = {11922--11940},
}

@article{apuli_inferring_2020,
	title = {Inferring the {Genomic} {Landscape} of {Recombination} {Rate} {Variation} in {European} {Aspen} ( {Populus} tremula )},
	volume = {10},
	issn = {2160-1836},
	url = {https://academic.oup.com/g3journal/article/10/1/299/6020315},
	doi = {10/gjctk2},
	abstract = {Abstract
            The rate of meiotic recombination is one of the central factors determining genome-wide levels of linkage disequilibrium which has important consequences for the efficiency of natural selection and for the dissection of quantitative traits. Here we present a new, high-resolution linkage map for Populus tremula that we use to anchor approximately two thirds of the P. tremula draft genome assembly on to the expected 19 chromosomes, providing us with the first chromosome-scale assembly for P. tremula (Table 2). We then use this resource to estimate variation in recombination rates across the P. tremula genome and compare these results to recombination rates based on linkage disequilibrium in a large number of unrelated individuals. We also assess how variation in recombination rates is associated with a number of genomic features, such as gene density, repeat density and methylation levels. We find that recombination rates obtained from the two methods largely agree, although the LD-based method identifies a number of genomic regions with very high recombination rates that the map-based method fails to detect. Linkage map and LD-based estimates of recombination rates are positively correlated and show similar correlations with other genomic features, showing that both methods can accurately infer recombination rate variation across the genome. Recombination rates are positively correlated with gene density and negatively correlated with repeat density and methylation levels, suggesting that recombination is largely directed toward gene regions in P. tremula.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {G3 Genes{\textbar}Genomes{\textbar}Genetics},
	author = {Apuli, Rami-Petteri and Bernhardsson, Carolina and Schiffthaler, Bastian and Robinson, Kathryn M and Jansson, Stefan and Street, Nathaniel R and Ingvarsson, Pär K},
	month = jan,
	year = {2020},
	pages = {299--309},
}

Abstract The rate of meiotic recombination is one of the central factors determining genome-wide levels of linkage disequilibrium which has important consequences for the efficiency of natural selection and for the dissection of quantitative traits. Here we present a new, high-resolution linkage map for Populus tremula that we use to anchor approximately two thirds of the P. tremula draft genome assembly on to the expected 19 chromosomes, providing us with the first chromosome-scale assembly for P. tremula (Table 2). We then use this resource to estimate variation in recombination rates across the P. tremula genome and compare these results to recombination rates based on linkage disequilibrium in a large number of unrelated individuals. We also assess how variation in recombination rates is associated with a number of genomic features, such as gene density, repeat density and methylation levels. We find that recombination rates obtained from the two methods largely agree, although the LD-based method identifies a number of genomic regions with very high recombination rates that the map-based method fails to detect. Linkage map and LD-based estimates of recombination rates are positively correlated and show similar correlations with other genomic features, showing that both methods can accurately infer recombination rate variation across the genome. Recombination rates are positively correlated with gene density and negatively correlated with repeat density and methylation levels, suggesting that recombination is largely directed toward gene regions in P. tremula.

@article{pozo_three-way_2020,
	title = {Three-way {Interactions} between {Plants}, {Microbes}, and {Arthropods} ({PMA}): {Impacts}, {Mechanisms}, and {Prospects} for {Sustainable} {Plant} {Protection}},
	volume = {32},
	issn = {1040-4651, 1532-298X},
	shorttitle = {Three-way {Interactions} between {Plants}, {Microbes}, and {Arthropods} ({PMA})},
	url = {https://academic.oup.com/plcell/article/doi/10.1105/tpc.120.tt0720/6115734},
	doi = {10.1105/tpc.120.tt0720},
	abstract = {Three-way Interactions between Plants, Microbes, and Arthropods (PMA): Impacts, Mechanisms, and Prospects for Sustainable Plant Protection (By Maria J. Pozo, Benedicte R. Albrectsen, Eduardo R. Bejarano, Eduardo de la Peña, Salva Herrero, Ainhoa Martinez-Medina, Victoria Pastor, Sabine Ravnskov, Mary Williams and Arjen Biere)
            Plants constantly interact with numerous of organisms and the outcome of these interactions determines plant health and growth. In other words, the phenotype of a plant is not only the result of the plant’s interaction with abiotic conditions, but also of multiple interactions in the living environment surrounding the plant, the phytobiome. In this Teaching Tool, we have focused on interactions between plants, microbes and arthropods (PMA). The organism groups that contribute to PMA interactions are presented as well as types of interactions between them, along with multiple examples of simple and more complex PMA interactions. The underlying mechanisms of plant responses are described in detail as well as the evolutionary aspects of PMA interactions. Finally, the use of PMA interactions for crop protection in sustainable plant production that supports the UN Sustainable Development Goals for 2030 is proposed.
            (Posted July 6, 2020)
            Click HERE to access Teaching Tool Components
            RECOMMENDED CITATION STYLE:
            Pozo, M.J., Albrectsen, B.R., Bejarano, E.R., de la Peña, E., Herrero, S., Martinez-Medina, A., Pastor, V., Ravnskov, S., Williams, M., and Biere, A. (July NN, 2020). Three-way interactions between plants, microbes, and arthropods (PMA): Impacts, mechanisms, and prospects for sustainable plant protection. Teaching Tools in Plant Biology: Lecture Notes. The Plant Cell (online), doi/10.1105/tpc.120.tt0720},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {The Plant Cell},
	author = {Pozo, M. J. and Albrectsen, B. R. and Bejarano, E. and de la Pena, E. and Herrero, S. and Martinez-Medina, A. and Pastor, V. and Ravnskov, S. and Biere, A.},
	month = jul,
	year = {2020},
	pages = {tpc.120.tt0720},
}

Three-way Interactions between Plants, Microbes, and Arthropods (PMA): Impacts, Mechanisms, and Prospects for Sustainable Plant Protection (By Maria J. Pozo, Benedicte R. Albrectsen, Eduardo R. Bejarano, Eduardo de la Peña, Salva Herrero, Ainhoa Martinez-Medina, Victoria Pastor, Sabine Ravnskov, Mary Williams and Arjen Biere) Plants constantly interact with numerous of organisms and the outcome of these interactions determines plant health and growth. In other words, the phenotype of a plant is not only the result of the plant’s interaction with abiotic conditions, but also of multiple interactions in the living environment surrounding the plant, the phytobiome. In this Teaching Tool, we have focused on interactions between plants, microbes and arthropods (PMA). The organism groups that contribute to PMA interactions are presented as well as types of interactions between them, along with multiple examples of simple and more complex PMA interactions. The underlying mechanisms of plant responses are described in detail as well as the evolutionary aspects of PMA interactions. Finally, the use of PMA interactions for crop protection in sustainable plant production that supports the UN Sustainable Development Goals for 2030 is proposed. (Posted July 6, 2020) Click HERE to access Teaching Tool Components RECOMMENDED CITATION STYLE: Pozo, M.J., Albrectsen, B.R., Bejarano, E.R., de la Peña, E., Herrero, S., Martinez-Medina, A., Pastor, V., Ravnskov, S., Williams, M., and Biere, A. (July NN, 2020). Three-way interactions between plants, microbes, and arthropods (PMA): Impacts, mechanisms, and prospects for sustainable plant protection. Teaching Tools in Plant Biology: Lecture Notes. The Plant Cell (online), doi/10.1105/tpc.120.tt0720

@incollection{raggi_auxin_2020,
	title = {Auxin},
	isbn = {978-1-119-35725-4},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/9781119357254.ch5},
	abstract = {As synthetic auxins are valuable tools for dissecting the chemistry and biology of auxin, it is important to understand the mechanisms of their transport compared to indole-3-acetic acid (IAA). The discovery of auxin was followed by enthusiastic attempts to synthesize more plant growth-promoting substances similar to IAA. The formation of auxin gradients is essential for many different developmental events such as specification of apical and basal axes in the embryo, maintenance of meristematic activity, formation of leaves, lateral roots, flowers and hypocotyls, and root bending. The application of structurally different auxin-like molecules, together with the development of molecular biology and biochemical techniques, has deepened the understanding of how auxin works and what its characteristics are. Furthermore, the use of small molecules as tools to perturb the complex pathways of auxin metabolism, transport and signalling has greatly assisted our journey of understanding.},
	language = {en},
	urldate = {2021-12-09},
	booktitle = {The {Chemical} {Biology} of {Plant} {Biostimulants}},
	publisher = {John Wiley \& Sons, Ltd},
	author = {Raggi, Sara and Doyle, Siamsa M. and Robert, Stéphanie},
	year = {2020},
	doi = {10.1002/9781119357254.ch5},
	note = {Section: 5
\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/9781119357254.ch5},
	keywords = {auxin biology, auxin chemistry, auxin gradient, auxin metabolism, indole-3-acetic acid, plant growth-promoting substances, synthetic auxins},
	pages = {123--153},
}

As synthetic auxins are valuable tools for dissecting the chemistry and biology of auxin, it is important to understand the mechanisms of their transport compared to indole-3-acetic acid (IAA). The discovery of auxin was followed by enthusiastic attempts to synthesize more plant growth-promoting substances similar to IAA. The formation of auxin gradients is essential for many different developmental events such as specification of apical and basal axes in the embryo, maintenance of meristematic activity, formation of leaves, lateral roots, flowers and hypocotyls, and root bending. The application of structurally different auxin-like molecules, together with the development of molecular biology and biochemical techniques, has deepened the understanding of how auxin works and what its characteristics are. Furthermore, the use of small molecules as tools to perturb the complex pathways of auxin metabolism, transport and signalling has greatly assisted our journey of understanding.

@article{lakehal_ethylene_2020,
	title = {{ETHYLENE} {RESPONSE} {FACTOR} 115 integrates jasmonate and cytokinin signaling machineries to repress adventitious rooting in {Arabidopsis}},
	volume = {228},
	copyright = {©2020 The Authors. New Phytologist ©2020 New Phytologist Trust},
	issn = {1469-8137},
	url = {https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.16794},
	doi = {10/ghhwk4},
	abstract = {Adventitious root initiation (ARI) is a de novo organogenesis program and a key adaptive trait in plants. Several hormones regulate ARI but the underlying genetic architecture that integrates the hormonal crosstalk governing this process remains largely elusive. In this study, we use genetics, genome editing, transcriptomics, hormone profiling and cell biological approaches to demonstrate a crucial role played by the APETALA2/ETHYLENE RESPONSE FACTOR 115 transcription factor. We demonstrate that ERF115 functions as a repressor of ARI by activating the cytokinin (CK) signaling machinery. We also demonstrate that ERF115 is transcriptionally activated by jasmonate (JA), an oxylipin-derived phytohormone, which represses ARI in NINJA-dependent and independent manners. Our data indicate that NINJA-dependent JA signaling in pericycle cells blocks early events of ARI. Altogether, our results reveal a previously unreported molecular network involving cooperative crosstalk between JA and CK machineries that represses ARI.},
	language = {en},
	number = {5},
	urldate = {2021-06-21},
	journal = {New Phytologist},
	author = {Lakehal, Abdellah and Dob, Asma and Rahneshan, Zahra and Novák, Ondřej and Escamez, Sacha and Alallaq, Sanaria and Strnad, Miroslav and Tuominen, Hannele and Bellini, Catherine},
	year = {2020},
	keywords = {AP2/ERF transcription factors, adventitious rooting, cytokinins, de novo organogenesis, jasmonate},
	pages = {1611--1626},
}

Adventitious root initiation (ARI) is a de novo organogenesis program and a key adaptive trait in plants. Several hormones regulate ARI but the underlying genetic architecture that integrates the hormonal crosstalk governing this process remains largely elusive. In this study, we use genetics, genome editing, transcriptomics, hormone profiling and cell biological approaches to demonstrate a crucial role played by the APETALA2/ETHYLENE RESPONSE FACTOR 115 transcription factor. We demonstrate that ERF115 functions as a repressor of ARI by activating the cytokinin (CK) signaling machinery. We also demonstrate that ERF115 is transcriptionally activated by jasmonate (JA), an oxylipin-derived phytohormone, which represses ARI in NINJA-dependent and independent manners. Our data indicate that NINJA-dependent JA signaling in pericycle cells blocks early events of ARI. Altogether, our results reveal a previously unreported molecular network involving cooperative crosstalk between JA and CK machineries that represses ARI.

@incollection{champion_multiple_2020,
	address = {New York, NY},
	title = {Multiple {Roles} of {Jasmonates} in {Shaping} {Rhizotaxis}: {Emerging} {Integrators}},
	volume = {2085},
	isbn = {978-1-07-160141-9 978-1-07-160142-6},
	shorttitle = {Multiple {Roles} of {Jasmonates} in {Shaping} {Rhizotaxis}},
	url = {http://link.springer.com/10.1007/978-1-0716-0142-6_1},
	language = {en},
	urldate = {2021-06-07},
	booktitle = {Jasmonate in {Plant} {Biology}},
	publisher = {Springer US},
	author = {Lakehal, Abdellah and Ranjan, Alok and Bellini, Catherine},
	editor = {Champion, Antony and Laplaze, Laurent},
	year = {2020},
	pages = {3--22},
}

@incollection{raggi_auxin_2020,
	title = {Auxin: at the crossroads between chemistry and biology},
	isbn = {978-1-119-35725-4},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/9781119357254.ch5},
	abstract = {As synthetic auxins are valuable tools for dissecting the chemistry and biology of auxin, it is important to understand the mechanisms of their transport compared to indole-3-acetic acid (IAA). The discovery of auxin was followed by enthusiastic attempts to synthesize more plant growth-promoting substances similar to IAA. The formation of auxin gradients is essential for many different developmental events such as specification of apical and basal axes in the embryo, maintenance of meristematic activity, formation of leaves, lateral roots, flowers and hypocotyls, and root bending. The application of structurally different auxin-like molecules, together with the development of molecular biology and biochemical techniques, has deepened the understanding of how auxin works and what its characteristics are. Furthermore, the use of small molecules as tools to perturb the complex pathways of auxin metabolism, transport and signalling has greatly assisted our journey of understanding.},
	language = {en},
	urldate = {2021-10-21},
	booktitle = {The {Chemical} {Biology} of {Plant} {Biostimulants}},
	publisher = {John Wiley \& Sons, Ltd},
	author = {Raggi, Sara and Doyle, Siamsa M. and Robert, Stéphanie},
	year = {2020},
	keywords = {auxin biology, auxin chemistry, auxin gradient, auxin metabolism, indole-3-acetic acid, plant growth-promoting substances, synthetic auxins},
	pages = {123--153},
}

As synthetic auxins are valuable tools for dissecting the chemistry and biology of auxin, it is important to understand the mechanisms of their transport compared to indole-3-acetic acid (IAA). The discovery of auxin was followed by enthusiastic attempts to synthesize more plant growth-promoting substances similar to IAA. The formation of auxin gradients is essential for many different developmental events such as specification of apical and basal axes in the embryo, maintenance of meristematic activity, formation of leaves, lateral roots, flowers and hypocotyls, and root bending. The application of structurally different auxin-like molecules, together with the development of molecular biology and biochemical techniques, has deepened the understanding of how auxin works and what its characteristics are. Furthermore, the use of small molecules as tools to perturb the complex pathways of auxin metabolism, transport and signalling has greatly assisted our journey of understanding.

@article{dhurva_prasad_establishment_2020,
	title = {Establishment of regenerative callus, cell suspension system, and molecular characterization of {Taxus} wallichiana {Zucc}. for the in vitro production of {Taxol}},
	issn = {22313354},
	url = {https://japsonline.com/abstract.php?article_id=3374&sts=2},
	doi = {10/gkfc6w},
	abstract = {Taxus wallichiana, an endangered Taxus species native to Nepal, is a source of Taxol (paclitaxel), an anticancer drug, which if produced via plant cell culture in vitro not only reduces the pressure on natural habitat but also allows continuous production throughout the seasons. Gamborg’s B5 medium was the culture medium to develop callus and suspension culture. Quantification of Taxol was carried out via high performance liquid chromatography (HPLC) using C18 column, water-acetonitrile mobile phase, and 1 ml/minute flowrate at 227 nm wavelength. Genetic variation among population was determined using the POPGEN32, version 1.31. Best callus response was in medium with 1 mg/l 2,4-D for both stem and needle explants. For cell suspension culture, callus from needle explants showed better response compared to stem. Fructose and sucrose proved to be the best carbon sources. Cell count increased as carbon concentration increased. 2,4-D at low concentration ({\textless}2 mg/l) and naphthaleneacetic acid at high concentration ({\textgreater}5 mg/l) showed higher cell growth rate. Inoculum volume was directly proportional to cell count. Extra addition of macronutrients had inhibitory effect on cell count, but the effect was reversed for MgSO4. Using HPLC, for bark, the highest Taxol yield was 0.057 mg/g distilled water (DW), while for needle was 0.056 mg/g DW. For suspension cultured HPLC samples, Taxol yield ranged at 0.004\%. Size range of amplified Deoxyribonucleic acids was between 200 and 2,000 bp. Thus, this investigation generated a concrete data for Taxus population of Nepal providing efficient protocols for establishment of callus and cell suspension culture with the aim of producing Taxol in in vitro conditions.},
	language = {en},
	urldate = {2021-08-12},
	journal = {Journal of Applied Pharmaceutical Science},
	author = {Dhurva Prasad, Gauchan and Sudina, Bhuju and Janardan, Lamichhane and Rajani, Shakya and María Rosario, García-Gil},
	month = jun,
	year = {2020},
}

Taxus wallichiana, an endangered Taxus species native to Nepal, is a source of Taxol (paclitaxel), an anticancer drug, which if produced via plant cell culture in vitro not only reduces the pressure on natural habitat but also allows continuous production throughout the seasons. Gamborg’s B5 medium was the culture medium to develop callus and suspension culture. Quantification of Taxol was carried out via high performance liquid chromatography (HPLC) using C18 column, water-acetonitrile mobile phase, and 1 ml/minute flowrate at 227 nm wavelength. Genetic variation among population was determined using the POPGEN32, version 1.31. Best callus response was in medium with 1 mg/l 2,4-D for both stem and needle explants. For cell suspension culture, callus from needle explants showed better response compared to stem. Fructose and sucrose proved to be the best carbon sources. Cell count increased as carbon concentration increased. 2,4-D at low concentration (\textless2 mg/l) and naphthaleneacetic acid at high concentration (\textgreater5 mg/l) showed higher cell growth rate. Inoculum volume was directly proportional to cell count. Extra addition of macronutrients had inhibitory effect on cell count, but the effect was reversed for MgSO4. Using HPLC, for bark, the highest Taxol yield was 0.057 mg/g distilled water (DW), while for needle was 0.056 mg/g DW. For suspension cultured HPLC samples, Taxol yield ranged at 0.004%. Size range of amplified Deoxyribonucleic acids was between 200 and 2,000 bp. Thus, this investigation generated a concrete data for Taxus population of Nepal providing efficient protocols for establishment of callus and cell suspension culture with the aim of producing Taxol in in vitro conditions.

@article{yu_ralf1-feronia_2020,
	title = {The {RALF1}-{FERONIA} interaction modulates endocytosis to mediate control of root growth in \textit{{Arabidopsis}}},
	issn = {1477-9129, 0950-1991},
	url = {https://journals.biologists.com/dev/article/doi/10.1242/dev.189902/266898/The-RALF1-FERONIA-interaction-modulates},
	doi = {10.1242/dev.189902},
	abstract = {The interaction between the receptor-like kinase (RLK) FERONIA (FER) and the secreted peptide Rapid Alkalinization Factor 1 (RALF1) is vital for development and stress responses in Arabidopsis. Ligand-induced membrane dynamics affect the function of several RLKs, but the effects of the RALF1-FER interaction on the dynamics of FER and the ensuing effects on its functionality are poorly understood. Here, we show that RALF1 modulated the dynamics and partitioning of FER-GFP at the plasma membrane (PM). Moreover, FER was internalized by both clathrin-mediated endocytosis (CME) and clathrin-independent endocytosis (CIE) under steady state conditions. After RALF1 treatment, FER-GFP internalization was primarily enhanced via the CME pathway, raising FER-GFP levels in the vacuole. RALF1 treatment also modulated trafficking of other PM proteins such as PIN2-GFP and BRI1-GFP, increasing their vacuolar levels by enhancing their internalization. Importantly, blocking CME attenuated RALF1-mediated root growth inhibition independently of RALF1-induced early signaling, suggesting that the RALF1 can also exert its effects via the CME pathway. These findings reveal that the RALF1-FER interaction modulates plant growth and development and this may also involve endocytosis of PM proteins.},
	language = {en},
	urldate = {2021-06-07},
	journal = {Development},
	author = {Yu, Meng and Li, Ruili and Cui, Yaning and Chen, Weijun and Li, Bin and Zhang, Xi and Bu, Yufen and Cao, Yangyang and Xing, Jingjing and Jewaria, Pawan Kumar and Li, Xiaojuan and Bhalerao, Rishikesh P. and Yu, Feng and Lin, Jinxing},
	month = jan,
	year = {2020},
	pages = {dev.189902},
}

The interaction between the receptor-like kinase (RLK) FERONIA (FER) and the secreted peptide Rapid Alkalinization Factor 1 (RALF1) is vital for development and stress responses in Arabidopsis. Ligand-induced membrane dynamics affect the function of several RLKs, but the effects of the RALF1-FER interaction on the dynamics of FER and the ensuing effects on its functionality are poorly understood. Here, we show that RALF1 modulated the dynamics and partitioning of FER-GFP at the plasma membrane (PM). Moreover, FER was internalized by both clathrin-mediated endocytosis (CME) and clathrin-independent endocytosis (CIE) under steady state conditions. After RALF1 treatment, FER-GFP internalization was primarily enhanced via the CME pathway, raising FER-GFP levels in the vacuole. RALF1 treatment also modulated trafficking of other PM proteins such as PIN2-GFP and BRI1-GFP, increasing their vacuolar levels by enhancing their internalization. Importantly, blocking CME attenuated RALF1-mediated root growth inhibition independently of RALF1-induced early signaling, suggesting that the RALF1 can also exert its effects via the CME pathway. These findings reveal that the RALF1-FER interaction modulates plant growth and development and this may also involve endocytosis of PM proteins.

@article{zhang_chromatin-modifying_2020,
	title = {The chromatin-modifying protein {HUB2} is involved in the regulation of lignin composition in xylem vessels},
	volume = {71},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article/71/18/5484/5849544},
	doi = {10.1093/jxb/eraa264},
	abstract = {Abstract
            PIRIN2 (PRN2) was earlier reported to suppress syringyl (S)-type lignin accumulation of xylem vessels of Arabidopsis thaliana. In the present study, we report yeast two-hybrid results supporting the interaction of PRN2 with HISTONE MONOUBIQUITINATION2 (HUB2) in Arabidopsis. HUB2 has been previously implicated in several plant developmental processes, but not in lignification. Interaction between PRN2 and HUB2 was verified by β-galactosidase enzymatic and co-immunoprecipitation assays. HUB2 promoted the deposition of S-type lignin in the secondary cell walls of both stem and hypocotyl tissues, as analysed by pyrolysis-GC/MS. Chemical fingerprinting of individual xylem vessel cell walls by Raman and Fourier transform infrared microspectroscopy supported the function of HUB2 in lignin deposition. These results, together with a genetic analysis of the hub2 prn2 double mutant, support the antagonistic function of PRN2 and HUB2 in deposition of S-type lignin. Transcriptome analyses indicated the opposite regulation of the S-type lignin biosynthetic gene FERULATE-5-HYDROXYLASE1 by PRN2 and HUB2 as the underlying mechanism. PRN2 and HUB2 promoter activities co-localized in cells neighbouring the xylem vessel elements, suggesting that the S-type lignin-promoting function of HUB2 is antagonized by PRN2 for the benefit of the guaiacyl (G)-type lignin enrichment of the neighbouring xylem vessel elements.},
	language = {en},
	number = {18},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Zhang, Bo and Sztojka, Bernadette and Seyfferth, Carolin and Escamez, Sacha and Miskolczi, Pál and Chantreau, Maxime and Bakó, László and Delhomme, Nicolas and Gorzsás, András and Bhalerao, Rishikesh P. and Tuominen, Hannele},
	editor = {Turner, Simon},
	month = sep,
	year = {2020},
	pages = {5484--5494},
}

Abstract PIRIN2 (PRN2) was earlier reported to suppress syringyl (S)-type lignin accumulation of xylem vessels of Arabidopsis thaliana. In the present study, we report yeast two-hybrid results supporting the interaction of PRN2 with HISTONE MONOUBIQUITINATION2 (HUB2) in Arabidopsis. HUB2 has been previously implicated in several plant developmental processes, but not in lignification. Interaction between PRN2 and HUB2 was verified by β-galactosidase enzymatic and co-immunoprecipitation assays. HUB2 promoted the deposition of S-type lignin in the secondary cell walls of both stem and hypocotyl tissues, as analysed by pyrolysis-GC/MS. Chemical fingerprinting of individual xylem vessel cell walls by Raman and Fourier transform infrared microspectroscopy supported the function of HUB2 in lignin deposition. These results, together with a genetic analysis of the hub2 prn2 double mutant, support the antagonistic function of PRN2 and HUB2 in deposition of S-type lignin. Transcriptome analyses indicated the opposite regulation of the S-type lignin biosynthetic gene FERULATE-5-HYDROXYLASE1 by PRN2 and HUB2 as the underlying mechanism. PRN2 and HUB2 promoter activities co-localized in cells neighbouring the xylem vessel elements, suggesting that the S-type lignin-promoting function of HUB2 is antagonized by PRN2 for the benefit of the guaiacyl (G)-type lignin enrichment of the neighbouring xylem vessel elements.

@article{espinal-centeno_conservation_2020,
	title = {Conservation analysis of core cell cycle regulators and their transcriptional behavior during limb regeneration in {Ambystoma} mexicanum},
	volume = {164},
	issn = {09254773},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0925477320300563},
	doi = {10.1016/j.mod.2020.103651},
	language = {en},
	urldate = {2021-06-07},
	journal = {Mechanisms of Development},
	author = {Espinal-Centeno, Annie and Dipp-Álvarez, Melissa and Saldaña, Carlos and Bakó, Laszlo and Cruz-Ramírez, Alfredo},
	month = dec,
	year = {2020},
	pages = {103651},
}

@article{fujita_schengen_2020,
	title = {{SCHENGEN} receptor module drives localized {ROS} production and lignification in plant roots},
	volume = {39},
	issn = {0261-4189},
	url = {https://www.embopress.org/doi/full/10.15252/embj.2019103894},
	doi = {10/gjct3x},
	abstract = {Abstract Production of reactive oxygen species (ROS) by NADPH oxidases (NOXs) impacts many processes in animals and plants, and many plant receptor pathways involve rapid, NOX-dependent increases of ROS. Yet, their general reactivity has made it challenging to pinpoint the precise role and immediate molecular action of ROS. A well-understood ROS action in plants is to provide the co-substrate for lignin peroxidases in the cell wall. Lignin can be deposited with exquisite spatial control, but the underlying mechanisms have remained elusive. Here, we establish a kinase signaling relay that exerts direct, spatial control over ROS production and lignification within the cell wall. We show that polar localization of a single kinase component is crucial for pathway function. Our data indicate that an intersection of more broadly localized components allows for micrometer-scale precision of lignification and that this system is triggered through initiation of ROS production as a critical peroxidase co-substrate.},
	number = {9},
	urldate = {2021-06-21},
	journal = {The EMBO Journal},
	author = {Fujita, Satoshi and De Bellis, Damien and Edel, Kai H and Köster, Philipp and Andersen, Tonni Grube and Schmid-Siegert, Emanuel and Dénervaud Tendon, Valérie and Pfister, Alexandre and Marhavý, Peter and Ursache, Robertas and Doblas, Verónica G and Barberon, Marie and Daraspe, Jean and Creff, Audrey and Ingram, Gwyneth and Kudla, Jörg and Geldner, Niko},
	month = may,
	year = {2020},
	note = {Publisher: John Wiley \& Sons, Ltd},
	keywords = {Casparian strips, extracellular diffusion barriers, lignin, localized ROS production, polarized signaling},
	pages = {e103894},
}

Abstract Production of reactive oxygen species (ROS) by NADPH oxidases (NOXs) impacts many processes in animals and plants, and many plant receptor pathways involve rapid, NOX-dependent increases of ROS. Yet, their general reactivity has made it challenging to pinpoint the precise role and immediate molecular action of ROS. A well-understood ROS action in plants is to provide the co-substrate for lignin peroxidases in the cell wall. Lignin can be deposited with exquisite spatial control, but the underlying mechanisms have remained elusive. Here, we establish a kinase signaling relay that exerts direct, spatial control over ROS production and lignification within the cell wall. We show that polar localization of a single kinase component is crucial for pathway function. Our data indicate that an intersection of more broadly localized components allows for micrometer-scale precision of lignification and that this system is triggered through initiation of ROS production as a critical peroxidase co-substrate.

@article{kawde_more_2020,
	title = {More than protection: the function of {TiO} $_{\textrm{2}}$ interlayers in hematite functionalized {Si} photoanodes},
	volume = {22},
	issn = {1463-9076, 1463-9084},
	shorttitle = {More than protection},
	url = {http://xlink.rsc.org/?DOI=D0CP04280C},
	doi = {10/gjdpf7},
	abstract = {Signature of performance-enhancing oxygen vacancies in the mesoporous TiO
              2
               interlayer of a hematite functionalized Si microwire photoanode revealed by hard energy X-ray spectroscopy.
            
          , 
            
              Worldwide significant efforts are ongoing to develop devices that store solar energy as fuels. In one such approach, solar energy is absorbed by semiconductors and utilized directly by catalysts at their surfaces to split water into H
              2
              and O
              2
              . To protect the semiconductors in these photo-electrochemical cells (PEC) from corrosion, frequently thin TiO
              2
              interlayers are applied. Employing a well-performing photoanode comprised of 1-D n-Si microwires (MWs) covered with a mesoporous (mp) TiO
              2
              interlayer fabricated by solution processing and functionalized with α-Fe
              2
              O
              3
              nanorods, we studied here the function of this TiO
              2
              interlayer by high-energy resolution fluorescence detected X-ray absorption near edge structure (HERFD-XANES) spectroscopy, along with X-ray emission spectroscopy (XES) and standard characterization techniques. Our data reveal that the TiO
              2
              interlayer not only protects the n-Si MW surface from corrosion, but that it also acts as a template for the hydrothermal growth of α-Fe
              2
              O
              3
              nanorods and improves the photocatalytic efficiency. We show that the latter effect correlates with the presence of stable oxygen vacancies at the interface between mp-TiO
              2
              and α-Fe
              2
              O
              3
              , which act as electron traps and thereby substantially reduce the charge recombination rate at the hematite surface.},
	language = {en},
	number = {48},
	urldate = {2021-06-07},
	journal = {Physical Chemistry Chemical Physics},
	author = {Kawde, Anurag and Annamalai, Alagappan and Sellstedt, Anita and Uhlig, Jens and Wågberg, Thomas and Glatzel, Pieter and Messinger, Johannes},
	year = {2020},
	pages = {28459--28467},
}

Signature of performance-enhancing oxygen vacancies in the mesoporous TiO 2  interlayer of a hematite functionalized Si microwire photoanode revealed by hard energy X-ray spectroscopy. , Worldwide significant efforts are ongoing to develop devices that store solar energy as fuels. In one such approach, solar energy is absorbed by semiconductors and utilized directly by catalysts at their surfaces to split water into H 2 and O 2 . To protect the semiconductors in these photo-electrochemical cells (PEC) from corrosion, frequently thin TiO 2 interlayers are applied. Employing a well-performing photoanode comprised of 1-D n-Si microwires (MWs) covered with a mesoporous (mp) TiO 2 interlayer fabricated by solution processing and functionalized with α-Fe 2 O 3 nanorods, we studied here the function of this TiO 2 interlayer by high-energy resolution fluorescence detected X-ray absorption near edge structure (HERFD-XANES) spectroscopy, along with X-ray emission spectroscopy (XES) and standard characterization techniques. Our data reveal that the TiO 2 interlayer not only protects the n-Si MW surface from corrosion, but that it also acts as a template for the hydrothermal growth of α-Fe 2 O 3 nanorods and improves the photocatalytic efficiency. We show that the latter effect correlates with the presence of stable oxygen vacancies at the interface between mp-TiO 2 and α-Fe 2 O 3 , which act as electron traps and thereby substantially reduce the charge recombination rate at the hematite surface.

@article{gil-munoz_transcriptomic_2020,
	title = {Transcriptomic {Analysis} {Reveals} {Salt} {Tolerance} {Mechanisms} {Present} in {Date}-{Plum} {Persimmon} {Rootstock} ({Diospyros} lotus {L}.)},
	volume = {10},
	issn = {2073-4395},
	url = {https://www.mdpi.com/2073-4395/10/11/1703},
	doi = {10/gjd6kb},
	abstract = {Agriculture needs solutions for adapting crops to increasing salinity globally. Research on physiological and molecular responses activated by salinity is needed to elucidate mechanisms of salinity tolerance. Transcriptome profiling (RNA-Seq) is a powerful tool to study the transcriptomic profile of genotypes under stress conditions. Persimmon species have different levels of tolerance to salinity, this variability may provide knowledge on persimmon species and development of salt--tolerant rootstocks. In this study, we conducted a physiological and transcriptomic profiling of roots and leaves in tolerant and sensitive plants of persimmon rootstock grown under saline and control conditions. Characterization of physiological responses along with gene expression changes in roots and leaves allowed the identification of several salt tolerance mechanisms related to ion transport and thermospermine synthesis. Differences were observed in putative H+/ATPases that allow transmembrane ionic transport and chloride channel protein-like genes. Furthermore, an overexpression of thermospermine synthase found in the roots of tolerant plants may indicate that alterations in root architecture could act as an additional mechanism of response to salt stress. These results indicate that Diospyros lotus L. exhibits genetically-controlled variability for salt tolerance traits which opens potential opportunities for breeding salt-tolerant persimmon rootstocks in a Mediterranean environment challenged by drought and salinity.},
	language = {en},
	number = {11},
	urldate = {2021-06-07},
	journal = {Agronomy},
	author = {Gil-Muñoz, Francisco and Delhomme, Nicolas and Quiñones, Ana and Naval, Maria del Mar and Badenes, Maria Luisa and García-Gil, M. Rosario},
	month = nov,
	year = {2020},
	pages = {1703},
}

Agriculture needs solutions for adapting crops to increasing salinity globally. Research on physiological and molecular responses activated by salinity is needed to elucidate mechanisms of salinity tolerance. Transcriptome profiling (RNA-Seq) is a powerful tool to study the transcriptomic profile of genotypes under stress conditions. Persimmon species have different levels of tolerance to salinity, this variability may provide knowledge on persimmon species and development of salt–tolerant rootstocks. In this study, we conducted a physiological and transcriptomic profiling of roots and leaves in tolerant and sensitive plants of persimmon rootstock grown under saline and control conditions. Characterization of physiological responses along with gene expression changes in roots and leaves allowed the identification of several salt tolerance mechanisms related to ion transport and thermospermine synthesis. Differences were observed in putative H+/ATPases that allow transmembrane ionic transport and chloride channel protein-like genes. Furthermore, an overexpression of thermospermine synthase found in the roots of tolerant plants may indicate that alterations in root architecture could act as an additional mechanism of response to salt stress. These results indicate that Diospyros lotus L. exhibits genetically-controlled variability for salt tolerance traits which opens potential opportunities for breeding salt-tolerant persimmon rootstocks in a Mediterranean environment challenged by drought and salinity.

@article{herrera-belaroussi_candidatus_2020,
	title = {Candidatus {Frankia} nodulisporulans sp. nov., an {Alnus} glutinosa-infective {Frankia} species unable to grow in pure culture and able to sporulate in-planta},
	volume = {43},
	issn = {07232020},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0723202020300898},
	doi = {10/gjdt2w},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Systematic and Applied Microbiology},
	author = {Herrera-Belaroussi, Aude and Normand, Philippe and Pawlowski, Katharina and Fernandez, Maria P. and Wibberg, Daniel and Kalinowski, Jörn and Brachmann, Andreas and Berckx, Fede and Lee, Natuschka and Blom, Jochen and Pozzi, Adrien C. and Fournier, Pascale and Bethencourt, Lorine and Dubost, Audrey and Abrouk, Danis and Sellstedt, Anita},
	month = nov,
	year = {2020},
	pages = {126134},
}

@article{gaillochet_hy5_2020,
	title = {{HY5} and phytochrome activity modulate shoot to root coordination during thermomorphogenesis},
	issn = {1477-9129, 0950-1991},
	url = {https://journals.biologists.com/dev/article/doi/10.1242/dev.192625/267053/HY5-and-phytochrome-activity-modulate-shoot-to},
	doi = {10/gjcxk6},
	abstract = {Temperature is one of the most impactful environmental factors to which plants adjust their growth and development. While the regulation of temperature signaling has been extensively investigated for the aerial part of plants, much less is known and understood about how roots sense and modulate their growth in response to fluctuating temperatures. Here we found that shoot and root growth responses to high ambient temperature are coordinated during early seedling development. A shoot signaling module that includes HY5, the phytochromes and the PIFs exerts a central function in coupling these growth responses and maintain auxin levels in the root. In addition to the HY5/PIF-dependent shoot module, a regulatory axis composed of auxin biosynthesis and auxin perception factors controls root responses to high ambient temperature. Together, our findings show that shoot and root developmental responses to temperature are tightly coupled during thermomorphogenesis and suggest that roots integrate energy signals with local hormonal inputs.},
	language = {en},
	urldate = {2021-06-07},
	journal = {Development},
	author = {Gaillochet, Christophe and Burko, Yogev and Platre, Matthieu Pierre and Zhang, Ling and Simura, Jan and Willige, Björn C. and Kumar, S. Vinod and Ljung, Karin and Chory, Joanne and Busch, Wolfgang},
	month = jan,
	year = {2020},
	pages = {dev.192625},
}

Temperature is one of the most impactful environmental factors to which plants adjust their growth and development. While the regulation of temperature signaling has been extensively investigated for the aerial part of plants, much less is known and understood about how roots sense and modulate their growth in response to fluctuating temperatures. Here we found that shoot and root growth responses to high ambient temperature are coordinated during early seedling development. A shoot signaling module that includes HY5, the phytochromes and the PIFs exerts a central function in coupling these growth responses and maintain auxin levels in the root. In addition to the HY5/PIF-dependent shoot module, a regulatory axis composed of auxin biosynthesis and auxin perception factors controls root responses to high ambient temperature. Together, our findings show that shoot and root developmental responses to temperature are tightly coupled during thermomorphogenesis and suggest that roots integrate energy signals with local hormonal inputs.

@article{goretti_terminal_2020,
	title = {{TERMINAL} {FLOWER1} {Functions} as a {Mobile} {Transcriptional} {Cofactor} in the {Shoot} {Apical} {Meristem}},
	volume = {182},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/182/4/2081-2095/6116513},
	doi = {10/ghqb3x},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Goretti, Daniela and Silvestre, Marina and Collani, Silvio and Langenecker, Tobias and Méndez, Carla and Madueño, Francisco and Schmid, Markus},
	month = apr,
	year = {2020},
	pages = {2081--2095},
}

@article{dong_spatial_2020,
	title = {Spatial and competition models increase the progeny testing efficiency of {Japanese} larch},
	volume = {50},
	issn = {0045-5067, 1208-6037},
	url = {https://cdnsciencepub.com/doi/10.1139/cjfr-2020-0007},
	doi = {10/gjcxch},
	abstract = {The main purpose of this study was to examine spatial and competition effects on estimates of genetic parameters, as well as on selection options for growth traits, including height (H), diameter at breast height (DBH), and volume (V), in a progeny test of Japanese larch (Larix kaempferi (Lam.) Carrière) at age 20 years. We compared performances among the individual-tree additive genetic base model (B) with design factors only, the spatial effect model (AR1), the competition model (C), and the combined competition and spatial model (CS). We found that spatial heterogeneity had significant effects on growth traits and that plot variance decreased by more than 80\% in the AR1 model relative to the B model. Competition had significant effects on DBH and V but a smaller effect on H. In the C model, direct additive genetic variances ([Formula: see text]) for DBH and V increased by 205\% and 93\%, respectively, whereas residual variances ([Formula: see text]) decreased by 8\% and 6\%, respectively. In the CS model, the correlations between direct and competitive genetic effects were 0.83, −0.97, and −0.98 for H, DBH, and V, respectively. Competition significantly affected the forward selection. The proportions of selected elite trees were only 39\% and 25\% common between the B and CS models for DBH and V, respectively, when selection intensity was 5\%. For breeding selection, depending on thinning regimes planned, trees of high additive breeding values but low competitive breeding values are preferable for plantation.},
	language = {en},
	number = {12},
	urldate = {2021-06-07},
	journal = {Canadian Journal of Forest Research},
	author = {Dong, Leiming and Xie, Yunhui and Wu, Harry X. and Sun, Xiaomei},
	month = dec,
	year = {2020},
	pages = {1373--1382},
}

The main purpose of this study was to examine spatial and competition effects on estimates of genetic parameters, as well as on selection options for growth traits, including height (H), diameter at breast height (DBH), and volume (V), in a progeny test of Japanese larch (Larix kaempferi (Lam.) Carrière) at age 20 years. We compared performances among the individual-tree additive genetic base model (B) with design factors only, the spatial effect model (AR1), the competition model (C), and the combined competition and spatial model (CS). We found that spatial heterogeneity had significant effects on growth traits and that plot variance decreased by more than 80% in the AR1 model relative to the B model. Competition had significant effects on DBH and V but a smaller effect on H. In the C model, direct additive genetic variances ([Formula: see text]) for DBH and V increased by 205% and 93%, respectively, whereas residual variances ([Formula: see text]) decreased by 8% and 6%, respectively. In the CS model, the correlations between direct and competitive genetic effects were 0.83, −0.97, and −0.98 for H, DBH, and V, respectively. Competition significantly affected the forward selection. The proportions of selected elite trees were only 39% and 25% common between the B and CS models for DBH and V, respectively, when selection intensity was 5%. For breeding selection, depending on thinning regimes planned, trees of high additive breeding values but low competitive breeding values are preferable for plantation.

@article{fundova_genetic_2020,
	title = {Genetic improvement of sawn-board shape stability in {Scots} pine ({Pinus} sylvestris {L}.)},
	volume = {157},
	issn = {09266690},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0926669020308566},
	doi = {10/gjcw67},
	language = {en},
	urldate = {2021-06-07},
	journal = {Industrial Crops and Products},
	author = {Fundova, Irena and Hallingbäck, Henrik R. and Jansson, Gunnar and Wu, Harry X.},
	month = dec,
	year = {2020},
	pages = {112939},
}

@article{forsmark_low_2020,
	title = {Low and {High} {Nitrogen} {Deposition} {Rates} in {Northern} {Coniferous} {Forests} {Have} {Different} {Impacts} on {Aboveground} {Litter} {Production}, {Soil} {Respiration}, and {Soil} {Carbon} {Stocks}},
	volume = {23},
	issn = {1432-9840, 1435-0629},
	url = {http://link.springer.com/10.1007/s10021-020-00478-8},
	doi = {10/gjcvpf},
	abstract = {Abstract
            
              Nitrogen (N) deposition can change the carbon (C) sink of northern coniferous forests by changing the balance between net primary production and soil respiration. We used a field experiment in an N poor
              Pinus sylvestris
              forest where five levels of N (0, 3, 6, 12, and 50 kg N ha
              −1
               yr
              −1
              ,
              n
               = 6) had been added annually for 12–13 years to investigate how litter C inputs and soil respiration, divided into its autotrophic and heterotrophic sources, respond to different rates of N input, and its subsequent effect on soil C storage. The highest N addition rate (50 kg N ha
              −1
               yr
              −1
              ) stimulated soil C accumulation in the organic layer by 22.3 kg C kg
              −1
               N added, increased litter inputs by 46\%, and decreased soil respiration per mass unit of soil C by 31.2\%, mainly by decreasing autotrophic respiration. Lower N addition rates (≤ 12 kg N ha
              −1
               yr
              −1
              ) had no effect on litter inputs or soil respiration. These results support previous studies reporting on increased litter inputs coupled to impeded soil C mineralization, contributing to enhancing the soil C sink when N is supplied at high rates, but add observations for lower N addition rates more realistic for N deposition. In doing so, we show that litter production in N poor northern coniferous forests can be relatively unresponsive to low N deposition levels, that stimulation of microbial activity at low N additions is unlikely to reduce the soil C sink, and that high levels of N deposition enhance the soil C sink by increasing litter inputs and decreasing soil respiration.},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {Ecosystems},
	author = {Forsmark, Benjamin and Nordin, Annika and Maaroufi, Nadia I. and Lundmark, Tomas and Gundale, Michael J.},
	month = nov,
	year = {2020},
	pages = {1423--1436},
}

Abstract Nitrogen (N) deposition can change the carbon (C) sink of northern coniferous forests by changing the balance between net primary production and soil respiration. We used a field experiment in an N poor Pinus sylvestris forest where five levels of N (0, 3, 6, 12, and 50 kg N ha −1  yr −1 , n  = 6) had been added annually for 12–13 years to investigate how litter C inputs and soil respiration, divided into its autotrophic and heterotrophic sources, respond to different rates of N input, and its subsequent effect on soil C storage. The highest N addition rate (50 kg N ha −1  yr −1 ) stimulated soil C accumulation in the organic layer by 22.3 kg C kg −1  N added, increased litter inputs by 46%, and decreased soil respiration per mass unit of soil C by 31.2%, mainly by decreasing autotrophic respiration. Lower N addition rates (≤ 12 kg N ha −1  yr −1 ) had no effect on litter inputs or soil respiration. These results support previous studies reporting on increased litter inputs coupled to impeded soil C mineralization, contributing to enhancing the soil C sink when N is supplied at high rates, but add observations for lower N addition rates more realistic for N deposition. In doing so, we show that litter production in N poor northern coniferous forests can be relatively unresponsive to low N deposition levels, that stimulation of microbial activity at low N additions is unlikely to reduce the soil C sink, and that high levels of N deposition enhance the soil C sink by increasing litter inputs and decreasing soil respiration.

@article{escamez_cell_2020,
	title = {Cell {Death} in {Cells} {Overlying} {Lateral} {Root} {Primordia} {Facilitates} {Organ} {Growth} in {Arabidopsis}},
	volume = {30},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982219315805},
	doi = {10/ggh2vm},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Current Biology},
	author = {Escamez, Sacha and André, Domenique and Sztojka, Bernadette and Bollhöner, Benjamin and Hall, Hardy and Berthet, Béatrice and Voß, Ute and Lers, Amnon and Maizel, Alexis and Andersson, Magnus and Bennett, Malcolm and Tuominen, Hannele},
	month = feb,
	year = {2020},
	pages = {455--464.e7},
}

@article{cheah_assessment_2020,
	title = {Assessment of the manganese cluster’s oxidation state via photoactivation of photosystem {II} microcrystals},
	volume = {117},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1915879117},
	doi = {10/gjd35c},
	abstract = {Knowledge of the manganese oxidation states of the oxygen-evolving Mn
              4
              CaO
              5
              cluster in photosystem II (PSII) is crucial toward understanding the mechanism of biological water oxidation. There is a 4 decade long debate on this topic that historically originates from the observation of a multiline electron paramagnetic resonance (EPR) signal with effective total spin of S = 1/2 in the singly oxidized S
              2
              state of this cluster. This signal implies an overall oxidation state of either Mn(III)
              3
              Mn(IV) or Mn(III)Mn(IV)
              3
              for the S
              2
              state. These 2 competing assignments are commonly known as “low oxidation (LO)” and “high oxidation (HO)” models of the Mn
              4
              CaO
              5
              cluster. Recent advanced EPR and Mn K-edge X-ray spectroscopy studies converge upon the HO model. However, doubts about these assignments have been voiced, fueled especially by studies counting the number of flash-driven electron removals required for the assembly of an active Mn
              4
              CaO
              5
              cluster starting from Mn(II) and Mn-free PSII. This process, known as photoactivation, appeared to support the LO model since the first oxygen is reported to evolve already after 7 flashes. In this study, we improved the quantum yield and sensitivity of the photoactivation experiment by employing PSII microcrystals that retained all protein subunits after complete manganese removal and by oxygen detection via a custom built thin-layer cell connected to a membrane inlet mass spectrometer. We demonstrate that 9 flashes by a nanosecond laser are required for the production of the first oxygen, which proves that the HO model provides the correct description of the Mn
              4
              CaO
              5
              cluster’s oxidation states.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Cheah, Mun Hon and Zhang, Miao and Shevela, Dmitry and Mamedov, Fikret and Zouni, Athina and Messinger, Johannes},
	month = jan,
	year = {2020},
	pages = {141--145},
}

Knowledge of the manganese oxidation states of the oxygen-evolving Mn 4 CaO 5 cluster in photosystem II (PSII) is crucial toward understanding the mechanism of biological water oxidation. There is a 4 decade long debate on this topic that historically originates from the observation of a multiline electron paramagnetic resonance (EPR) signal with effective total spin of S = 1/2 in the singly oxidized S 2 state of this cluster. This signal implies an overall oxidation state of either Mn(III) 3 Mn(IV) or Mn(III)Mn(IV) 3 for the S 2 state. These 2 competing assignments are commonly known as “low oxidation (LO)” and “high oxidation (HO)” models of the Mn 4 CaO 5 cluster. Recent advanced EPR and Mn K-edge X-ray spectroscopy studies converge upon the HO model. However, doubts about these assignments have been voiced, fueled especially by studies counting the number of flash-driven electron removals required for the assembly of an active Mn 4 CaO 5 cluster starting from Mn(II) and Mn-free PSII. This process, known as photoactivation, appeared to support the LO model since the first oxygen is reported to evolve already after 7 flashes. In this study, we improved the quantum yield and sensitivity of the photoactivation experiment by employing PSII microcrystals that retained all protein subunits after complete manganese removal and by oxygen detection via a custom built thin-layer cell connected to a membrane inlet mass spectrometer. We demonstrate that 9 flashes by a nanosecond laser are required for the production of the first oxygen, which proves that the HO model provides the correct description of the Mn 4 CaO 5 cluster’s oxidation states.

@article{antunes_differentiation_2020,
	title = {Differentiation of two {Maytenus} species and their hybrid via untargeted metabolomics},
	volume = {158},
	issn = {09266690},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0926669020309316},
	doi = {10/gjcxhq},
	language = {en},
	urldate = {2021-06-07},
	journal = {Industrial Crops and Products},
	author = {Antunes, Elisa Ribeiro Miranda and Duarte, Rodolfo Santos and Moritz, Thomas and Sawaya, Alexandra Christine Helena Frankland},
	month = dec,
	year = {2020},
	pages = {113014},
}

@article{bag_direct_2020,
	title = {Direct energy transfer from photosystem {II} to photosystem {I} confers winter sustainability in {Scots} {Pine}},
	volume = {11},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/s41467-020-20137-9},
	doi = {10/gjd6p3},
	abstract = {Abstract
            
              Evergreen conifers in boreal forests can survive extremely cold (freezing) temperatures during long dark winter and fully recover during summer. A phenomenon called “sustained quenching” putatively provides photoprotection and enables their survival, but its precise molecular and physiological mechanisms are not understood. To unveil them, here we have analyzed seasonal adjustment of the photosynthetic machinery of Scots pine (
              Pinus sylvestris
              ) trees by monitoring multi-year changes in weather, chlorophyll fluorescence, chloroplast ultrastructure, and changes in pigment-protein composition. Analysis of Photosystem II and Photosystem I performance parameters indicate that highly dynamic structural and functional seasonal rearrangements of the photosynthetic apparatus occur. Although several mechanisms might contribute to ‘sustained quenching’ of winter/early spring pine needles, time-resolved fluorescence analysis shows that extreme down-regulation of photosystem II activity along with direct energy transfer from photosystem II to photosystem I play a major role. This mechanism is enabled by extensive thylakoid destacking allowing for the mixing of PSII with PSI complexes. These two linked phenomena play crucial roles in winter acclimation and protection.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Bag, Pushan and Chukhutsina, Volha and Zhang, Zishan and Paul, Suman and Ivanov, Alexander G. and Shutova, Tatyana and Croce, Roberta and Holzwarth, Alfred R. and Jansson, Stefan},
	month = dec,
	year = {2020},
	pages = {6388},
}

Abstract Evergreen conifers in boreal forests can survive extremely cold (freezing) temperatures during long dark winter and fully recover during summer. A phenomenon called “sustained quenching” putatively provides photoprotection and enables their survival, but its precise molecular and physiological mechanisms are not understood. To unveil them, here we have analyzed seasonal adjustment of the photosynthetic machinery of Scots pine ( Pinus sylvestris ) trees by monitoring multi-year changes in weather, chlorophyll fluorescence, chloroplast ultrastructure, and changes in pigment-protein composition. Analysis of Photosystem II and Photosystem I performance parameters indicate that highly dynamic structural and functional seasonal rearrangements of the photosynthetic apparatus occur. Although several mechanisms might contribute to ‘sustained quenching’ of winter/early spring pine needles, time-resolved fluorescence analysis shows that extreme down-regulation of photosystem II activity along with direct energy transfer from photosystem II to photosystem I play a major role. This mechanism is enabled by extensive thylakoid destacking allowing for the mixing of PSII with PSI complexes. These two linked phenomena play crucial roles in winter acclimation and protection.

@article{abedi_spatio-temporal_2020,
	title = {The {Spatio}-{Temporal} {Distribution} of {Cell} {Wall}-{Associated} {Glycoproteins} {During} {Wood} {Formation} in {Populus}},
	volume = {11},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2020.611607/full},
	doi = {10/gjcxhp},
	abstract = {Plant cell wall associated hydroxyproline-rich glycoproteins (HRGPs) are involved in several aspects of plant growth and development, including wood formation in trees. HRGPs such as arabinogalactan-proteins (AGPs), extensins (EXTs), and proline rich proteins (PRPs) are important for the development and architecture of plant cell walls. Analysis of publicly available gene expression data revealed that many
              HRGP
              encoding genes show tight spatio-temporal expression patterns in the developing wood of
              Populus
              that are indicative of specific functions during wood formation. Similar results were obtained for the expression of glycosyl transferases putatively involved in HRGP glycosylation.
              In situ
              immunolabelling of transverse wood sections using AGP and EXT antibodies revealed the cell type specificity of different epitopes. In mature wood AGP epitopes were located in xylem ray cell walls, whereas EXT epitopes were specifically observed between neighboring xylem vessels, and on the ray cell side of the vessel walls, likely in association with pits. Molecular mass and glycan analysis of AGPs and EXTs in phloem/cambium, developing xylem, and mature xylem revealed clear differences in glycan structures and size between the tissues. Separation of AGPs by agarose gel electrophoresis and staining with β-D-glucosyl Yariv confirmed the presence of different AGP populations in phloem/cambium and xylem. These results reveal the diverse changes in HRGP-related processes that occur during wood formation at the gene expression and HRGP glycan biosynthesis levels, and relate HRGPs and glycosylation processes to the developmental processes of wood formation.},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Abedi, Tayebeh and Castilleux, Romain and Nibbering, Pieter and Niittylä, Totte},
	month = dec,
	year = {2020},
	pages = {611607},
}

Plant cell wall associated hydroxyproline-rich glycoproteins (HRGPs) are involved in several aspects of plant growth and development, including wood formation in trees. HRGPs such as arabinogalactan-proteins (AGPs), extensins (EXTs), and proline rich proteins (PRPs) are important for the development and architecture of plant cell walls. Analysis of publicly available gene expression data revealed that many HRGP encoding genes show tight spatio-temporal expression patterns in the developing wood of Populus that are indicative of specific functions during wood formation. Similar results were obtained for the expression of glycosyl transferases putatively involved in HRGP glycosylation. In situ immunolabelling of transverse wood sections using AGP and EXT antibodies revealed the cell type specificity of different epitopes. In mature wood AGP epitopes were located in xylem ray cell walls, whereas EXT epitopes were specifically observed between neighboring xylem vessels, and on the ray cell side of the vessel walls, likely in association with pits. Molecular mass and glycan analysis of AGPs and EXTs in phloem/cambium, developing xylem, and mature xylem revealed clear differences in glycan structures and size between the tissues. Separation of AGPs by agarose gel electrophoresis and staining with β-D-glucosyl Yariv confirmed the presence of different AGP populations in phloem/cambium and xylem. These results reveal the diverse changes in HRGP-related processes that occur during wood formation at the gene expression and HRGP glycan biosynthesis levels, and relate HRGPs and glycosylation processes to the developmental processes of wood formation.

@article{abreu_changes_2020,
	title = {Changes in lipid and carotenoid metabolism in {Chlamydomonas} reinhardtii during induction of {CO2}-concentrating mechanism: {Cellular} response to low {CO2} stress},
	volume = {52},
	issn = {22119264},
	shorttitle = {Changes in lipid and carotenoid metabolism in {Chlamydomonas} reinhardtii during induction of {CO2}-concentrating mechanism},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S221192642030967X},
	doi = {10/gjcxj6},
	language = {en},
	urldate = {2021-06-07},
	journal = {Algal Research},
	author = {Abreu, Ilka N. and Aksmann, Anna and Bajhaiya, Amit K. and Benlloch, Reyes and Giordano, Mario and Pokora, Wojciech and Selstam, Eva and Moritz, Thomas},
	month = dec,
	year = {2020},
	pages = {102099},
}

@article{arias_nuclear_2020,
	title = {Nuclear proteome analysis of {Chlamydomonas} with response to {CO2} limitation},
	volume = {46},
	issn = {22119264},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S221192641930133X},
	doi = {10/gh9mnq},
	language = {en},
	urldate = {2021-06-07},
	journal = {Algal Research},
	author = {Arias, Carolina and Obudulu, Ogonna and Zhao, Xiaoling and Ansolia, Preeti and Zhang, Xueyang and Paul, Suman and Bygdell, Joakim and Pirmoradian, Mohammad and Zubarev, Roman A. and Samuelsson, Göran and Wingsle, Gunnar and Bajhaiya, Amit K.},
	month = mar,
	year = {2020},
	pages = {101765},
}

@article{bai_seed-stored_2020,
	title = {Seed-{Stored} {mRNAs} that {Are} {Specifically} {Associated} to {Monosomes} {Are} {Translationally} {Regulated} during {Germination1}  [{OPEN}]},
	volume = {182},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.19.00644},
	doi = {10.1104/pp.19.00644},
	abstract = {The life cycle of many organisms includes a quiescent stage, such as bacterial or fungal spores, insect larvae, or plant seeds. Common to these stages is their low water content and high survivability during harsh conditions. Upon rehydration, organisms need to reactivate metabolism and protein synthesis. Plant seeds contain many mRNAs that are transcribed during seed development. Translation of these mRNAs occurs during early seed germination, even before the requirement of transcription. Therefore, stored mRNAs are postulated to be important for germination. How these mRNAs are stored and protected during long-term storage is unknown. The aim of this study was to investigate how mRNAs are stored in dry seeds and whether they are indeed translated during seed germination. We investigated seed polysome profiles and the mRNAs and protein complexes that are associated with these ribosomes in seeds of the model organism Arabidopsis (Arabidopsis thaliana). We showed that most stored mRNAs are associated with monosomes in dry seeds; therefore, we focus on monosomes in this study. Seed ribosome complexes are associated with mRNA-binding proteins, stress granule, and P-body proteins, which suggests regulated packing of seed mRNAs. Interestingly, ∼17\% of the mRNAs that are specifically associated with monosomes are translationally up-regulated during seed germination. These mRNAs are transcribed during seed maturation, suggesting a role for this developmental stage in determining the translational fate of mRNAs during early germination.},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Bai, Bing and van der Horst, Sjors and Cordewener, Jan H.G. and America, Twan A.H.P. and Hanson, Johannes and Bentsink, Leónie},
	month = jan,
	year = {2020},
	pages = {378--392},
}

The life cycle of many organisms includes a quiescent stage, such as bacterial or fungal spores, insect larvae, or plant seeds. Common to these stages is their low water content and high survivability during harsh conditions. Upon rehydration, organisms need to reactivate metabolism and protein synthesis. Plant seeds contain many mRNAs that are transcribed during seed development. Translation of these mRNAs occurs during early seed germination, even before the requirement of transcription. Therefore, stored mRNAs are postulated to be important for germination. How these mRNAs are stored and protected during long-term storage is unknown. The aim of this study was to investigate how mRNAs are stored in dry seeds and whether they are indeed translated during seed germination. We investigated seed polysome profiles and the mRNAs and protein complexes that are associated with these ribosomes in seeds of the model organism Arabidopsis (Arabidopsis thaliana). We showed that most stored mRNAs are associated with monosomes in dry seeds; therefore, we focus on monosomes in this study. Seed ribosome complexes are associated with mRNA-binding proteins, stress granule, and P-body proteins, which suggests regulated packing of seed mRNAs. Interestingly, ∼17% of the mRNAs that are specifically associated with monosomes are translationally up-regulated during seed germination. These mRNAs are transcribed during seed maturation, suggesting a role for this developmental stage in determining the translational fate of mRNAs during early germination.

@article{van_der_horst_metabolite_2020,
	title = {Metabolite {Control} of {Translation} by {Conserved} {Peptide} {uORFs}: {The} {Ribosome} as a {Metabolite} {Multisensor}},
	volume = {182},
	issn = {0032-0889, 1532-2548},
	shorttitle = {Metabolite {Control} of {Translation} by {Conserved} {Peptide} {uORFs}},
	url = {https://academic.oup.com/plphys/article/182/1/110-122/6116065},
	doi = {10.1104/pp.19.00940},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {van der Horst, Sjors and Filipovska, Teodora and Hanson, Johannes and Smeekens, Sjef},
	month = jan,
	year = {2020},
	pages = {110--122},
}

@article{maurya_branching_2020,
	title = {Branching {Regulator} {BRC1} {Mediates} {Photoperiodic} {Control} of {Seasonal} {Growth} in {Hybrid} {Aspen}},
	volume = {30},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S096098221931440X},
	doi = {10.1016/j.cub.2019.11.001},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Current Biology},
	author = {Maurya, Jay P. and Singh, Rajesh Kumar and Miskolczi, Pal C. and Prasad, Amritha N. and Jonsson, Kristoffer and Wu, Feng and Bhalerao, Rishikesh P.},
	month = jan,
	year = {2020},
	pages = {122--126.e2},
}

@article{kindgren_native_2020,
	title = {Native elongation transcript sequencing reveals temperature dependent dynamics of nascent {RNAPII} transcription in {Arabidopsis}},
	volume = {48},
	issn = {0305-1048, 1362-4962},
	url = {https://academic.oup.com/nar/article/48/5/2332/5682908},
	doi = {10.1093/nar/gkz1189},
	abstract = {Abstract
            Temperature profoundly affects the kinetics of biochemical reactions, yet how large molecular complexes such as the transcription machinery accommodate changing temperatures to maintain cellular function is poorly understood. Here, we developed plant native elongating transcripts sequencing (plaNET-seq) to profile genome-wide nascent RNA polymerase II (RNAPII) transcription during the cold-response of Arabidopsis thaliana with single-nucleotide resolution. Combined with temporal resolution, these data revealed transient genome-wide reprogramming of nascent RNAPII transcription during cold, including characteristics of RNAPII elongation and thousands of non-coding transcripts connected to gene expression. Our results suggest a role for promoter–proximal RNAPII stalling in predisposing genes for transcriptional activation during plant–environment interactions. At gene 3′-ends, cold initially facilitated transcriptional termination by limiting the distance of read-through transcription. Within gene bodies, cold reduced the kinetics of co-transcriptional splicing leading to increased intragenic stalling. Our data resolved multiple distinct mechanisms by which temperature transiently altered the dynamics of nascent RNAPII transcription and associated RNA processing, illustrating potential biotechnological solutions and future focus areas to promote food security in the context of a changing climate.},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Nucleic Acids Research},
	author = {Kindgren, Peter and Ivanov, Maxim and Marquardt, Sebastian},
	month = mar,
	year = {2020},
	pages = {2332--2347},
}

Abstract Temperature profoundly affects the kinetics of biochemical reactions, yet how large molecular complexes such as the transcription machinery accommodate changing temperatures to maintain cellular function is poorly understood. Here, we developed plant native elongating transcripts sequencing (plaNET-seq) to profile genome-wide nascent RNA polymerase II (RNAPII) transcription during the cold-response of Arabidopsis thaliana with single-nucleotide resolution. Combined with temporal resolution, these data revealed transient genome-wide reprogramming of nascent RNAPII transcription during cold, including characteristics of RNAPII elongation and thousands of non-coding transcripts connected to gene expression. Our results suggest a role for promoter–proximal RNAPII stalling in predisposing genes for transcriptional activation during plant–environment interactions. At gene 3′-ends, cold initially facilitated transcriptional termination by limiting the distance of read-through transcription. Within gene bodies, cold reduced the kinetics of co-transcriptional splicing leading to increased intragenic stalling. Our data resolved multiple distinct mechanisms by which temperature transiently altered the dynamics of nascent RNAPII transcription and associated RNA processing, illustrating potential biotechnological solutions and future focus areas to promote food security in the context of a changing climate.

@article{sullivan_mitogenome_2020,
	title = {The {Mitogenome} of {Norway} {Spruce} and a {Reappraisal} of {Mitochondrial} {Recombination} in {Plants}},
	volume = {12},
	issn = {1759-6653},
	url = {https://academic.oup.com/gbe/article/12/1/3586/5644343},
	doi = {10.1093/gbe/evz263},
	abstract = {Abstract
            Plant mitogenomes can be difficult to assemble because they are structurally dynamic and prone to intergenomic DNA transfers, leading to the unusual situation where an organelle genome is far outnumbered by its nuclear counterparts. As a result, comparative mitogenome studies are in their infancy and some key aspects of genome evolution are still known mainly from pregenomic, qualitative methods. To help address these limitations, we combined machine learning and in silico enrichment of mitochondrial-like long reads to assemble the bacterial-sized mitogenome of Norway spruce (Pinaceae: Picea abies). We conducted comparative analyses of repeat abundance, intergenomic transfers, substitution and rearrangement rates, and estimated repeat-by-repeat homologous recombination rates. Prompted by our discovery of highly recombinogenic small repeats in P. abies, we assessed the genomic support for the prevailing hypothesis that intramolecular recombination is predominantly driven by repeat length, with larger repeats facilitating DNA exchange more readily. Overall, we found mixed support for this view: Recombination dynamics were heterogeneous across vascular plants and highly active small repeats (ca. 200 bp) were present in about one-third of studied mitogenomes. As in previous studies, we did not observe any robust relationships among commonly studied genome attributes, but we identify variation in recombination rates as a underinvestigated source of plant mitogenome diversity.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Genome Biology and Evolution},
	author = {Sullivan, Alexis R and Eldfjell, Yrin and Schiffthaler, Bastian and Delhomme, Nicolas and Asp, Torben and Hebelstrup, Kim H and Keech, Olivier and Öberg, Lisa and Møller, Ian Max and Arvestad, Lars and Street, Nathaniel R and Wang, Xiao-Ru},
	editor = {Vision, Todd},
	month = jan,
	year = {2020},
	pages = {3586--3598},
}

Abstract Plant mitogenomes can be difficult to assemble because they are structurally dynamic and prone to intergenomic DNA transfers, leading to the unusual situation where an organelle genome is far outnumbered by its nuclear counterparts. As a result, comparative mitogenome studies are in their infancy and some key aspects of genome evolution are still known mainly from pregenomic, qualitative methods. To help address these limitations, we combined machine learning and in silico enrichment of mitochondrial-like long reads to assemble the bacterial-sized mitogenome of Norway spruce (Pinaceae: Picea abies). We conducted comparative analyses of repeat abundance, intergenomic transfers, substitution and rearrangement rates, and estimated repeat-by-repeat homologous recombination rates. Prompted by our discovery of highly recombinogenic small repeats in P. abies, we assessed the genomic support for the prevailing hypothesis that intramolecular recombination is predominantly driven by repeat length, with larger repeats facilitating DNA exchange more readily. Overall, we found mixed support for this view: Recombination dynamics were heterogeneous across vascular plants and highly active small repeats (ca. 200 bp) were present in about one-third of studied mitogenomes. As in previous studies, we did not observe any robust relationships among commonly studied genome attributes, but we identify variation in recombination rates as a underinvestigated source of plant mitogenome diversity.

@article{kucukoglu_peptide_2020,
	title = {Peptide encoding \textit{{Populus} {CLV3}/{ESR}‐{RELATED} 47} ( \textit{{PttCLE47}} ) promotes cambial development and secondary xylem formation in hybrid aspen},
	volume = {226},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.16331},
	doi = {10.1111/nph.16331},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Kucukoglu, Melis and Chaabouni, Salma and Zheng, Bo and Mähönen, Ari Pekka and Helariutta, Ykä and Nilsson, Ove},
	month = apr,
	year = {2020},
	pages = {75--85},
}

@article{elfstrand_genotypic_2020,
	title = {Genotypic variation in {Norway} spruce correlates to fungal communities in vegetative buds},
	volume = {29},
	issn = {0962-1083, 1365-294X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.15314},
	doi = {10.1111/mec.15314},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Molecular Ecology},
	author = {Elfstrand, Malin and Zhou, Linghua and Baison, John and Olson, Åke and Lundén, Karl and Karlsson, Bo and Wu, Harry X. and Stenlid, Jan and García‐Gil, M. Rosario},
	month = jan,
	year = {2020},
	pages = {199--213},
}

@article{zhang_pirin2_2020,
	title = {{PIRIN2} suppresses {S}‐type lignin accumulation in a noncell‐autonomous manner in {Arabidopsis} xylem elements},
	volume = {225},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.16271},
	doi = {10.1111/nph.16271},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Zhang, Bo and Sztojka, Bernadette and Escamez, Sacha and Vanholme, Ruben and Hedenström, Mattias and Wang, Yin and Turumtay, Halbay and Gorzsás, András and Boerjan, Wout and Tuominen, Hannele},
	month = mar,
	year = {2020},
	pages = {1923--1935},
}

@article{rogers_global_2020,
	title = {A global view of aspen: {Conservation} science for widespread keystone systems},
	volume = {21},
	issn = {23519894},
	shorttitle = {A global view of aspen},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S2351989419305803},
	doi = {10.1016/j.gecco.2019.e00828},
	language = {en},
	urldate = {2021-06-07},
	journal = {Global Ecology and Conservation},
	author = {Rogers, Paul C. and Pinno, Bradley D. and Šebesta, Jan and Albrectsen, Benedicte R. and Li, Guoqing and Ivanova, Natalya and Kusbach, Antonín and Kuuluvainen, Timo and Landhäusser, Simon M. and Liu, Hongyan and Myking, Tor and Pulkkinen, Pertti and Wen, Zhongming and Kulakowski, Dominik},
	month = mar,
	year = {2020},
	pages = {e00828},
}

@article{jonasson_isolation_2020,
	title = {Isolation and characterization of cellulose nanofibers from aspen wood using derivatizing and non-derivatizing pretreatments},
	volume = {27},
	issn = {0969-0239, 1572-882X},
	url = {http://link.springer.com/10.1007/s10570-019-02754-w},
	doi = {10.1007/s10570-019-02754-w},
	abstract = {Abstract
              The link between wood and corresponding cellulose nanofiber (CNF) behavior is complex owing the multiple chemical pretreatments required for successful preparation. In this study we apply a few pretreatments on aspen wood and compare the final CNF behavior in order to rationalize quantitative studies of CNFs derived from aspen wood with variable properties. This is relevant for efforts to improve the properties of woody biomass through tree breeding. Three different types of pretreatments were applied prior to disintegration (microfluidizer) after a mild pulping step; derivatizing TEMPO-oxidation, carboxymethylation and non-derivatizing soaking in deep-eutectic solvents. TEMPO-oxidation was also performed directly on the plain wood powder without pulping. Obtained CNFs (44–55\% yield) had hemicellulose content between 8 and 26 wt\% and were characterized primarily by fine (height ≈ 2 nm) and coarser (2 nm {\textless} height {\textless} 100 nm) grade CNFs from the derivatizing and non-derivatizing treatments, respectively. Nanopapers from non-derivatized CNFs had higher thermal stability (280 °C) compared to carboxymethylated (260 °C) and TEMPO-oxidized (220 °C). Stiffness of nanopapers made from non-derivatized treatments was higher whilst having less tensile strength and elongation-at-break than those made from derivatized CNFs. The direct TEMPO-oxidized CNFs and nanopapers were furthermore morphologically and mechanically indistinguishable from those that also underwent a pulping step. The results show that utilizing both derivatizing and non-derivatizing pretreatments can facilitate studies of the relationship between wood properties and final CNF behavior. This can be valuable when studying engineered trees for the purpose of decreasing resource consumption when isolation cellulose nanomaterials.
            
            
              Graphic abstract},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Cellulose},
	author = {Jonasson, Simon and Bünder, Anne and Niittylä, Totte and Oksman, Kristiina},
	month = jan,
	year = {2020},
	pages = {185--203},
}

Abstract The link between wood and corresponding cellulose nanofiber (CNF) behavior is complex owing the multiple chemical pretreatments required for successful preparation. In this study we apply a few pretreatments on aspen wood and compare the final CNF behavior in order to rationalize quantitative studies of CNFs derived from aspen wood with variable properties. This is relevant for efforts to improve the properties of woody biomass through tree breeding. Three different types of pretreatments were applied prior to disintegration (microfluidizer) after a mild pulping step; derivatizing TEMPO-oxidation, carboxymethylation and non-derivatizing soaking in deep-eutectic solvents. TEMPO-oxidation was also performed directly on the plain wood powder without pulping. Obtained CNFs (44–55% yield) had hemicellulose content between 8 and 26 wt% and were characterized primarily by fine (height ≈ 2 nm) and coarser (2 nm \textless height \textless 100 nm) grade CNFs from the derivatizing and non-derivatizing treatments, respectively. Nanopapers from non-derivatized CNFs had higher thermal stability (280 °C) compared to carboxymethylated (260 °C) and TEMPO-oxidized (220 °C). Stiffness of nanopapers made from non-derivatized treatments was higher whilst having less tensile strength and elongation-at-break than those made from derivatized CNFs. The direct TEMPO-oxidized CNFs and nanopapers were furthermore morphologically and mechanically indistinguishable from those that also underwent a pulping step. The results show that utilizing both derivatizing and non-derivatizing pretreatments can facilitate studies of the relationship between wood properties and final CNF behavior. This can be valuable when studying engineered trees for the purpose of decreasing resource consumption when isolation cellulose nanomaterials. Graphic abstract

@article{khoomrung_metabolic_2020,
	title = {Metabolic {Profiling} and {Compound}-{Class} {Identification} {Reveal} {Alterations} in {Serum} {Triglyceride} {Levels} in {Mice} {Immunized} with {Human} {Vaccine} {Adjuvant} {Alum}},
	volume = {19},
	issn = {1535-3893, 1535-3907},
	url = {https://pubs.acs.org/doi/10.1021/acs.jproteome.9b00517},
	doi = {10.1021/acs.jproteome.9b00517},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Journal of Proteome Research},
	author = {Khoomrung, Sakda and Nookaew, Intawat and Sen, Partho and Olafsdottir, Thorunn A. and Persson, Josefine and Moritz, Thomas and Andersen, Peter and Harandi, Ali M. and Nielsen, Jens},
	month = jan,
	year = {2020},
	pages = {269--278},
}

@article{kleczkowski_optimization_2020,
	title = {Optimization of nucleotide sugar supply for polysaccharide formation via thermodynamic buffering},
	volume = {477},
	issn = {0264-6021, 1470-8728},
	url = {https://portlandpress.com/biochemj/article/477/2/341/221922/Optimization-of-nucleotide-sugar-supply-for},
	doi = {10.1042/BCJ20190807},
	abstract = {Plant polysaccharides (cellulose, hemicellulose, pectin, starch) are either direct (i.e. leaf starch) or indirect products of photosynthesis, and they belong to the most abundant organic compounds in nature. Although each of these polymers is made by a specific enzymatic machinery, frequently in different cell locations, details of their synthesis share certain common features. Thus, the production of these polysaccharides is preceded by the formation of nucleotide sugars catalyzed by fully reversible reactions of various enzymes, mostly pyrophosphorylases. These ‘buffering’ enzymes are, generally, quite active and operate close to equilibrium. The nucleotide sugars are then used as substrates for irreversible reactions of various polysaccharide-synthesizing glycosyltransferases (‘engine’ enzymes), e.g. plastidial starch synthases, or plasma membrane-bound cellulose synthase and callose synthase, or ER/Golgi-located variety of glycosyltransferases forming hemicellulose and pectin backbones. Alternatively, the irreversible step might also be provided by a carrier transporting a given immediate precursor across a membrane. Here, we argue that local equilibria, established within metabolic pathways and cycles resulting in polysaccharide production, bring stability to the system via the arrangement of a flexible supply of nucleotide sugars. This metabolic system is itself under control of adenylate kinase and nucleoside-diphosphate kinase, which determine the availability of nucleotides (adenylates, uridylates, guanylates and cytidylates) and Mg2+, the latter serving as a feedback signal from the nucleotide metabolome. Under these conditions, the supply of nucleotide sugars to engine enzymes is stable and constant, and the metabolic process becomes optimized in its load and consumption, making the system steady and self-regulated.},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Biochemical Journal},
	author = {Kleczkowski, Leszek A. and Igamberdiev, Abir U.},
	month = jan,
	year = {2020},
	pages = {341--356},
}

Plant polysaccharides (cellulose, hemicellulose, pectin, starch) are either direct (i.e. leaf starch) or indirect products of photosynthesis, and they belong to the most abundant organic compounds in nature. Although each of these polymers is made by a specific enzymatic machinery, frequently in different cell locations, details of their synthesis share certain common features. Thus, the production of these polysaccharides is preceded by the formation of nucleotide sugars catalyzed by fully reversible reactions of various enzymes, mostly pyrophosphorylases. These ‘buffering’ enzymes are, generally, quite active and operate close to equilibrium. The nucleotide sugars are then used as substrates for irreversible reactions of various polysaccharide-synthesizing glycosyltransferases (‘engine’ enzymes), e.g. plastidial starch synthases, or plasma membrane-bound cellulose synthase and callose synthase, or ER/Golgi-located variety of glycosyltransferases forming hemicellulose and pectin backbones. Alternatively, the irreversible step might also be provided by a carrier transporting a given immediate precursor across a membrane. Here, we argue that local equilibria, established within metabolic pathways and cycles resulting in polysaccharide production, bring stability to the system via the arrangement of a flexible supply of nucleotide sugars. This metabolic system is itself under control of adenylate kinase and nucleoside-diphosphate kinase, which determine the availability of nucleotides (adenylates, uridylates, guanylates and cytidylates) and Mg2+, the latter serving as a feedback signal from the nucleotide metabolome. Under these conditions, the supply of nucleotide sugars to engine enzymes is stable and constant, and the metabolic process becomes optimized in its load and consumption, making the system steady and self-regulated.

@article{milhinhos_acaulis5_2020,
	title = {{ACAULIS5} {Is} {Required} for {Cytokinin} {Accumulation} and {Function} {During} {Secondary} {Growth} of {Populus} {Trees}},
	volume = {11},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2020.601858/full},
	doi = {10.3389/fpls.2020.601858},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Milhinhos, Ana and Bollhöner, Benjamin and Blazquez, Miguel A. and Novák, Ondřej and Miguel, Célia M. and Tuominen, Hannele},
	month = nov,
	year = {2020},
	pages = {601858},
}

@article{raggi_polar_2020,
	title = {Polar expedition: mechanisms for protein polar localization},
	volume = {53},
	issn = {13695266},
	shorttitle = {Polar expedition},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1369526619301165},
	doi = {10.1016/j.pbi.2019.12.001},
	language = {en},
	urldate = {2021-06-07},
	journal = {Current Opinion in Plant Biology},
	author = {Raggi, Sara and Demes, Elsa and Liu, Sijia and Verger, Stéphane and Robert, Stéphanie},
	month = feb,
	year = {2020},
	pages = {134--140},
}

@article{wang_demography_2020,
	title = {Demography and {Natural} {Selection} {Have} {Shaped} {Genetic} {Variation} in the {Widely} {Distributed} {Conifer} {Norway} {Spruce} ({Picea} abies)},
	volume = {12},
	issn = {1759-6653},
	url = {https://academic.oup.com/gbe/article/12/2/3803/5709816},
	doi = {10.1093/gbe/evaa005},
	abstract = {Abstract
            Under the neutral theory, species with larger effective population size are expected to harbor higher genetic diversity. However, across a wide variety of organisms, the range of genetic diversity is orders of magnitude more narrow than the range of effective population size. This observation has become known as Lewontin’s paradox and although aspects of this phenomenon have been extensively studied, the underlying causes for the paradox remain unclear. Norway spruce (Picea abies) is a widely distributed conifer species across the northern hemisphere, and it consequently plays a major role in European forestry. Here, we use whole-genome resequencing data from 35 individuals to perform population genomic analyses in P. abies in an effort to understand what drives genome-wide patterns of variation in this species. Despite having a very wide geographic distribution and an corresponding enormous current population size, our analyses find that genetic diversity of P. abies is low across a number of populations (π = 0.0049 in Central-Europe, π = 0.0063 in Sweden-Norway, π = 0.0063 in Finland). To assess the reasons for the low levels of genetic diversity, we infer the demographic history of the species and find that it is characterized by several reoccurring bottlenecks with concomitant decreases in effective population size can, at least partly, provide an explanation for low polymorphism we observe in P. abies. Further analyses suggest that recurrent natural selection, both purifying and positive selection, can also contribute to the loss of genetic diversity in Norway spruce by reducing genetic diversity at linked sites. Finally, the overall low mutation rates seen in conifers can also help explain the low genetic diversity maintained in Norway spruce.},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Genome Biology and Evolution},
	author = {Wang, Xi and Bernhardsson, Carolina and Ingvarsson, Pär K},
	editor = {Chaw, Shu-Miaw},
	month = feb,
	year = {2020},
	pages = {3803--3817},
}

Abstract Under the neutral theory, species with larger effective population size are expected to harbor higher genetic diversity. However, across a wide variety of organisms, the range of genetic diversity is orders of magnitude more narrow than the range of effective population size. This observation has become known as Lewontin’s paradox and although aspects of this phenomenon have been extensively studied, the underlying causes for the paradox remain unclear. Norway spruce (Picea abies) is a widely distributed conifer species across the northern hemisphere, and it consequently plays a major role in European forestry. Here, we use whole-genome resequencing data from 35 individuals to perform population genomic analyses in P. abies in an effort to understand what drives genome-wide patterns of variation in this species. Despite having a very wide geographic distribution and an corresponding enormous current population size, our analyses find that genetic diversity of P. abies is low across a number of populations (π = 0.0049 in Central-Europe, π = 0.0063 in Sweden-Norway, π = 0.0063 in Finland). To assess the reasons for the low levels of genetic diversity, we infer the demographic history of the species and find that it is characterized by several reoccurring bottlenecks with concomitant decreases in effective population size can, at least partly, provide an explanation for low polymorphism we observe in P. abies. Further analyses suggest that recurrent natural selection, both purifying and positive selection, can also contribute to the loss of genetic diversity in Norway spruce by reducing genetic diversity at linked sites. Finally, the overall low mutation rates seen in conifers can also help explain the low genetic diversity maintained in Norway spruce.

@article{yang_two_2020,
	title = {Two dominant boreal conifers use contrasting mechanisms to reactivate photosynthesis in the spring},
	volume = {11},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/s41467-019-13954-0},
	doi = {10.1038/s41467-019-13954-0},
	abstract = {Abstract
            
              Boreal forests are dominated by evergreen conifers that show strongly regulated seasonal photosynthetic activity. Understanding the mechanisms behind seasonal modulation of photosynthesis is crucial for predicting how these forests will respond to changes in seasonal patterns and how this will affect their role in the terrestrial carbon cycle. We demonstrate that the two co-occurring dominant boreal conifers, Scots pine (
              Pinus sylvestris L
              .) and Norway spruce
              (Picea abies
              ), use contrasting mechanisms to reactivate photosynthesis in the spring. Scots pine downregulates its capacity for CO
              2
              assimilation during winter and activates alternative electron sinks through accumulation of PGR5 and PGRL1 during early spring until the capacity for CO
              2
              assimilation is recovered. In contrast, Norway spruce lacks this ability to actively switch between different electron sinks over the year and as a consequence suffers severe photooxidative damage during the critical spring period.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Yang, Qi and Blanco, Nicolás E. and Hermida-Carrera, Carmen and Lehotai, Nóra and Hurry, Vaughan and Strand, Åsa},
	month = dec,
	year = {2020},
	pages = {128},
}

Abstract Boreal forests are dominated by evergreen conifers that show strongly regulated seasonal photosynthetic activity. Understanding the mechanisms behind seasonal modulation of photosynthesis is crucial for predicting how these forests will respond to changes in seasonal patterns and how this will affect their role in the terrestrial carbon cycle. We demonstrate that the two co-occurring dominant boreal conifers, Scots pine ( Pinus sylvestris L .) and Norway spruce (Picea abies ), use contrasting mechanisms to reactivate photosynthesis in the spring. Scots pine downregulates its capacity for CO 2 assimilation during winter and activates alternative electron sinks through accumulation of PGR5 and PGRL1 during early spring until the capacity for CO 2 assimilation is recovered. In contrast, Norway spruce lacks this ability to actively switch between different electron sinks over the year and as a consequence suffers severe photooxidative damage during the critical spring period.

@article{zhang_woxauxin_2020,
	title = {A {WOX}/{Auxin} {Biosynthesis} {Module} {Controls} {Growth} to {Shape} {Leaf} {Form}},
	volume = {30},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982220313683},
	doi = {10.1016/j.cub.2020.09.037},
	language = {en},
	number = {24},
	urldate = {2021-06-07},
	journal = {Current Biology},
	author = {Zhang, Zhongjuan and Runions, Adam and Mentink, Remco A. and Kierzkowski, Daniel and Karady, Michal and Hashemi, Babak and Huijser, Peter and Strauss, Sören and Gan, Xiangchao and Ljung, Karin and Tsiantis, Miltos},
	month = dec,
	year = {2020},
	pages = {4857--4868.e6},
}

@article{de_zio_reaction_2020,
	title = {Reaction {Wood} {Anatomical} {Traits} and {Hormonal} {Profiles} in {Poplar} {Bent} {Stem} and {Root}},
	volume = {11},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2020.590985/full},
	doi = {10.3389/fpls.2020.590985},
	abstract = {Reaction wood (RW) formation is an innate physiological response of woody plants to counteract mechanical constraints in nature, reinforce structure and redirect growth toward the vertical direction. Differences and/or similarities between stem and root response to mechanical constraints remain almost unknown especially in relation to phytohormones distribution and RW characteristics. Thus,
              Populus nigra
              stem and root subjected to static non-destructive mid-term bending treatment were analyzed. The distribution of tension and compression forces was firstly modeled along the main bent stem and root axis; then, anatomical features, chemical composition, and a complete auxin and cytokinin metabolite profiles of the stretched convex and compressed concave side of three different bent stem and root sectors were analyzed. The results showed that in bent stems RW was produced on the upper stretched convex side whereas in bent roots it was produced on the lower compressed concave side. Anatomical features and chemical analysis showed that bent stem RW was characterized by a low number of vessel, poor lignification, and high carbohydrate, and thus gelatinous layer in fiber cell wall. Conversely, in bent root, RW was characterized by high vessel number and area, without any significant variation in carbohydrate and lignin content. An antagonistic interaction of auxins and different cytokinin forms/conjugates seems to regulate critical aspects of RW formation/development in stem and root to facilitate upward/downward organ bending. The observed differences between the response stem and root to bending highlight how hormonal signaling is highly organ-dependent.},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {De Zio, Elena and Montagnoli, Antonio and Karady, Michal and Terzaghi, Mattia and Sferra, Gabriella and Antoniadi, Ioanna and Scippa, Gabriella S. and Ljung, Karin and Chiatante, Donato and Trupiano, Dalila},
	month = dec,
	year = {2020},
	pages = {590985},
}

Reaction wood (RW) formation is an innate physiological response of woody plants to counteract mechanical constraints in nature, reinforce structure and redirect growth toward the vertical direction. Differences and/or similarities between stem and root response to mechanical constraints remain almost unknown especially in relation to phytohormones distribution and RW characteristics. Thus, Populus nigra stem and root subjected to static non-destructive mid-term bending treatment were analyzed. The distribution of tension and compression forces was firstly modeled along the main bent stem and root axis; then, anatomical features, chemical composition, and a complete auxin and cytokinin metabolite profiles of the stretched convex and compressed concave side of three different bent stem and root sectors were analyzed. The results showed that in bent stems RW was produced on the upper stretched convex side whereas in bent roots it was produced on the lower compressed concave side. Anatomical features and chemical analysis showed that bent stem RW was characterized by a low number of vessel, poor lignification, and high carbohydrate, and thus gelatinous layer in fiber cell wall. Conversely, in bent root, RW was characterized by high vessel number and area, without any significant variation in carbohydrate and lignin content. An antagonistic interaction of auxins and different cytokinin forms/conjugates seems to regulate critical aspects of RW formation/development in stem and root to facilitate upward/downward organ bending. The observed differences between the response stem and root to bending highlight how hormonal signaling is highly organ-dependent.

@article{bru_genetic_2020,
	title = {A {Genetic} {Screen} to {Identify} {New} {Molecular} {Players} {Involved} in {Photoprotection} {qH} in {Arabidopsis} thaliana},
	volume = {9},
	issn = {2223-7747},
	url = {https://www.mdpi.com/2223-7747/9/11/1565},
	doi = {10.3390/plants9111565},
	abstract = {Photosynthesis is a biological process which converts light energy into chemical energy that is used in the Calvin–Benson cycle to produce organic compounds. An excess of light can induce damage to the photosynthetic machinery. Therefore, plants have evolved photoprotective mechanisms such as non-photochemical quenching (NPQ). To focus molecular insights on slowly relaxing NPQ processes in Arabidopsis thaliana, previously, a qE-deficient line—the PsbS mutant—was mutagenized and a mutant with high and slowly relaxing NPQ was isolated. The mutated gene was named suppressor of quenching 1, or SOQ1, to describe its function. Indeed, when present, SOQ1 negatively regulates or suppresses a form of antenna NPQ that is slow to relax and is photoprotective. We have now termed this component qH and identified the plastid lipocalin, LCNP, as the effector for this energy dissipation mode to occur. Recently, we found that the relaxation of qH1, ROQH1, protein is required to turn off qH. The aim of this study is to identify new molecular players involved in photoprotection qH by a whole genome sequencing approach of chemically mutagenized Arabidopsis thaliana. We conducted an EMS-mutagenesis on the soq1 npq4 double mutant and used chlorophyll fluorescence imaging to screen for suppressors and enhancers of qH. Out of 22,000 mutagenized plants screened, the molecular players cited above were found using a mapping-by-sequencing approach. Here, we describe the phenotypic characterization of the other mutants isolated from this genetic screen and an additional 8000 plants screened. We have classified them in several classes based on their fluorescence parameters, NPQ kinetics, and pigment content. A high-throughput whole genome sequencing approach on 65 mutants will identify the causal mutations thanks to allelic mutations from having reached saturation of the genetic screen. The candidate genes could be involved in the formation or maintenance of quenching sites for qH, in the regulation of qH at the transcriptional level, or be part of the quenching site itself.},
	language = {en},
	number = {11},
	urldate = {2021-06-07},
	journal = {Plants},
	author = {Bru, Pierrick and Nanda, Sanchali and Malnoë, Alizée},
	month = nov,
	year = {2020},
	pages = {1565},
}

Photosynthesis is a biological process which converts light energy into chemical energy that is used in the Calvin–Benson cycle to produce organic compounds. An excess of light can induce damage to the photosynthetic machinery. Therefore, plants have evolved photoprotective mechanisms such as non-photochemical quenching (NPQ). To focus molecular insights on slowly relaxing NPQ processes in Arabidopsis thaliana, previously, a qE-deficient line—the PsbS mutant—was mutagenized and a mutant with high and slowly relaxing NPQ was isolated. The mutated gene was named suppressor of quenching 1, or SOQ1, to describe its function. Indeed, when present, SOQ1 negatively regulates or suppresses a form of antenna NPQ that is slow to relax and is photoprotective. We have now termed this component qH and identified the plastid lipocalin, LCNP, as the effector for this energy dissipation mode to occur. Recently, we found that the relaxation of qH1, ROQH1, protein is required to turn off qH. The aim of this study is to identify new molecular players involved in photoprotection qH by a whole genome sequencing approach of chemically mutagenized Arabidopsis thaliana. We conducted an EMS-mutagenesis on the soq1 npq4 double mutant and used chlorophyll fluorescence imaging to screen for suppressors and enhancers of qH. Out of 22,000 mutagenized plants screened, the molecular players cited above were found using a mapping-by-sequencing approach. Here, we describe the phenotypic characterization of the other mutants isolated from this genetic screen and an additional 8000 plants screened. We have classified them in several classes based on their fluorescence parameters, NPQ kinetics, and pigment content. A high-throughput whole genome sequencing approach on 65 mutants will identify the causal mutations thanks to allelic mutations from having reached saturation of the genetic screen. The candidate genes could be involved in the formation or maintenance of quenching sites for qH, in the regulation of qH at the transcriptional level, or be part of the quenching site itself.

@article{colesie_differences_2020,
	title = {Differences in growth-economics of fast vs. slow growing grass species in response to temperature and nitrogen limitation individually, and in combination},
	volume = {20},
	issn = {1472-6785},
	url = {https://bmcecol.biomedcentral.com/articles/10.1186/s12898-020-00333-3},
	doi = {10.1186/s12898-020-00333-3},
	abstract = {Abstract
            
              Background
              
                Fast growing invasive alien species are highly efficient with little investment in their tissues. They often outcompete slower growing species with severe consequences for diversity and community composition. The plant economics trait-based approach provides a theoretical framework, allowing the classification of plants with different performance characteristics. However, in multifaceted background, this approach needs testing. The evaluation and prediction of plant performance outcomes in ecologically relevant settings is among the most pressing topics to understand and predict ecosystem functioning, especially in a quickly changing environment. Temperature and nutrient availability are major components of the global environmental change and this study examines the response of growth economic traits, photosynthesis and respiration to such changes for an invasive fast-growing (
                Bromus hordaceus
                ) and a slow-growing perennial (
                Bromus erectus
                ) grass species.
              
            
            
              Results
              
                The fully controlled growth chamber experiment simulated temperature—and changes in nitrogen availability individually and in combination. We therefore provide maximum control and monitoring of growth responses allowing general growth trait response patterns to be tested. Under optimal nitrogen availability the slow growing
                B. erectus
                was better able to handle the lower temperatures (7 °C) whilst both species had problems at higher temperatures (30 °C). Stresses produced by a combination of heat and nutrient availability were identified to be less limiting for the slow growing species but the combination of chilling with low nutrient availability was most detrimental to both species.
              
            
            
              Conclusions
              
                For the fast-growing invader
                B. hordeaceus
                a reduction of nitrogen availability in combination with a temperature increase, leads to limited growth performance in comparison to the slow-growing perennial species
                B.erectus
                and this may explain why nutrient-rich habitats often experience more invasion than resource-poor habitats.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Ecology},
	author = {Colesie, Claudia and Stangl, Zsofia Reka and Hurry, Vaughan},
	month = dec,
	year = {2020},
	pages = {63},
}

Abstract Background Fast growing invasive alien species are highly efficient with little investment in their tissues. They often outcompete slower growing species with severe consequences for diversity and community composition. The plant economics trait-based approach provides a theoretical framework, allowing the classification of plants with different performance characteristics. However, in multifaceted background, this approach needs testing. The evaluation and prediction of plant performance outcomes in ecologically relevant settings is among the most pressing topics to understand and predict ecosystem functioning, especially in a quickly changing environment. Temperature and nutrient availability are major components of the global environmental change and this study examines the response of growth economic traits, photosynthesis and respiration to such changes for an invasive fast-growing ( Bromus hordaceus ) and a slow-growing perennial ( Bromus erectus ) grass species. Results The fully controlled growth chamber experiment simulated temperature—and changes in nitrogen availability individually and in combination. We therefore provide maximum control and monitoring of growth responses allowing general growth trait response patterns to be tested. Under optimal nitrogen availability the slow growing B. erectus was better able to handle the lower temperatures (7 °C) whilst both species had problems at higher temperatures (30 °C). Stresses produced by a combination of heat and nutrient availability were identified to be less limiting for the slow growing species but the combination of chilling with low nutrient availability was most detrimental to both species. Conclusions For the fast-growing invader B. hordeaceus a reduction of nitrogen availability in combination with a temperature increase, leads to limited growth performance in comparison to the slow-growing perennial species B.erectus and this may explain why nutrient-rich habitats often experience more invasion than resource-poor habitats.

@article{calleja-rodriguez_evaluation_2020,
	title = {Evaluation of the efficiency of genomic versus pedigree predictions for growth and wood quality traits in {Scots} pine},
	volume = {21},
	issn = {1471-2164},
	url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-07188-4},
	doi = {10.1186/s12864-020-07188-4},
	abstract = {Abstract
            
              Background
              
                Genomic selection (GS) or genomic prediction is a promising approach for tree breeding to obtain higher genetic gains by shortening time of progeny testing in breeding programs. As proof-of-concept for Scots pine (
                Pinus sylvestris
                L.), a genomic prediction study was conducted with 694 individuals representing 183 full-sib families that were genotyped with genotyping-by-sequencing (GBS) and phenotyped for growth and wood quality traits. 8719 SNPs were used to compare different genomic with pedigree prediction models. Additionally, four prediction efficiency methods were used to evaluate the impact of genomic breeding value estimations by assigning diverse ratios of training and validation sets, as well as several subsets of SNP markers.
              
            
            
              Results
              Genomic Best Linear Unbiased Prediction (GBLUP) and Bayesian Ridge Regression (BRR) combined with expectation maximization (EM) imputation algorithm showed slightly higher prediction efficiencies than Pedigree Best Linear Unbiased Prediction (PBLUP) and Bayesian LASSO, with some exceptions. A subset of approximately 6000 SNP markers, was enough to provide similar prediction efficiencies as the full set of 8719 markers. Additionally, prediction efficiencies of genomic models were enough to achieve a higher selection response, that varied between 50-143\% higher than the traditional pedigree-based selection.
            
            
              Conclusions
              Although prediction efficiencies were similar for genomic and pedigree models, the relative selection response was doubled for genomic models by assuming that earlier selections can be done at the seedling stage, reducing the progeny testing time, thus shortening the breeding cycle length roughly by 50\%.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Genomics},
	author = {Calleja-Rodriguez, Ainhoa and Pan, Jin and Funda, Tomas and Chen, Zhiqiang and Baison, John and Isik, Fikret and Abrahamsson, Sara and Wu, Harry X.},
	month = dec,
	year = {2020},
	pages = {796},
}

Abstract Background Genomic selection (GS) or genomic prediction is a promising approach for tree breeding to obtain higher genetic gains by shortening time of progeny testing in breeding programs. As proof-of-concept for Scots pine ( Pinus sylvestris L.), a genomic prediction study was conducted with 694 individuals representing 183 full-sib families that were genotyped with genotyping-by-sequencing (GBS) and phenotyped for growth and wood quality traits. 8719 SNPs were used to compare different genomic with pedigree prediction models. Additionally, four prediction efficiency methods were used to evaluate the impact of genomic breeding value estimations by assigning diverse ratios of training and validation sets, as well as several subsets of SNP markers. Results Genomic Best Linear Unbiased Prediction (GBLUP) and Bayesian Ridge Regression (BRR) combined with expectation maximization (EM) imputation algorithm showed slightly higher prediction efficiencies than Pedigree Best Linear Unbiased Prediction (PBLUP) and Bayesian LASSO, with some exceptions. A subset of approximately 6000 SNP markers, was enough to provide similar prediction efficiencies as the full set of 8719 markers. Additionally, prediction efficiencies of genomic models were enough to achieve a higher selection response, that varied between 50-143% higher than the traditional pedigree-based selection. Conclusions Although prediction efficiencies were similar for genomic and pedigree models, the relative selection response was doubled for genomic models by assuming that earlier selections can be done at the seedling stage, reducing the progeny testing time, thus shortening the breeding cycle length roughly by 50%.

@article{miguel_gdsl_2020,
	title = {A {GDSL} lipase-like from {Ipomoea} batatas catalyzes efficient production of 3,5-{diCQA} when expressed in {Pichia} pastoris},
	volume = {3},
	issn = {2399-3642},
	url = {http://www.nature.com/articles/s42003-020-01387-1},
	doi = {10.1038/s42003-020-01387-1},
	abstract = {Abstract
            
              The synthesis of 3,5-dicaffeoylquinic acid (3,5-DiCQA) has attracted the interest of many researchers for more than 30 years. Recently, enzymes belonging to the BAHD acyltransferase family were shown to mediate its synthesis, albeit with notably low efficiency. In this study, a new enzyme belonging to the GDSL lipase-like family was identified and proven to be able to transform chlorogenic acid (5-
              O
              -caffeoylquinic acid, 5-CQA, CGA) in 3,5-DiCQA with a conversion rate of more than 60\%. The enzyme has been produced in different expression systems but has only been shown to be active when transiently synthesized in
              Nicotiana benthamiana
              or stably expressed in
              Pichia pastoris
              . The synthesis of the molecule could be performed in vitro but also by a bioconversion approach beginning from pure 5-CQA or from green coffee bean extract, thereby paving the road for producing it on an industrial scale.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Communications Biology},
	author = {Miguel, Sissi and Legrand, Guillaume and Duriot, Léonor and Delporte, Marianne and Menin, Barbara and Michel, Cindy and Olry, Alexandre and Chataigné, Gabrielle and Salwinski, Aleksander and Bygdell, Joakim and Vercaigne, Dominique and Wingsle, Gunnar and Hilbert, Jean Louis and Bourgaud, Frédéric and Hehn, Alain and Gagneul, David},
	month = dec,
	year = {2020},
	pages = {673},
}

Abstract The synthesis of 3,5-dicaffeoylquinic acid (3,5-DiCQA) has attracted the interest of many researchers for more than 30 years. Recently, enzymes belonging to the BAHD acyltransferase family were shown to mediate its synthesis, albeit with notably low efficiency. In this study, a new enzyme belonging to the GDSL lipase-like family was identified and proven to be able to transform chlorogenic acid (5- O -caffeoylquinic acid, 5-CQA, CGA) in 3,5-DiCQA with a conversion rate of more than 60%. The enzyme has been produced in different expression systems but has only been shown to be active when transiently synthesized in Nicotiana benthamiana or stably expressed in Pichia pastoris . The synthesis of the molecule could be performed in vitro but also by a bioconversion approach beginning from pure 5-CQA or from green coffee bean extract, thereby paving the road for producing it on an industrial scale.

@article{harinikumar_bioethanol_2020,
	title = {Bioethanol production from four abundant {Indian} agricultural wastes},
	volume = {11},
	issn = {1759-7269, 1759-7277},
	url = {https://www.tandfonline.com/doi/full/10.1080/17597269.2017.1387744},
	doi = {10.1080/17597269.2017.1387744},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Biofuels},
	author = {Harinikumar, K. M. and Kudahettige-Nilsson, R. L. and Devadas, A. and Holmgren, M. and Sellstedt, A.},
	month = jul,
	year = {2020},
	pages = {607--613},
}

@article{shchukarev_cryo-xps_2020,
	title = {Cryo-{XPS} analysis reveals surface composition of microalgae},
	volume = {526},
	issn = {01694332},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0169433220312952},
	doi = {10.1016/j.apsusc.2020.146538},
	language = {en},
	urldate = {2021-06-07},
	journal = {Applied Surface Science},
	author = {Shchukarev, A. and Gojkovic, Z. and Funk, C. and Ramstedt, M.},
	month = oct,
	year = {2020},
	pages = {146538},
}

@article{gauchan_evaluation_2020,
	title = {Evaluation of antimicrobial, antioxidant and cytotoxic properties of bioactive compounds produced from endophytic fungi of {Himalayan} yew ({Taxus} wallichiana) in {Nepal}},
	volume = {9},
	issn = {2046-1402},
	url = {https://f1000research.com/articles/9-379/v2},
	doi = {10.12688/f1000research.23250.2},
	abstract = {Background:
              Endophytic fungi are largely underexplored in the discovery of natural bioactive products though being rich sources of novel compounds with promising pharmaceutical potential. In this study,
              Taxus wallichiana,
              which has huge medicinal value, was investigated for its endophytic diversity and capability to produce bioactive secondary metabolites by analyzing antioxidant, antimicrobial and cytotoxic properties.
            
            
              Methods:
              The endophytes were identified by ITS-PCR using genomic DNA samples. The secondary metabolites were extracted by solvent extraction method using ethyl acetate. The antioxidant activity was analyzed by Thin Layer Chromatography, Total Phenol Content (TPC), Total Flavonoid Content (TFC) and DPPH assay, and the antimicrobial activity was analyzed by agar-well diffusion method. Brine shrimp lethality assay was used to analyze the cytotoxicity of the fungal extracts.
            
            
              Results:
              Out of 16 different
              Taxus
              trees sampled from different locations of Dhorpatan, 13 distinctive endophytic fungi were isolated and grouped into 9 different genera:
              Bjerkandera, Trichoderma, Preussia, Botrytis, Arthrinium, Alternaria, Cladosporium, Sporormiella
              and
              Daldinia
              . The ethyl acetate extracts isolated from three endophytic fungi:
              Alternaria alternata
              ,
              Cladosporium cladosporioides
              and
              Alternaria brassicae
              showed significant TPC values of 204±6.144, 312.3±2.147 and 152.7±4.958µg GAE/mg of dry extract, respectively, and TFC values of 177.9±2.911, 644.1±4.202 and 96.38±3.851µg RE/mg of dry extract, respectively. Furthermore, these three extracts showed a dose dependent radical scavenging activity with IC
              50
              concentration of 22.85, 22.15 and 23.001 µg/ml, respectively. The extracts of
              C. cladosporioides
              and
              A. brassicae
              also showed promising antimicrobial activity against
              Escherichia coli
              ,
              Staphylococcus aureus
              and
              Bacillus subtilis
              with a minimum inhibitory concentration of 250μg/ml for all bacteria. Both the samples showed cytotoxic property against shrimp nauplii with LC
              50
              of 104.2 and 125.9µg/ml, respectively.
            
            
              Conclusions:
              The crude fungal extracts obtained from endophytes:
              A. alternata
              ,
              C. cladosporioides
              and
              A. brassicae
              upon purification and further identification of the bioactive compounds can be a fascinating source for novel pharmaceutical agents.},
	language = {en},
	urldate = {2021-06-07},
	journal = {F1000Research},
	author = {Gauchan, Dhurva Prasad and Kandel, Pratistha and Tuladhar, Astha and Acharya, Ashesh and Kadel, Upendra and Baral, Aayush and Shahi, Arjan Bir and García-Gil, María Rosario},
	month = oct,
	year = {2020},
	pages = {379},
}

Background: Endophytic fungi are largely underexplored in the discovery of natural bioactive products though being rich sources of novel compounds with promising pharmaceutical potential. In this study, Taxus wallichiana, which has huge medicinal value, was investigated for its endophytic diversity and capability to produce bioactive secondary metabolites by analyzing antioxidant, antimicrobial and cytotoxic properties. Methods: The endophytes were identified by ITS-PCR using genomic DNA samples. The secondary metabolites were extracted by solvent extraction method using ethyl acetate. The antioxidant activity was analyzed by Thin Layer Chromatography, Total Phenol Content (TPC), Total Flavonoid Content (TFC) and DPPH assay, and the antimicrobial activity was analyzed by agar-well diffusion method. Brine shrimp lethality assay was used to analyze the cytotoxicity of the fungal extracts. Results: Out of 16 different Taxus trees sampled from different locations of Dhorpatan, 13 distinctive endophytic fungi were isolated and grouped into 9 different genera: Bjerkandera, Trichoderma, Preussia, Botrytis, Arthrinium, Alternaria, Cladosporium, Sporormiella and Daldinia . The ethyl acetate extracts isolated from three endophytic fungi: Alternaria alternata , Cladosporium cladosporioides and Alternaria brassicae showed significant TPC values of 204±6.144, 312.3±2.147 and 152.7±4.958µg GAE/mg of dry extract, respectively, and TFC values of 177.9±2.911, 644.1±4.202 and 96.38±3.851µg RE/mg of dry extract, respectively. Furthermore, these three extracts showed a dose dependent radical scavenging activity with IC 50 concentration of 22.85, 22.15 and 23.001 µg/ml, respectively. The extracts of C. cladosporioides and A. brassicae also showed promising antimicrobial activity against Escherichia coli , Staphylococcus aureus and Bacillus subtilis with a minimum inhibitory concentration of 250μg/ml for all bacteria. Both the samples showed cytotoxic property against shrimp nauplii with LC 50 of 104.2 and 125.9µg/ml, respectively. Conclusions: The crude fungal extracts obtained from endophytes: A. alternata , C. cladosporioides and A. brassicae upon purification and further identification of the bioactive compounds can be a fascinating source for novel pharmaceutical agents.

@article{baison_genetic_2020,
	title = {Genetic control of tracheid properties in {Norway} spruce wood},
	volume = {10},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/s41598-020-72586-3},
	doi = {10.1038/s41598-020-72586-3},
	abstract = {Abstract
            
              Through the use of genome-wide association studies (GWAS) mapping it is possible to establish the genetic basis of phenotypic trait variation. Our GWAS study presents the first such effort in Norway spruce (
              Picea abies
              (L). Karst.) for the traits related to wood tracheid characteristics. The study employed an exome capture genotyping approach that generated 178 101 Single Nucleotide Polymorphisms (SNPs) from 40 018 probes within a population of 517 Norway spruce mother trees. We applied a least absolute shrinkage and selection operator (LASSO) based association mapping method using a functional multi-locus mapping approach, with a stability selection probability method as the hypothesis testing approach to determine significant Quantitative Trait Loci (QTLs). The analysis has provided 30 significant associations, the majority of which show specific expression in wood-forming tissues or high ubiquitous expression, potentially controlling tracheids dimensions, their cell wall thickness and microfibril angle. Among the most promising candidates based on our results and prior information for other species are:
              Picea abies BIG GRAIN 2
              (
              PabBG2)
              with a predicted function in auxin transport and sensitivity, and
              MA\_373300g0010
              encoding a protein similar to wall-associated receptor kinases, which were both associated with cell wall thickness. The results demonstrate feasibility of GWAS to identify novel candidate genes controlling industrially-relevant tracheid traits in Norway spruce.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	author = {Baison, J. and Zhou, Linghua and Forsberg, Nils and Mörling, Tommy and Grahn, Thomas and Olsson, Lars and Karlsson, Bo and Wu, Harry X. and Mellerowicz, Ewa J. and Lundqvist, Sven-Olof and García-Gil, María Rosario},
	month = dec,
	year = {2020},
	pages = {18089},
}

Abstract Through the use of genome-wide association studies (GWAS) mapping it is possible to establish the genetic basis of phenotypic trait variation. Our GWAS study presents the first such effort in Norway spruce ( Picea abies (L). Karst.) for the traits related to wood tracheid characteristics. The study employed an exome capture genotyping approach that generated 178 101 Single Nucleotide Polymorphisms (SNPs) from 40 018 probes within a population of 517 Norway spruce mother trees. We applied a least absolute shrinkage and selection operator (LASSO) based association mapping method using a functional multi-locus mapping approach, with a stability selection probability method as the hypothesis testing approach to determine significant Quantitative Trait Loci (QTLs). The analysis has provided 30 significant associations, the majority of which show specific expression in wood-forming tissues or high ubiquitous expression, potentially controlling tracheids dimensions, their cell wall thickness and microfibril angle. Among the most promising candidates based on our results and prior information for other species are: Picea abies BIG GRAIN 2 ( PabBG2) with a predicted function in auxin transport and sensitivity, and MA_373300g0010 encoding a protein similar to wall-associated receptor kinases, which were both associated with cell wall thickness. The results demonstrate feasibility of GWAS to identify novel candidate genes controlling industrially-relevant tracheid traits in Norway spruce.

@article{yang_chromosome-level_2020,
	title = {Chromosome-level genome assembly of a parent species of widely cultivated azaleas},
	volume = {11},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/s41467-020-18771-4},
	doi = {10.1038/s41467-020-18771-4},
	abstract = {Abstract
            
              Azaleas (Ericaceae) comprise one of the most diverse ornamental plants, renowned for their cultural and economic importance. We present a chromosome-scale genome assembly for
              Rhododendron simsii
              , the primary ancestor of azalea cultivars. Genome analyses unveil the remnants of an ancient whole-genome duplication preceding the radiation of most Ericaceae, likely contributing to the genomic architecture of flowering time. Small-scale gene duplications contribute to the expansion of gene families involved in azalea pigment biosynthesis. We reconstruct entire metabolic pathways for anthocyanins and carotenoids and their potential regulatory networks by detailed analysis of time-ordered gene co-expression networks. MYB, bHLH, and WD40 transcription factors may collectively regulate anthocyanin accumulation in
              R. simsii
              , particularly at the initial stages of flower coloration, and with WRKY transcription factors controlling progressive flower coloring at later stages. This work provides a cornerstone for understanding the underlying genetics governing flower timing and coloration and could accelerate selective breeding in azalea.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Yang, Fu-Sheng and Nie, Shuai and Liu, Hui and Shi, Tian-Le and Tian, Xue-Chan and Zhou, Shan-Shan and Bao, Yu-Tao and Jia, Kai-Hua and Guo, Jing-Fang and Zhao, Wei and An, Na and Zhang, Ren-Gang and Yun, Quan-Zheng and Wang, Xin-Zhu and Mannapperuma, Chanaka and Porth, Ilga and El-Kassaby, Yousry Aly and Street, Nathaniel Robert and Wang, Xiao-Ru and Van de Peer, Yves and Mao, Jian-Feng},
	month = dec,
	year = {2020},
	pages = {5269},
}

Abstract Azaleas (Ericaceae) comprise one of the most diverse ornamental plants, renowned for their cultural and economic importance. We present a chromosome-scale genome assembly for Rhododendron simsii , the primary ancestor of azalea cultivars. Genome analyses unveil the remnants of an ancient whole-genome duplication preceding the radiation of most Ericaceae, likely contributing to the genomic architecture of flowering time. Small-scale gene duplications contribute to the expansion of gene families involved in azalea pigment biosynthesis. We reconstruct entire metabolic pathways for anthocyanins and carotenoids and their potential regulatory networks by detailed analysis of time-ordered gene co-expression networks. MYB, bHLH, and WD40 transcription factors may collectively regulate anthocyanin accumulation in R. simsii , particularly at the initial stages of flower coloration, and with WRKY transcription factors controlling progressive flower coloring at later stages. This work provides a cornerstone for understanding the underlying genetics governing flower timing and coloration and could accelerate selective breeding in azalea.

@article{alallaq_red_2020,
	title = {Red {Light} {Controls} {Adventitious} {Root} {Regeneration} by {Modulating} {Hormone} {Homeostasis} in {Picea} abies {Seedlings}},
	volume = {11},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2020.586140/full},
	doi = {10.3389/fpls.2020.586140},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Alallaq, Sanaria and Ranjan, Alok and Brunoni, Federica and Novák, Ondřej and Lakehal, Abdellah and Bellini, Catherine},
	month = sep,
	year = {2020},
	pages = {586140},
}

@article{ferro_dna_2020,
	title = {{DNA} metabarcoding reveals microbial community dynamics in a microalgae-based municipal wastewater treatment open photobioreactor},
	volume = {51},
	issn = {22119264},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S2211926419311476},
	doi = {10.1016/j.algal.2020.102043},
	language = {en},
	urldate = {2021-06-07},
	journal = {Algal Research},
	author = {Ferro, Lorenza and Hu, Yue O.O. and Gentili, Francesco G. and Andersson, Anders F. and Funk, Christiane},
	month = oct,
	year = {2020},
	pages = {102043},
}

@article{putintseva_siberian_2020,
	title = {Siberian larch ({Larix} sibirica {Ledeb}.) mitochondrial genome assembled using both short and long nucleotide sequence reads is currently the largest known mitogenome},
	volume = {21},
	issn = {1471-2164},
	url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-07061-4},
	doi = {10.1186/s12864-020-07061-4},
	abstract = {Abstract
            
              Background
              
                Plant mitochondrial genomes (mitogenomes) can be structurally complex while their size can vary from {\textasciitilde} 222 Kbp in
                Brassica napus
                to 11.3 Mbp in
                Silene conica
                . To date, in comparison with the number of plant species, only a few plant mitogenomes have been sequenced and released, particularly for conifers (the Pinaceae family). Conifers cover an ancient group of land plants that includes about 600 species, and which are of great ecological and economical value. Among them, Siberian larch (
                Larix sibirica
                Ledeb.) represents one of the keystone species in Siberian boreal forests. Yet, despite its importance for evolutionary and population studies, the mitogenome of Siberian larch has not yet been assembled and studied.
              
            
            
              Results
              Two sources of DNA sequences were used to search for mitochondrial DNA (mtDNA) sequences: mtDNA enriched samples and nucleotide reads generated in the de novo whole genome sequencing project, respectively. The assembly of the Siberian larch mitogenome contained nine contigs, with the shortest and the largest contigs being 24,767 bp and 4,008,762 bp, respectively. The total size of the genome was estimated at 11.7 Mbp. In total, 40 protein-coding, 34 tRNA, and 3 rRNA genes and numerous repetitive elements (REs) were annotated in this mitogenome. In total, 864 C-to-U RNA editing sites were found for 38 out of 40 protein-coding genes. The immense size of this genome, currently the largest reported, can be partly explained by variable numbers of mobile genetic elements, and introns, but unlikely by plasmid-related sequences. We found few plasmid-like insertions representing only 0.11\% of the entire Siberian larch mitogenome.
            
            
              Conclusions
              
                Our study showed that the size of the Siberian larch mitogenome is much larger than in other so far studied Gymnosperms, and in the same range as for the annual flowering plant
                Silene conica
                (11.3 Mbp). Similar to other species, the Siberian larch mitogenome contains relatively few genes, and despite its huge size, the repeated and low complexity regions cover only 14.46\% of the mitogenome sequence.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Genomics},
	author = {Putintseva, Yuliya A. and Bondar, Eugeniya I. and Simonov, Evgeniy P. and Sharov, Vadim V. and Oreshkova, Natalya V. and Kuzmin, Dmitry A. and Konstantinov, Yuri M. and Shmakov, Vladimir N. and Belkov, Vadim I. and Sadovsky, Michael G. and Keech, Olivier and Krutovsky, Konstantin V.},
	month = dec,
	year = {2020},
	pages = {654},
}

Abstract Background Plant mitochondrial genomes (mitogenomes) can be structurally complex while their size can vary from ~ 222 Kbp in Brassica napus to 11.3 Mbp in Silene conica . To date, in comparison with the number of plant species, only a few plant mitogenomes have been sequenced and released, particularly for conifers (the Pinaceae family). Conifers cover an ancient group of land plants that includes about 600 species, and which are of great ecological and economical value. Among them, Siberian larch ( Larix sibirica Ledeb.) represents one of the keystone species in Siberian boreal forests. Yet, despite its importance for evolutionary and population studies, the mitogenome of Siberian larch has not yet been assembled and studied. Results Two sources of DNA sequences were used to search for mitochondrial DNA (mtDNA) sequences: mtDNA enriched samples and nucleotide reads generated in the de novo whole genome sequencing project, respectively. The assembly of the Siberian larch mitogenome contained nine contigs, with the shortest and the largest contigs being 24,767 bp and 4,008,762 bp, respectively. The total size of the genome was estimated at 11.7 Mbp. In total, 40 protein-coding, 34 tRNA, and 3 rRNA genes and numerous repetitive elements (REs) were annotated in this mitogenome. In total, 864 C-to-U RNA editing sites were found for 38 out of 40 protein-coding genes. The immense size of this genome, currently the largest reported, can be partly explained by variable numbers of mobile genetic elements, and introns, but unlikely by plasmid-related sequences. We found few plasmid-like insertions representing only 0.11% of the entire Siberian larch mitogenome. Conclusions Our study showed that the size of the Siberian larch mitogenome is much larger than in other so far studied Gymnosperms, and in the same range as for the annual flowering plant Silene conica (11.3 Mbp). Similar to other species, the Siberian larch mitogenome contains relatively few genes, and despite its huge size, the repeated and low complexity regions cover only 14.46% of the mitogenome sequence.

@article{tebani_integration_2020,
	title = {Integration of molecular profiles in a longitudinal wellness profiling cohort},
	volume = {11},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/s41467-020-18148-7},
	doi = {10.1038/s41467-020-18148-7},
	abstract = {Abstract
            An important aspect of precision medicine is to probe the stability in molecular profiles among healthy individuals over time. Here, we sample a longitudinal wellness cohort with 100 healthy individuals and analyze blood molecular profiles including proteomics, transcriptomics, lipidomics, metabolomics, autoantibodies and immune cell profiling, complemented with gut microbiota composition and routine clinical chemistry. Overall, our results show high variation between individuals across different molecular readouts, while the intra-individual baseline variation is low. The analyses show that each individual has a unique and stable plasma protein profile throughout the study period and that many individuals also show distinct profiles with regards to the other omics datasets, with strong underlying connections between the blood proteome and the clinical chemistry parameters. In conclusion, the results support an individual-based definition of health and show that comprehensive omics profiling in a longitudinal manner is a path forward for precision medicine.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Tebani, Abdellah and Gummesson, Anders and Zhong, Wen and Koistinen, Ina Schuppe and Lakshmikanth, Tadepally and Olsson, Lisa M. and Boulund, Fredrik and Neiman, Maja and Stenlund, Hans and Hellström, Cecilia and Karlsson, Max J. and Arif, Muhammad and Dodig-Crnković, Tea and Mardinoglu, Adil and Lee, Sunjae and Zhang, Cheng and Chen, Yang and Olin, Axel and Mikes, Jaromir and Danielsson, Hanna and von Feilitzen, Kalle and Jansson, Per-Anders and Angerås, Oskar and Huss, Mikael and Kjellqvist, Sanela and Odeberg, Jacob and Edfors, Fredrik and Tremaroli, Valentina and Forsström, Björn and Schwenk, Jochen M. and Nilsson, Peter and Moritz, Thomas and Bäckhed, Fredrik and Engstrand, Lars and Brodin, Petter and Bergström, Göran and Uhlen, Mathias and Fagerberg, Linn},
	month = dec,
	year = {2020},
	pages = {4487},
}

Abstract An important aspect of precision medicine is to probe the stability in molecular profiles among healthy individuals over time. Here, we sample a longitudinal wellness cohort with 100 healthy individuals and analyze blood molecular profiles including proteomics, transcriptomics, lipidomics, metabolomics, autoantibodies and immune cell profiling, complemented with gut microbiota composition and routine clinical chemistry. Overall, our results show high variation between individuals across different molecular readouts, while the intra-individual baseline variation is low. The analyses show that each individual has a unique and stable plasma protein profile throughout the study period and that many individuals also show distinct profiles with regards to the other omics datasets, with strong underlying connections between the blood proteome and the clinical chemistry parameters. In conclusion, the results support an individual-based definition of health and show that comprehensive omics profiling in a longitudinal manner is a path forward for precision medicine.

@article{kubiasova_cytokinin_2020,
	title = {Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum},
	volume = {11},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/s41467-020-17949-0},
	doi = {10.1038/s41467-020-17949-0},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Kubiasová, Karolina and Montesinos, Juan Carlos and Šamajová, Olga and Nisler, Jaroslav and Mik, Václav and Semerádová, Hana and Plíhalová, Lucie and Novák, Ondřej and Marhavý, Peter and Cavallari, Nicola and Zalabák, David and Berka, Karel and Doležal, Karel and Galuszka, Petr and Šamaj, Jozef and Strnad, Miroslav and Benková, Eva and Plíhal, Ondřej and Spíchal, Lukáš},
	month = dec,
	year = {2020},
	pages = {4285},
}

@article{antoniadi_cell-surface_2020,
	title = {Cell-surface receptors enable perception of extracellular cytokinins},
	volume = {11},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/s41467-020-17700-9},
	doi = {10.1038/s41467-020-17700-9},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Antoniadi, Ioanna and Novák, Ondřej and Gelová, Zuzana and Johnson, Alexander and Plíhal, Ondřej and Simerský, Radim and Mik, Václav and Vain, Thomas and Mateo-Bonmatí, Eduardo and Karady, Michal and Pernisová, Markéta and Plačková, Lenka and Opassathian, Korawit and Hejátko, Jan and Robert, Stéphanie and Friml, Jiří and Doležal, Karel and Ljung, Karin and Turnbull, Colin},
	month = dec,
	year = {2020},
	pages = {4284},
}

@article{lim_effects_2020,
	title = {Effects of whole‐tree harvesting at thinning and subsequent compensatory nutrient additions on carbon sequestration and soil acidification in a boreal forest},
	volume = {12},
	issn = {1757-1693, 1757-1707},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/gcbb.12737},
	doi = {10.1111/gcbb.12737},
	language = {en},
	number = {11},
	urldate = {2021-06-07},
	journal = {GCB Bioenergy},
	author = {Lim, Hyungwoo and Olsson, Bengt A. and Lundmark, Tomas and Dahl, Jenny and Nordin, Annika},
	month = nov,
	year = {2020},
	pages = {992--1001},
}

@article{kauppi_carbon_2020,
	title = {Carbon benefits from {Forest} {Transitions} promoting biomass expansions and thickening},
	volume = {26},
	issn = {1354-1013, 1365-2486},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/gcb.15292},
	doi = {10.1111/gcb.15292},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {Global Change Biology},
	author = {Kauppi, Pekka E. and Ciais, Philippe and Högberg, Peter and Nordin, Annika and Lappi, Juha and Lundmark, Tomas and Wernick, Iddo K.},
	month = oct,
	year = {2020},
	pages = {5365--5370},
}

@article{moazzami_farida_silver_2020,
	title = {Silver nanoparticle pollutants activate oxidative stress responses and rosmarinic acid accumulation in sage},
	volume = {170},
	issn = {0031-9317, 1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/ppl.13172},
	doi = {10.1111/ppl.13172},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Moazzami Farida, Seyed Hamed and Karamian, Roya and Albrectsen, Benedicte R},
	month = nov,
	year = {2020},
	pages = {415--432},
}

@article{dong_heartbreak_2020,
	title = {{HEARTBREAK} {Controls} {Post}-translational {Modification} of {INDEHISCENT} to {Regulate} {Fruit} {Morphology} in {Capsella}},
	volume = {30},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982220310800},
	doi = {10.1016/j.cub.2020.07.055},
	language = {en},
	number = {19},
	urldate = {2021-06-07},
	journal = {Current Biology},
	author = {Dong, Yang and Majda, Mateusz and Šimura, Jan and Horvath, Robert and Srivastava, Anjil K. and Łangowski, Łukasz and Eldridge, Tilly and Stacey, Nicola and Slotte, Tanja and Sadanandom, Ari and Ljung, Karin and Smith, Richard S. and Østergaard, Lars},
	month = oct,
	year = {2020},
	pages = {3880--3888.e5},
}

@article{ponnu_trehalose_2020,
	title = {The trehalose 6‐phosphate pathway impacts vegetative phase change in \textit{{Arabidopsis} thaliana}},
	volume = {104},
	issn = {0960-7412, 1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/tpj.14965},
	doi = {10.1111/tpj.14965},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {The Plant Journal},
	author = {Ponnu, Jathish and Schlereth, Armin and Zacharaki, Vasiliki and Działo, Magdalena A. and Abel, Christin and Feil, Regina and Schmid, Markus and Wahl, Vanessa},
	month = nov,
	year = {2020},
	pages = {768--780},
}

@article{vaisanen_hunting_2020,
	title = {Hunting monolignol transporters: membrane proteomics and biochemical transport assays with membrane vesicles of {Norway} spruce},
	volume = {71},
	issn = {0022-0957, 1460-2431},
	shorttitle = {Hunting monolignol transporters},
	url = {https://academic.oup.com/jxb/article/71/20/6379/5890496},
	doi = {10.1093/jxb/eraa368},
	abstract = {Abstract
            Both the mechanisms of monolignol transport and the transported form of monolignols in developing xylem of trees are unknown. We tested the hypothesis of an active, plasma membrane-localized transport of monolignol monomers, dimers, and/or glucosidic forms with membrane vesicles prepared from developing xylem and lignin-forming tissue-cultured cells of Norway spruce (Picea abies L. Karst.), as well as from control materials, comprising non-lignifying Norway spruce phloem and tobacco (Nicotiana tabacum L.) BY-2 cells. Xylem and BY-2 vesicles transported both coniferin and p-coumaryl alcohol glucoside, but inhibitor assays suggested that this transport was through the tonoplast. Membrane vesicles prepared from lignin-forming spruce cells showed coniferin transport, but the Km value for coniferin was much higher than those of xylem and BY-2 cells. Liquid chromatography-mass spectrometry analysis of membrane proteins isolated from spruce developing xylem, phloem, and lignin-forming cultured cells revealed multiple transporters. These were compared with a transporter gene set obtained by a correlation analysis with a selected set of spruce monolignol biosynthesis genes. Biochemical membrane vesicle assays showed no support for ABC-transporter-mediated monolignol transport but point to a role for secondary active transporters (such as MFS or MATE transporters). In contrast, proteomic and co-expression analyses suggested a role for ABC transporters and MFS transporters.},
	language = {en},
	number = {20},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Väisänen, Enni and Takahashi, Junko and Obudulu, Ogonna and Bygdell, Joakim and Karhunen, Pirkko and Blokhina, Olga and Laitinen, Teresa and Teeri, Teemu H and Wingsle, Gunnar and Fagerstedt, Kurt V and Kärkönen, Anna},
	editor = {Zhao, Qiao},
	month = oct,
	year = {2020},
	pages = {6379--6395},
}

Abstract Both the mechanisms of monolignol transport and the transported form of monolignols in developing xylem of trees are unknown. We tested the hypothesis of an active, plasma membrane-localized transport of monolignol monomers, dimers, and/or glucosidic forms with membrane vesicles prepared from developing xylem and lignin-forming tissue-cultured cells of Norway spruce (Picea abies L. Karst.), as well as from control materials, comprising non-lignifying Norway spruce phloem and tobacco (Nicotiana tabacum L.) BY-2 cells. Xylem and BY-2 vesicles transported both coniferin and p-coumaryl alcohol glucoside, but inhibitor assays suggested that this transport was through the tonoplast. Membrane vesicles prepared from lignin-forming spruce cells showed coniferin transport, but the Km value for coniferin was much higher than those of xylem and BY-2 cells. Liquid chromatography-mass spectrometry analysis of membrane proteins isolated from spruce developing xylem, phloem, and lignin-forming cultured cells revealed multiple transporters. These were compared with a transporter gene set obtained by a correlation analysis with a selected set of spruce monolignol biosynthesis genes. Biochemical membrane vesicle assays showed no support for ABC-transporter-mediated monolignol transport but point to a role for secondary active transporters (such as MFS or MATE transporters). In contrast, proteomic and co-expression analyses suggested a role for ABC transporters and MFS transporters.

@article{funda_genetic_2020,
	title = {Genetic improvement of the chemical composition of {Scots} pine ( \textit{{Pinus} sylvestris} {L}.) juvenile wood for bioenergy production},
	volume = {12},
	issn = {1757-1693, 1757-1707},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/gcbb.12723},
	doi = {10.1111/gcbb.12723},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {GCB Bioenergy},
	author = {Funda, Tomáš and Fundová, Irena and Fries, Anders and Wu, Harry X.},
	month = oct,
	year = {2020},
	pages = {848--863},
}

@article{grebe_specific_2020,
	title = {Specific thylakoid protein phosphorylations are prerequisites for overwintering of {Norway} spruce ( \textit{{Picea} abies} ) photosynthesis},
	volume = {117},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.2004165117},
	doi = {10.1073/pnas.2004165117},
	abstract = {Coping of evergreen conifers in boreal forests with freezing temperatures on bright winter days puts the photosynthetic machinery in great risk of oxidative damage. To survive harsh winter conditions, conifers have evolved a unique but poorly characterized photoprotection mechanism, a sustained form of nonphotochemical quenching (sustained NPQ). Here we focused on functional properties and underlying molecular mechanisms related to the development of sustained NPQ in Norway spruce (
              Picea abies
              ). Data were collected during 4 consecutive years (2016 to 2019) from trees growing in sun and shade habitats. When day temperatures dropped below −4 °C, the specific N-terminally triply phosphorylated LHCB1 isoform (3p-LHCII) and phosphorylated PSBS (p-PSBS) could be detected in the thylakoid membrane. Development of sustained NPQ coincided with the highest level of 3p-LHCII and p-PSBS, occurring after prolonged coincidence of bright winter days and temperatures close to −10 °C. Artificial induction of both the sustained NPQ and recovery from naturally induced sustained NPQ provided information on differential dynamics and light-dependence of 3p-LHCII and p-PSBS accumulation as prerequisites for sustained NPQ. Data obtained collectively suggest three components related to sustained NPQ in spruce: 1) Freezing temperatures induce 3p-LHCII accumulation independently of light, which is suggested to initiate destacking of appressed thylakoid membranes due to increased electrostatic repulsion of adjacent membranes; 2) p-PSBS accumulation is both light- and temperature-dependent and closely linked to the initiation of sustained NPQ, which 3) in concert with PSII photoinhibition, is suggested to trigger sustained NPQ in spruce.},
	language = {en},
	number = {30},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Grebe, Steffen and Trotta, Andrea and Bajwa, Azfar Ali and Mancini, Ilaria and Bag, Pushan and Jansson, Stefan and Tikkanen, Mikko and Aro, Eva-Mari},
	month = jul,
	year = {2020},
	pages = {17499--17509},
}

Coping of evergreen conifers in boreal forests with freezing temperatures on bright winter days puts the photosynthetic machinery in great risk of oxidative damage. To survive harsh winter conditions, conifers have evolved a unique but poorly characterized photoprotection mechanism, a sustained form of nonphotochemical quenching (sustained NPQ). Here we focused on functional properties and underlying molecular mechanisms related to the development of sustained NPQ in Norway spruce ( Picea abies ). Data were collected during 4 consecutive years (2016 to 2019) from trees growing in sun and shade habitats. When day temperatures dropped below −4 °C, the specific N-terminally triply phosphorylated LHCB1 isoform (3p-LHCII) and phosphorylated PSBS (p-PSBS) could be detected in the thylakoid membrane. Development of sustained NPQ coincided with the highest level of 3p-LHCII and p-PSBS, occurring after prolonged coincidence of bright winter days and temperatures close to −10 °C. Artificial induction of both the sustained NPQ and recovery from naturally induced sustained NPQ provided information on differential dynamics and light-dependence of 3p-LHCII and p-PSBS accumulation as prerequisites for sustained NPQ. Data obtained collectively suggest three components related to sustained NPQ in spruce: 1) Freezing temperatures induce 3p-LHCII accumulation independently of light, which is suggested to initiate destacking of appressed thylakoid membranes due to increased electrostatic repulsion of adjacent membranes; 2) p-PSBS accumulation is both light- and temperature-dependent and closely linked to the initiation of sustained NPQ, which 3) in concert with PSII photoinhibition, is suggested to trigger sustained NPQ in spruce.

@incollection{popper_expression_2020,
	address = {New York, NY},
	title = {Expression of {Cell} {Wall}–{Modifying} {Enzymes} in {Aspen} for {Improved} {Lignocellulose} {Processing}},
	volume = {2149},
	isbn = {978-1-07-160619-3 978-1-07-160621-6},
	url = {http://link.springer.com/10.1007/978-1-0716-0621-6_9},
	language = {en},
	urldate = {2021-06-07},
	booktitle = {The {Plant} {Cell} {Wall}},
	publisher = {Springer New York},
	author = {Derba-Maceluch, Marta and Mellerowicz, Ewa J.},
	editor = {Popper, Zoë A.},
	year = {2020},
	doi = {10.1007/978-1-0716-0621-6_9},
	note = {Series Title: Methods in Molecular Biology},
	pages = {145--164},
}

@article{grones_fluctuating_2020,
	title = {Fluctuating auxin response gradients determine pavement cell-shape acquisition},
	volume = {117},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.2007400117},
	doi = {10.1073/pnas.2007400117},
	abstract = {Puzzle-shaped pavement cells provide a powerful model system to investigate the cellular and subcellular processes underlying complex cell-shape determination in plants. To better understand pavement cell-shape acquisition and the role of auxin in this process, we focused on the spirals of young stomatal lineage ground cells of
              Arabidopsis
              leaf epidermis. The predictability of lobe formation in these cells allowed us to demonstrate that the auxin response gradient forms within the cells of the spiral and fluctuates based on the particular stage of lobe development. We revealed that specific localization of auxin transporters at the different membranes of these young cells changes during the course of lobe formation, suggesting that these fluctuating auxin response gradients are orchestrated via auxin transport to control lobe formation and determine pavement cell shape.},
	language = {en},
	number = {27},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Grones, Peter and Majda, Mateusz and Doyle, Siamsa M. and Van Damme, Daniël and Robert, Stéphanie},
	month = jul,
	year = {2020},
	pages = {16027--16034},
}

Puzzle-shaped pavement cells provide a powerful model system to investigate the cellular and subcellular processes underlying complex cell-shape determination in plants. To better understand pavement cell-shape acquisition and the role of auxin in this process, we focused on the spirals of young stomatal lineage ground cells of Arabidopsis leaf epidermis. The predictability of lobe formation in these cells allowed us to demonstrate that the auxin response gradient forms within the cells of the spiral and fluctuates based on the particular stage of lobe development. We revealed that specific localization of auxin transporters at the different membranes of these young cells changes during the course of lobe formation, suggesting that these fluctuating auxin response gradients are orchestrated via auxin transport to control lobe formation and determine pavement cell shape.

@article{hubert_lipid_2020,
	title = {Lipid accumulation controls the balance between surface connection and scission of caveolae},
	volume = {9},
	issn = {2050-084X},
	url = {https://elifesciences.org/articles/55038},
	doi = {10.7554/eLife.55038},
	abstract = {Caveolae are bulb-shaped invaginations of the plasma membrane (PM) that undergo scission and fusion at the cell surface and are enriched in specific lipids. However, the influence of lipid composition on caveolae surface stability is not well described or understood. Accordingly, we inserted specific lipids into the cell PM via membrane fusion and studied their acute effects on caveolae dynamics. We demonstrate that sphingomyelin stabilizes caveolae to the cell surface, whereas cholesterol and glycosphingolipids drive caveolae scission from the PM. Although all three lipids accumulated specifically in caveolae, cholesterol and sphingomyelin were actively sequestered, whereas glycosphingolipids diffused freely. The ATPase EHD2 restricts lipid diffusion and counteracts lipid-induced scission. We propose that specific lipid accumulation in caveolae generates an intrinsically unstable domain prone to scission if not restrained by EHD2 at the caveolae neck. This work provides a mechanistic link between caveolae and their ability to sense the PM lipid composition.},
	language = {en},
	urldate = {2021-06-07},
	journal = {eLife},
	author = {Hubert, Madlen and Larsson, Elin and Vegesna, Naga Venkata Gayathri and Ahnlund, Maria and Johansson, Annika I and Moodie, Lindon WK and Lundmark, Richard},
	month = may,
	year = {2020},
	pages = {e55038},
}

Caveolae are bulb-shaped invaginations of the plasma membrane (PM) that undergo scission and fusion at the cell surface and are enriched in specific lipids. However, the influence of lipid composition on caveolae surface stability is not well described or understood. Accordingly, we inserted specific lipids into the cell PM via membrane fusion and studied their acute effects on caveolae dynamics. We demonstrate that sphingomyelin stabilizes caveolae to the cell surface, whereas cholesterol and glycosphingolipids drive caveolae scission from the PM. Although all three lipids accumulated specifically in caveolae, cholesterol and sphingomyelin were actively sequestered, whereas glycosphingolipids diffused freely. The ATPase EHD2 restricts lipid diffusion and counteracts lipid-induced scission. We propose that specific lipid accumulation in caveolae generates an intrinsically unstable domain prone to scission if not restrained by EHD2 at the caveolae neck. This work provides a mechanistic link between caveolae and their ability to sense the PM lipid composition.

@article{lim_planta_2020,
	title = {In planta study of photosynthesis and photorespiration using {NADPH} and {NADH}/{NAD}+ fluorescent protein sensors},
	volume = {11},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/s41467-020-17056-0},
	doi = {10.1038/s41467-020-17056-0},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Lim, Shey-Li and Voon, Chia Pao and Guan, Xiaoqian and Yang, Yi and Gardeström, Per and Lim, Boon Leong},
	month = dec,
	year = {2020},
	pages = {3238},
}

@article{lagercrantz_nyctinastic_2020,
	title = {Nyctinastic thallus movement in the liverwort {Marchantia} polymorpha is regulated by a circadian clock},
	volume = {10},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/s41598-020-65372-8},
	doi = {10.1038/s41598-020-65372-8},
	abstract = {Abstract
            
              The circadian clock coordinates an organism’s growth, development and physiology with environmental factors. One illuminating example is the rhythmic growth of hypocotyls and cotyledons in
              Arabidopsis thaliana
              . Such daily oscillations in leaf position are often referred to as sleep movements or nyctinasty. Here, we report that plantlets of the liverwort
              Marchantia polymorpha
              show analogous rhythmic movements of thallus lobes, and that the circadian clock controls this rhythm, with auxin a likely output pathway affecting these movements. The mechanisms of this circadian clock are partly conserved as compared to angiosperms, with homologs to the core clock genes
              PRR
              ,
              RVE
              and
              TOC1
              forming a core transcriptional feedback loop also in
              M. polymorpha
              .},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	author = {Lagercrantz, Ulf and Billhardt, Anja and Rousku, Sabine N. and Ljung, Karin and Eklund, D. Magnus},
	month = dec,
	year = {2020},
	pages = {8658},
}

Abstract The circadian clock coordinates an organism’s growth, development and physiology with environmental factors. One illuminating example is the rhythmic growth of hypocotyls and cotyledons in Arabidopsis thaliana . Such daily oscillations in leaf position are often referred to as sleep movements or nyctinasty. Here, we report that plantlets of the liverwort Marchantia polymorpha show analogous rhythmic movements of thallus lobes, and that the circadian clock controls this rhythm, with auxin a likely output pathway affecting these movements. The mechanisms of this circadian clock are partly conserved as compared to angiosperms, with homologs to the core clock genes PRR , RVE and TOC1 forming a core transcriptional feedback loop also in M. polymorpha .

@article{bunder_cellulose_2020,
	title = {{CELLULOSE} {SYNTHASE} {INTERACTING} 1 is required for wood mechanics and leaf morphology in aspen},
	volume = {103},
	issn = {0960-7412, 1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.14873},
	doi = {10.1111/tpj.14873},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {The Plant Journal},
	author = {Bünder, Anne and Sundman, Ola and Mahboubi, Amir and Persson, Staffan and Mansfield, Shawn D. and Rüggeberg, Markus and Niittylä, Totte},
	month = aug,
	year = {2020},
	pages = {1858--1868},
}

@article{ware_auxin_2020,
	title = {Auxin export from proximal fruits drives arrest in temporally competent inflorescences},
	volume = {6},
	issn = {2055-0278},
	url = {http://www.nature.com/articles/s41477-020-0661-z},
	doi = {10.1038/s41477-020-0661-z},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Nature Plants},
	author = {Ware, Alexander and Walker, Catriona H. and Šimura, Jan and González-Suárez, Pablo and Ljung, Karin and Bishopp, Anthony and Wilson, Zoe A. and Bennett, Tom},
	month = jun,
	year = {2020},
	pages = {699--707},
}

@article{muller_single_2020,
	title = {A single gene underlies the dynamic evolution of poplar sex determination},
	volume = {6},
	issn = {2055-0278},
	url = {http://www.nature.com/articles/s41477-020-0672-9},
	doi = {10.1038/s41477-020-0672-9},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Nature Plants},
	author = {Müller, Niels A. and Kersten, Birgit and Leite Montalvão, Ana P. and Mähler, Niklas and Bernhardsson, Carolina and Bräutigam, Katharina and Carracedo Lorenzo, Zulema and Hoenicka, Hans and Kumar, Vikash and Mader, Malte and Pakull, Birte and Robinson, Kathryn M. and Sabatti, Maurizio and Vettori, Cristina and Ingvarsson, Pär K. and Cronk, Quentin and Street, Nathaniel R. and Fladung, Matthias},
	month = jun,
	year = {2020},
	pages = {630--637},
}

@article{lee_gibberellin_2020,
	title = {A gibberellin methyltransferase modulates the timing of floral transition at the {Arabidopsis} shoot meristem},
	volume = {170},
	issn = {0031-9317, 1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/ppl.13146},
	doi = {10.1111/ppl.13146},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Lee, Joanne E. and Goretti, Daniela and Neumann, Manuela and Schmid, Markus and You, Yuan},
	month = dec,
	year = {2020},
	pages = {474--487},
}

@article{hallberg-sramek_framing_2020,
	title = {Framing woodland key habitats in the {Swedish} media – how has the framing changed over time?},
	volume = {35},
	issn = {0282-7581, 1651-1891},
	url = {https://www.tandfonline.com/doi/full/10.1080/02827581.2020.1761444},
	doi = {10.1080/02827581.2020.1761444},
	language = {en},
	number = {3-4},
	urldate = {2021-06-07},
	journal = {Scandinavian Journal of Forest Research},
	author = {Hallberg-Sramek, Isabella and Bjärstig, Therese and Nordin, Annika},
	month = may,
	year = {2020},
	pages = {198--209},
}

@article{law_centralization_2020,
	title = {Centralization {Within} {Sub}-{Experiments} {Enhances} the {Biological} {Relevance} of {Gene} {Co}-expression {Networks}: {A} {Plant} {Mitochondrial} {Case} {Study}},
	volume = {11},
	issn = {1664-462X},
	shorttitle = {Centralization {Within} {Sub}-{Experiments} {Enhances} the {Biological} {Relevance} of {Gene} {Co}-expression {Networks}},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2020.00524/full},
	doi = {10.3389/fpls.2020.00524},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Law, Simon R. and Kellgren, Therese G. and Björk, Rafael and Ryden, Patrik and Keech, Olivier},
	month = jun,
	year = {2020},
	pages = {524},
}

@article{nibbering_golgi-localized_2020,
	title = {Golgi-localized exo-β1,3-galactosidases involved in cell expansion and root growth in {Arabidopsis}},
	volume = {295},
	issn = {00219258},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S002192581750099X},
	doi = {10.1074/jbc.RA120.013878},
	language = {en},
	number = {31},
	urldate = {2021-06-07},
	journal = {Journal of Biological Chemistry},
	author = {Nibbering, Pieter and Petersen, Bent L. and Motawia, Mohammed Saddik and Jørgensen, Bodil and Ulvskov, Peter and Niittylä, Totte},
	month = jul,
	year = {2020},
	pages = {10581--10592},
}

@article{gojkovic_cryogenic_2020,
	title = {Cryogenic {X}-ray photoelectron spectroscopy determines surface composition of algal cells and gives insights into their spontaneous sedimentation},
	volume = {47},
	issn = {22119264},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S2211926419306149},
	doi = {10.1016/j.algal.2020.101836},
	language = {en},
	urldate = {2021-06-07},
	journal = {Algal Research},
	author = {Gojkovic, Zivan and Shchukarev, Andrey and Ramstedt, Madeleine and Funk, Christiane},
	month = may,
	year = {2020},
	pages = {101836},
}

@article{maurya_genetic_2020,
	title = {A genetic framework for regulation and seasonal adaptation of shoot architecture in hybrid aspen},
	volume = {117},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.2004705117},
	doi = {10.1073/pnas.2004705117},
	abstract = {Shoot architecture is critical for optimizing plant adaptation and productivity. In contrast with annuals, branching in perennials native to temperate and boreal regions must be coordinated with seasonal growth cycles. How branching is coordinated with seasonal growth is poorly understood. We identified key components of the genetic network that controls branching and its regulation by seasonal cues in the model tree hybrid aspen. Our results demonstrate that branching and its control by seasonal cues is mediated by mutually antagonistic action of aspen orthologs of the flowering regulators
              TERMINAL FLOWER 1
              (
              TFL1
              ) and
              APETALA1
              (
              LIKE APETALA 1/LAP1
              ).
              LAP1
              promotes branching through local action in axillary buds.
              LAP1
              acts in a cytokinin-dependent manner, stimulating expression of the cell-cycle regulator
              AIL1
              and suppressing
              BRANCHED1
              expression to promote branching. Short photoperiod and low temperature, the major seasonal cues heralding winter, suppress branching by simultaneous activation of
              TFL1
              and repression of the
              LAP1
              pathway. Our results thus reveal the genetic network mediating control of branching and its regulation by environmental cues facilitating integration of branching with seasonal growth control in perennial trees.},
	language = {en},
	number = {21},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Maurya, Jay P. and Miskolczi, Pal C. and Mishra, Sanatkumar and Singh, Rajesh Kumar and Bhalerao, Rishikesh P.},
	month = may,
	year = {2020},
	pages = {11523--11530},
}

Shoot architecture is critical for optimizing plant adaptation and productivity. In contrast with annuals, branching in perennials native to temperate and boreal regions must be coordinated with seasonal growth cycles. How branching is coordinated with seasonal growth is poorly understood. We identified key components of the genetic network that controls branching and its regulation by seasonal cues in the model tree hybrid aspen. Our results demonstrate that branching and its control by seasonal cues is mediated by mutually antagonistic action of aspen orthologs of the flowering regulators TERMINAL FLOWER 1 ( TFL1 ) and APETALA1 ( LIKE APETALA 1/LAP1 ). LAP1 promotes branching through local action in axillary buds. LAP1 acts in a cytokinin-dependent manner, stimulating expression of the cell-cycle regulator AIL1 and suppressing BRANCHED1 expression to promote branching. Short photoperiod and low temperature, the major seasonal cues heralding winter, suppress branching by simultaneous activation of TFL1 and repression of the LAP1 pathway. Our results thus reveal the genetic network mediating control of branching and its regulation by environmental cues facilitating integration of branching with seasonal growth control in perennial trees.

@article{gojkovic_modeling_2020,
	title = {Modeling biomass production during progressive nitrogen starvation by {North} {Swedish} green microalgae},
	volume = {47},
	issn = {22119264},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S2211926419306162},
	doi = {10.1016/j.algal.2020.101835},
	language = {en},
	urldate = {2021-06-07},
	journal = {Algal Research},
	author = {Gojkovic, Zivan and Lu, Yi and Ferro, Lorenza and Toffolo, Andrea and Funk, Christiane},
	month = may,
	year = {2020},
	pages = {101835},
}

@article{derba-maceluch_cell_2020,
	title = {Cell {Wall} {Acetylation} in {Hybrid} {Aspen} {Affects} {Field} {Performance}, {Foliar} {Phenolic} {Composition} and {Resistance} to {Biological} {Stress} {Factors} in a {Construct}-{Dependent} {Fashion}},
	volume = {11},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2020.00651/full},
	doi = {10.3389/fpls.2020.00651},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Derba-Maceluch, Marta and Amini, Fariba and Donev, Evgeniy N. and Pawar, Prashant Mohan-Anupama and Michaud, Lisa and Johansson, Ulf and Albrectsen, Benedicte R. and Mellerowicz, Ewa J.},
	month = may,
	year = {2020},
	pages = {651},
}

@article{nzayisenga_screening_2020,
	title = {Screening {Suitability} of {Northern} {Hemisphere} {Algal} {Strains} for {Heterotrophic} {Cultivation} and {Fatty} {Acid} {Methyl} {Ester} {Production}},
	volume = {25},
	issn = {1420-3049},
	url = {https://www.mdpi.com/1420-3049/25/9/2107},
	doi = {10.3390/molecules25092107},
	abstract = {Rapid rises in atmospheric CO2 levels derived from fossil fuel combustion are imposing urgent needs for renewable substitutes. One environmentally friendly alternative is biodiesel produced from suitable microalgal fatty acids. Algal strains normally grow photoautotrophically, but this is problematic in Northern areas because of the light limitations for much of the year. Mixotrophic and particularly heterotrophic strains could be valuable, especially if they can be cultivated in municipal wastewater with contents of nutrients such as nitrogen and phosphorous that should be reduced before release into receiving water. Thus, the aim of this study was to screen for microalgal strains suitable for heterotrophic cultivation with a cheap carbon source (glycerol) for biodiesel production in Nordic, and other high-latitude, countries. One of the examined strains, a Desmodesmus sp. strain designated 2-6, accumulated biomass at similar rates in heterotrophic conditions with 40 mM glycerol as in autotrophic conditions. Furthermore, in heterotrophic conditions it produced more fatty acids, and ca. 50\% more C18:1 fatty acids, as well as showing a significant decrease in C18:3 fatty acids, all of which are highly desirable features for biodiesel production.},
	language = {en},
	number = {9},
	urldate = {2021-06-07},
	journal = {Molecules},
	author = {Nzayisenga, Jean Claude and Niemi, Calle and Ferro, Lorenza and Gorzsas, Andras and Gentili, Francesco G. and Funk, Christiane and Sellstedt, Anita},
	month = apr,
	year = {2020},
	pages = {2107},
}

Rapid rises in atmospheric CO2 levels derived from fossil fuel combustion are imposing urgent needs for renewable substitutes. One environmentally friendly alternative is biodiesel produced from suitable microalgal fatty acids. Algal strains normally grow photoautotrophically, but this is problematic in Northern areas because of the light limitations for much of the year. Mixotrophic and particularly heterotrophic strains could be valuable, especially if they can be cultivated in municipal wastewater with contents of nutrients such as nitrogen and phosphorous that should be reduced before release into receiving water. Thus, the aim of this study was to screen for microalgal strains suitable for heterotrophic cultivation with a cheap carbon source (glycerol) for biodiesel production in Nordic, and other high-latitude, countries. One of the examined strains, a Desmodesmus sp. strain designated 2-6, accumulated biomass at similar rates in heterotrophic conditions with 40 mM glycerol as in autotrophic conditions. Furthermore, in heterotrophic conditions it produced more fatty acids, and ca. 50% more C18:1 fatty acids, as well as showing a significant decrease in C18:3 fatty acids, all of which are highly desirable features for biodiesel production.

@article{minina_classification_2020,
	title = {Classification and {Nomenclature} of {Metacaspases} and {Paracaspases}: {No} {More} {Confusion} with {Caspases}},
	volume = {77},
	issn = {10972765},
	shorttitle = {Classification and {Nomenclature} of {Metacaspases} and {Paracaspases}},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1097276519309505},
	doi = {10.1016/j.molcel.2019.12.020},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Molecular Cell},
	author = {Minina, Elena A. and Staal, Jens and Alvarez, Vanina E. and Berges, John A. and Berman-Frank, Ilana and Beyaert, Rudi and Bidle, Kay D. and Bornancin, Frédéric and Casanova, Magali and Cazzulo, Juan J. and Choi, Chang Jae and Coll, Nuria S. and Dixit, Vishva M. and Dolinar, Marko and Fasel, Nicolas and Funk, Christiane and Gallois, Patrick and Gevaert, Kris and Gutierrez-Beltran, Emilio and Hailfinger, Stephan and Klemenčič, Marina and Koonin, Eugene V. and Krappmann, Daniel and Linusson, Anna and Machado, Maurício F.M. and Madeo, Frank and Megeney, Lynn A. and Moschou, Panagiotis N. and Mottram, Jeremy C. and Nyström, Thomas and Osiewacz, Heinz D. and Overall, Christopher M. and Pandey, Kailash C. and Ruland, Jürgen and Salvesen, Guy S. and Shi, Yigong and Smertenko, Andrei and Stael, Simon and Ståhlberg, Jerry and Suárez, María Fernanda and Thome, Margot and Tuominen, Hannele and Van Breusegem, Frank and van der Hoorn, Renier A.L. and Vardi, Assaf and Zhivotovsky, Boris and Lam, Eric and Bozhkov, Peter V.},
	month = mar,
	year = {2020},
	pages = {927--929},
}

@article{hernandezverdeja_emerging_2020,
	title = {Emerging from the darkness: interplay between light and plastid signaling during chloroplast biogenesis},
	volume = {169},
	issn = {0031-9317, 1399-3054},
	shorttitle = {Emerging from the darkness},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/ppl.13100},
	doi = {10.1111/ppl.13100},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Hernández‐Verdeja, Tamara and Vuorijoki, Linda and Strand, Åsa},
	month = jul,
	year = {2020},
	pages = {397--406},
}

@article{takatani_microtubule_2020,
	title = {Microtubule {Response} to {Tensile} {Stress} {Is} {Curbed} by {NEK6} to {Buffer} {Growth} {Variation} in the {Arabidopsis} {Hypocotyl}},
	volume = {30},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982220301974},
	doi = {10.1016/j.cub.2020.02.024},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {Current Biology},
	author = {Takatani, Shogo and Verger, Stéphane and Okamoto, Takashi and Takahashi, Taku and Hamant, Olivier and Motose, Hiroyasu},
	month = apr,
	year = {2020},
	pages = {1491--1503.e2},
}

@article{smith_cep5_2020,
	title = {The {CEP5} {Peptide} {Promotes} {Abiotic} {Stress} {Tolerance}, {As} {Revealed} by {Quantitative} {Proteomics}, and {Attenuates} the {AUX}/{IAA} {Equilibrium} in {Arabidopsis}},
	volume = {19},
	issn = {15359476},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1535947620349604},
	doi = {10.1074/mcp.RA119.001826},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {Molecular \& Cellular Proteomics},
	author = {Smith, Stephanie and Zhu, Shanshuo and Joos, Lisa and Roberts, Ianto and Nikonorova, Natalia and Vu, Lam Dai and Stes, Elisabeth and Cho, Hyunwoo and Larrieu, Antoine and Xuan, Wei and Goodall, Benjamin and van de Cotte, Brigitte and Waite, Jessic Marie and Rigal, Adeline and Ramans Harborough, Sigurd and Persiau, Geert and Vanneste, Steffen and Kirschner, Gwendolyn K. and Vandermarliere, Elien and Martens, Lennart and Stahl, Yvonne and Audenaert, Dominique and Friml, Jirí and Felix, Georg and Simon, Rüdiger and Bennett, Malcolm J. and Bishopp, Anthony and De Jaeger, Geert and Ljung, Karin and Kepinski, Stefan and Robert, Stephanie and Nemhauser, Jennifer and Hwang, Ildoo and Gevaert, Kris and Beeckman, Tom and De Smet, Ive},
	month = aug,
	year = {2020},
	pages = {1248--1262},
}

@article{hurny_synergistic_2020,
	title = {{SYNERGISTIC} {ON} {AUXIN} {AND} {CYTOKININ} 1 positively regulates growth and attenuates soil pathogen resistance},
	volume = {11},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/s41467-020-15895-5},
	doi = {10.1038/s41467-020-15895-5},
	abstract = {Abstract
            
              Plants as non-mobile organisms constantly integrate varying environmental signals to flexibly adapt their growth and development. Local fluctuations in water and nutrient availability, sudden changes in temperature or other abiotic and biotic stresses can trigger changes in the growth of plant organs. Multiple mutually interconnected hormonal signaling cascades act as essential endogenous translators of these exogenous signals in the adaptive responses of plants. Although the molecular backbones of hormone transduction pathways have been identified, the mechanisms underlying their interactions are largely unknown. Here, using genome wide transcriptome profiling we identify an auxin and cytokinin cross-talk component;
              SYNERGISTIC ON AUXIN AND CYTOKININ 1
              (
              SYAC1
              ), whose expression in roots is strictly dependent on both of these hormonal pathways. We show that SYAC1 is a regulator of secretory pathway, whose enhanced activity interferes with deposition of cell wall components and can fine-tune organ growth and sensitivity to soil pathogens.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Hurný, Andrej and Cuesta, Candela and Cavallari, Nicola and Ötvös, Krisztina and Duclercq, Jerome and Dokládal, Ladislav and Montesinos, Juan Carlos and Gallemí, Marçal and Semerádová, Hana and Rauter, Thomas and Stenzel, Irene and Persiau, Geert and Benade, Freia and Bhalearo, Rishikesh and Sýkorová, Eva and Gorzsás, András and Sechet, Julien and Mouille, Gregory and Heilmann, Ingo and De Jaeger, Geert and Ludwig-Müller, Jutta and Benková, Eva},
	month = dec,
	year = {2020},
	pages = {2170},
}

Abstract Plants as non-mobile organisms constantly integrate varying environmental signals to flexibly adapt their growth and development. Local fluctuations in water and nutrient availability, sudden changes in temperature or other abiotic and biotic stresses can trigger changes in the growth of plant organs. Multiple mutually interconnected hormonal signaling cascades act as essential endogenous translators of these exogenous signals in the adaptive responses of plants. Although the molecular backbones of hormone transduction pathways have been identified, the mechanisms underlying their interactions are largely unknown. Here, using genome wide transcriptome profiling we identify an auxin and cytokinin cross-talk component; SYNERGISTIC ON AUXIN AND CYTOKININ 1 ( SYAC1 ), whose expression in roots is strictly dependent on both of these hormonal pathways. We show that SYAC1 is a regulator of secretory pathway, whose enhanced activity interferes with deposition of cell wall components and can fine-tune organ growth and sensitivity to soil pathogens.

@article{zhou_effect_2020,
	title = {Effect of number of annual rings and tree ages on genomic predictive ability for solid wood properties of {Norway} spruce},
	volume = {21},
	issn = {1471-2164},
	url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-6737-3},
	doi = {10.1186/s12864-020-6737-3},
	abstract = {Abstract
            
              Background
              
                Genomic selection (GS) or genomic prediction is considered as a promising approach to accelerate tree breeding and increase genetic gain by shortening breeding cycle, but the efforts to develop routines for operational breeding are so far limited. We investigated the predictive ability (PA) of GS based on 484 progeny trees from 62 half-sib families in Norway spruce (
                Picea abies
                (L.) Karst.) for wood density, modulus of elasticity (MOE) and microfibril angle (MFA) measured with SilviScan, as well as for measurements on standing trees by Pilodyn and Hitman instruments.
              
            
            
              Results
              GS predictive abilities were comparable with those based on pedigree-based prediction. Marker-based PAs were generally 25–30\% higher for traits density, MFA and MOE measured with SilviScan than for their respective standing tree-based method which measured with Pilodyn and Hitman. Prediction accuracy (PC) of the standing tree-based methods were similar or even higher than increment core-based method. 78–95\% of the maximal PAs of density, MFA and MOE obtained from coring to the pith at high age were reached by using data possible to obtain by drilling 3–5 rings towards the pith at tree age 10–12.
            
            
              Conclusions
              This study indicates standing tree-based measurements is a cost-effective alternative method for GS. PA of GS methods were comparable with those pedigree-based prediction. The highest PAs were reached with at least 80–90\% of the dataset used as training set. Selection for trait density could be conducted at an earlier age than for MFA and MOE. Operational breeding can also be optimized by training the model at an earlier age or using 3 to 5 outermost rings at tree age 10 to 12 years, thereby shortening the cycle and reducing the impact on the tree.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Genomics},
	author = {Zhou, Linghua and Chen, Zhiqiang and Olsson, Lars and Grahn, Thomas and Karlsson, Bo and Wu, Harry X. and Lundqvist, Sven-Olof and García-Gil, María Rosario},
	month = dec,
	year = {2020},
	pages = {323},
}

Abstract Background Genomic selection (GS) or genomic prediction is considered as a promising approach to accelerate tree breeding and increase genetic gain by shortening breeding cycle, but the efforts to develop routines for operational breeding are so far limited. We investigated the predictive ability (PA) of GS based on 484 progeny trees from 62 half-sib families in Norway spruce ( Picea abies (L.) Karst.) for wood density, modulus of elasticity (MOE) and microfibril angle (MFA) measured with SilviScan, as well as for measurements on standing trees by Pilodyn and Hitman instruments. Results GS predictive abilities were comparable with those based on pedigree-based prediction. Marker-based PAs were generally 25–30% higher for traits density, MFA and MOE measured with SilviScan than for their respective standing tree-based method which measured with Pilodyn and Hitman. Prediction accuracy (PC) of the standing tree-based methods were similar or even higher than increment core-based method. 78–95% of the maximal PAs of density, MFA and MOE obtained from coring to the pith at high age were reached by using data possible to obtain by drilling 3–5 rings towards the pith at tree age 10–12. Conclusions This study indicates standing tree-based measurements is a cost-effective alternative method for GS. PA of GS methods were comparable with those pedigree-based prediction. The highest PAs were reached with at least 80–90% of the dataset used as training set. Selection for trait density could be conducted at an earlier age than for MFA and MOE. Operational breeding can also be optimized by training the model at an earlier age or using 3 to 5 outermost rings at tree age 10 to 12 years, thereby shortening the cycle and reducing the impact on the tree.

@article{wang_hybrid_2020,
	title = {Hybrid {Aspen} {Expressing} a {Carbohydrate} {Esterase} {Family} 5 {Acetyl} {Xylan} {Esterase} {Under} {Control} of a {Wood}-{Specific} {Promoter} {Shows} {Improved} {Saccharification}},
	volume = {11},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2020.00380/full},
	doi = {10.3389/fpls.2020.00380},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Wang, Zhao and Pawar, Prashant Mohan-Anupama and Derba-Maceluch, Marta and Hedenström, Mattias and Chong, Sun-Li and Tenkanen, Maija and Jönsson, Leif J. and Mellerowicz, Ewa J.},
	month = apr,
	year = {2020},
	pages = {380},
}

@article{elfstrand_association_2020,
	title = {Association genetics identifies a specifically regulated {Norway} spruce laccase gene, {\textless}span style="font-variant:small-caps;"{\textgreater} \textit{{PaLAC5}} {\textless}/span{\textgreater} , linked to \textit{{Heterobasidion} parviporum} resistance},
	volume = {43},
	issn = {0140-7791, 1365-3040},
	shorttitle = {Association genetics identifies a specifically regulated {Norway} spruce laccase gene, {\textless}span style="font-variant},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.13768},
	doi = {10.1111/pce.13768},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {Plant, Cell \& Environment},
	author = {Elfstrand, Malin and Baison, John and Lundén, Karl and Zhou, Linghua and Vos, Ingrid and Capador, Hernan Dario and Åslund, Matilda Stein and Chen, Zhiqiang and Chaudhary, Rajiv and Olson, Åke and Wu, Harry X. and Karlsson, Bo and Stenlid, Jan and García‐Gil, María Rosario},
	month = jul,
	year = {2020},
	pages = {1779--1791},
}

@article{aryal_interplay_2020,
	title = {Interplay between {Cell} {Wall} and {Auxin} {Mediates} the {Control} of {Differential} {Cell} {Elongation} during {Apical} {Hook} {Development}},
	volume = {30},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982220302621},
	doi = {10.1016/j.cub.2020.02.055},
	language = {en},
	number = {9},
	urldate = {2021-06-07},
	journal = {Current Biology},
	author = {Aryal, Bibek and Jonsson, Kristoffer and Baral, Anirban and Sancho-Andres, Gloria and Routier- Kierzkowska, Anne-Lise and Kierzkowski, Daniel and Bhalerao, Rishikesh P.},
	month = may,
	year = {2020},
	pages = {1733--1739.e3},
}

@article{blaschek_cellular_2020,
	title = {Cellular and {Genetic} {Regulation} of {Coniferaldehyde} {Incorporation} in {Lignin} of {Herbaceous} and {Woody} {Plants} by {Quantitative} {Wiesner} {Staining}},
	volume = {11},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2020.00109/full},
	doi = {10.3389/fpls.2020.00109},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Blaschek, Leonard and Champagne, Antoine and Dimotakis, Charilaos and {Nuoendagula} and Decou, Raphaël and Hishiyama, Shojiro and Kratzer, Susanne and Kajita, Shinya and Pesquet, Edouard},
	month = mar,
	year = {2020},
	pages = {109},
}

@article{kemppainen_fluorescent_2020,
	title = {Fluorescent protein expression in the ectomycorrhizal fungus {Laccaria} bicolor: a plasmid toolkit for easy use of fluorescent markers in basidiomycetes},
	volume = {66},
	issn = {0172-8083, 1432-0983},
	shorttitle = {Fluorescent protein expression in the ectomycorrhizal fungus {Laccaria} bicolor},
	url = {http://link.springer.com/10.1007/s00294-020-01060-4},
	doi = {10.1007/s00294-020-01060-4},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Current Genetics},
	author = {Kemppainen, Minna and Chowdhury, Jamil and Lundberg-Felten, Judith and Pardo, Alejandro},
	month = aug,
	year = {2020},
	pages = {791--811},
}

@article{sandstrom_policy_2020,
	title = {Policy goals and instruments for achieving a desirable future forest: {Experiences} from backcasting with stakeholders in {Sweden}},
	volume = {111},
	issn = {13899341},
	shorttitle = {Policy goals and instruments for achieving a desirable future forest},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1389934119300012},
	doi = {10.1016/j.forpol.2019.102051},
	language = {en},
	urldate = {2021-06-07},
	journal = {Forest Policy and Economics},
	author = {Sandström, Camilla and Kanyama, Annika Carlsson and Räty, Riitta and Sonnek, Karin Mossberg and Nordström, Eva-Maria and Mossing, Annika and Nordin, Annika},
	month = feb,
	year = {2020},
	pages = {102051},
}

@article{fundova_genetic_2020,
	title = {Genetic {Improvement} of {Sawn}-{Board} {Stiffness} and {Strength} in {Scots} {Pine} ({Pinus} sylvestris {L}.)},
	volume = {20},
	issn = {1424-8220},
	url = {https://www.mdpi.com/1424-8220/20/4/1129},
	doi = {10.3390/s20041129},
	abstract = {Given an overall aim of improving Scots pine structural wood quality by selective tree breeding, we investigated the potential of non-destructive acoustic sensing tools to accurately predict wood stiffness (modulus of elasticity, MOE) and strength (modulus of rupture, MOR) of sawn boards. Non-destructive measurements of wood density (DEN), acoustic velocity (VEL) and MOE were carried out at different stages of wood processing chain (standing trees, felled logs and sawn boards), whilst destructively measured stiffness and strength served as benchmark traits. All acoustic based MOE and VEL estimates proved to be good proxies (rA {\textgreater} 0.65) for sawn-board stiffness while MOETREE, VELHIT and resistograph wood density (DENRES) measured on standing trees and MOELOG and VELFAK measured on felled logs well reflected board strength. Individual-tree narrow-sense heritability (     h i 2     ) for VEL, MOE and MOR were weak (0.05–0.26) but were substantially stronger for wood density (0.34–0.40). Moreover, additive genetic coefficients of variation for MOE and MOR were in the range from 5.4\% to 9.1\%, offering potential targets for exploitation by selective breeding. Consequently, selective breeding based on MOETREE, DENRES or stem straightness (STR) could improve several structural wood traits simultaneously.},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Sensors},
	author = {Fundova, Irena and Hallingbäck, Henrik R. and Jansson, Gunnar and Wu, Harry X.},
	month = feb,
	year = {2020},
	pages = {1129},
}

Given an overall aim of improving Scots pine structural wood quality by selective tree breeding, we investigated the potential of non-destructive acoustic sensing tools to accurately predict wood stiffness (modulus of elasticity, MOE) and strength (modulus of rupture, MOR) of sawn boards. Non-destructive measurements of wood density (DEN), acoustic velocity (VEL) and MOE were carried out at different stages of wood processing chain (standing trees, felled logs and sawn boards), whilst destructively measured stiffness and strength served as benchmark traits. All acoustic based MOE and VEL estimates proved to be good proxies (rA \textgreater 0.65) for sawn-board stiffness while MOETREE, VELHIT and resistograph wood density (DENRES) measured on standing trees and MOELOG and VELFAK measured on felled logs well reflected board strength. Individual-tree narrow-sense heritability ( h i 2 ) for VEL, MOE and MOR were weak (0.05–0.26) but were substantially stronger for wood density (0.34–0.40). Moreover, additive genetic coefficients of variation for MOE and MOR were in the range from 5.4% to 9.1%, offering potential targets for exploitation by selective breeding. Consequently, selective breeding based on MOETREE, DENRES or stem straightness (STR) could improve several structural wood traits simultaneously.

@article{leng_organismal_2020,
	title = {Organismal benefits of transcription speed control at gene boundaries},
	volume = {21},
	issn = {1469-221X, 1469-3178},
	url = {https://onlinelibrary.wiley.com/doi/10.15252/embr.201949315},
	doi = {10.15252/embr.201949315},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {EMBO reports},
	author = {Leng, Xueyuan and Ivanov, Maxim and Kindgren, Peter and Malik, Indranil and Thieffry, Axel and Brodersen, Peter and Sandelin, Albin and Kaplan, Craig D and Marquardt, Sebastian},
	month = apr,
	year = {2020},
}

@article{nzayisenga_effects_2020,
	title = {Effects of light intensity on growth and lipid production in microalgae grown in wastewater},
	volume = {13},
	issn = {1754-6834},
	url = {https://biotechnologyforbiofuels.biomedcentral.com/articles/10.1186/s13068-019-1646-x},
	doi = {10.1186/s13068-019-1646-x},
	abstract = {Abstract
            
              Background
              
                Cultivation of microalgae in wastewater could significantly contribute to wastewater treatment, biodiesel production, and thus the transition to renewable energy. However, more information on effects of environmental factors, including light intensity, on their growth and composition (particularly fatty acid contents) is required. Therefore, we investigated the biomass and fatty acid production of four microalgal species, isolated in the Northern hemisphere and grown at three light intensities (50, 150 and 300 μE m
                −2
                s
                −1
                ).
              
            
            
              Results
              
                Increases in light intensities resulted in higher biomass of all four species and, importantly, raised fatty acid contents of both
                Desmodesmus
                sp. and
                Scenedesmus obliquus
                . Fourier-transform IR spectrometry analysis showed that the increases in fatty acid content were associated with reductions in protein, but not carbohydrate, contents. Assessment of fatty acid composition revealed that increasing light intensity led to higher and lower contents of oleic (18:1) and linolenic (18:3) acids, respectively. The microalgae consumed more than 75\% of the nitrogen and phosphorus present in the wastewater used as growth medium.
              
            
            
              Conclusion
              The results show the importance of optimizing light intensities to improve fatty acid production by microalgae and their quality as sources of biodiesel. In addition, increase in fatty acid content is associated with decrease in protein content.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Biotechnology for Biofuels},
	author = {Nzayisenga, Jean Claude and Farge, Xavier and Groll, Sophia Leticia and Sellstedt, Anita},
	month = dec,
	year = {2020},
	pages = {4},
}

Abstract Background Cultivation of microalgae in wastewater could significantly contribute to wastewater treatment, biodiesel production, and thus the transition to renewable energy. However, more information on effects of environmental factors, including light intensity, on their growth and composition (particularly fatty acid contents) is required. Therefore, we investigated the biomass and fatty acid production of four microalgal species, isolated in the Northern hemisphere and grown at three light intensities (50, 150 and 300 μE m −2 s −1 ). Results Increases in light intensities resulted in higher biomass of all four species and, importantly, raised fatty acid contents of both Desmodesmus sp. and Scenedesmus obliquus . Fourier-transform IR spectrometry analysis showed that the increases in fatty acid content were associated with reductions in protein, but not carbohydrate, contents. Assessment of fatty acid composition revealed that increasing light intensity led to higher and lower contents of oleic (18:1) and linolenic (18:3) acids, respectively. The microalgae consumed more than 75% of the nitrogen and phosphorus present in the wastewater used as growth medium. Conclusion The results show the importance of optimizing light intensities to improve fatty acid production by microalgae and their quality as sources of biodiesel. In addition, increase in fatty acid content is associated with decrease in protein content.

@article{crawford_specific_2020,
	title = {Specific functions for {Mediator} complex subunits from different modules in the transcriptional response of {Arabidopsis} thaliana to abiotic stress},
	volume = {10},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/s41598-020-61758-w},
	doi = {10.1038/s41598-020-61758-w},
	abstract = {Abstract
            
              Adverse environmental conditions are detrimental to plant growth and development. Acclimation to abiotic stress conditions involves activation of signaling pathways which often results in changes in gene expression via networks of transcription factors (TFs). Mediator is a highly conserved co-regulator complex and an essential component of the transcriptional machinery in eukaryotes. Some Mediator subunits have been implicated in stress-responsive signaling pathways; however, much remains unknown regarding the role of plant Mediator in abiotic stress responses. Here, we use RNA-seq to analyze the transcriptional response of
              Arabidopsis thaliana
              to heat, cold and salt stress conditions. We identify a set of common abiotic stress regulons and describe the sequential and combinatorial nature of TFs involved in their transcriptional regulation. Furthermore, we identify stress-specific roles for the Mediator subunits MED9, MED16, MED18 and CDK8, and putative TFs connecting them to different stress signaling pathways. Our data also indicate different modes of action for subunits or modules of Mediator at the same gene loci, including a co-repressor function for MED16 prior to stress. These results illuminate a poorly understood but important player in the transcriptional response of plants to abiotic stress and identify target genes and mechanisms as a prelude to further biochemical characterization.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	author = {Crawford, Tim and Karamat, Fazeelat and Lehotai, Nóra and Rentoft, Matilda and Blomberg, Jeanette and Strand, Åsa and Björklund, Stefan},
	month = dec,
	year = {2020},
	pages = {5073},
}

Abstract Adverse environmental conditions are detrimental to plant growth and development. Acclimation to abiotic stress conditions involves activation of signaling pathways which often results in changes in gene expression via networks of transcription factors (TFs). Mediator is a highly conserved co-regulator complex and an essential component of the transcriptional machinery in eukaryotes. Some Mediator subunits have been implicated in stress-responsive signaling pathways; however, much remains unknown regarding the role of plant Mediator in abiotic stress responses. Here, we use RNA-seq to analyze the transcriptional response of Arabidopsis thaliana to heat, cold and salt stress conditions. We identify a set of common abiotic stress regulons and describe the sequential and combinatorial nature of TFs involved in their transcriptional regulation. Furthermore, we identify stress-specific roles for the Mediator subunits MED9, MED16, MED18 and CDK8, and putative TFs connecting them to different stress signaling pathways. Our data also indicate different modes of action for subunits or modules of Mediator at the same gene loci, including a co-repressor function for MED16 prior to stress. These results illuminate a poorly understood but important player in the transcriptional response of plants to abiotic stress and identify target genes and mechanisms as a prelude to further biochemical characterization.

@article{funda_predicting_2020,
	title = {Predicting the chemical composition of juvenile and mature woods in {Scots} pine ({Pinus} sylvestris {L}.) using {FTIR} spectroscopy},
	volume = {54},
	issn = {0043-7719, 1432-5225},
	url = {http://link.springer.com/10.1007/s00226-020-01159-4},
	doi = {10.1007/s00226-020-01159-4},
	abstract = {Abstract
            
              The chemical composition of wood is one of the key features that determine wood quality. The focus of this study was on identifying differences between juvenile and mature woods in Scots pine (
              Pinus sylvestris
              L.) and developing models for predicting the chemical composition of these two wood types. Chemical traits, determined by traditional wet chemistry techniques, included the proportion of lignin, polysaccharides and extractives. Partial least squares regression of Fourier transform infrared (FTIR) spectra was used for model building. The model performance was primarily evaluated by root mean squared error of predictions (RMSEP). High predictive power was attained for the content of lignin (RMSEP of 0.476 and 0.495 for juvenile and mature woods, respectively) and extractives (0.302 and 0.471), good predictive power for cellulose (0.715 and 0.696) and hemicelluloses in juvenile wood (0.719) and low predictive power for hemicelluloses in mature wood (0.823). A distinct band was observed at 1693 cm
              −1
              , and its intensity was strongly associated with the content of extractives (
              r
               = 0.968 and 0.861 in juvenile and mature woods, respectively). FTIR has proved suitable for the rapid, non-destructive, cost-efficient assessment of the chemical composition of juvenile and mature woods in Scots pine. The band at 1693 cm
              −1
              is to be further investigated to unravel its link with individual extractive components.},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Wood Science and Technology},
	author = {Funda, Tomas and Fundova, Irena and Gorzsás, András and Fries, Anders and Wu, Harry X.},
	month = mar,
	year = {2020},
	pages = {289--311},
}

Abstract The chemical composition of wood is one of the key features that determine wood quality. The focus of this study was on identifying differences between juvenile and mature woods in Scots pine ( Pinus sylvestris L.) and developing models for predicting the chemical composition of these two wood types. Chemical traits, determined by traditional wet chemistry techniques, included the proportion of lignin, polysaccharides and extractives. Partial least squares regression of Fourier transform infrared (FTIR) spectra was used for model building. The model performance was primarily evaluated by root mean squared error of predictions (RMSEP). High predictive power was attained for the content of lignin (RMSEP of 0.476 and 0.495 for juvenile and mature woods, respectively) and extractives (0.302 and 0.471), good predictive power for cellulose (0.715 and 0.696) and hemicelluloses in juvenile wood (0.719) and low predictive power for hemicelluloses in mature wood (0.823). A distinct band was observed at 1693 cm −1 , and its intensity was strongly associated with the content of extractives ( r  = 0.968 and 0.861 in juvenile and mature woods, respectively). FTIR has proved suitable for the rapid, non-destructive, cost-efficient assessment of the chemical composition of juvenile and mature woods in Scots pine. The band at 1693 cm −1 is to be further investigated to unravel its link with individual extractive components.

@article{chen_advantage_2020,
	title = {Advantage of clonal deployment in {Norway} spruce ({Picea} abies ({L}.) {H}. {Karst})},
	volume = {77},
	issn = {1286-4560, 1297-966X},
	url = {http://link.springer.com/10.1007/s13595-020-0920-1},
	doi = {10.1007/s13595-020-0920-1},
	abstract = {Abstract
            
              
                
                  Key message
                
              
              
                There is considerable genetic gain of tree volume from clonal deployment in Norway spruce (
                
                  Picea abies
                
                (L.) H. Karst) and clonal deployment will have at least 50\% more or double genetic gain than the seedling deployment.
              
            
            
              
                
                  Context
                
              
              Genetic parameters and genetic gains for wood quality and growth traits were estimated in six large clonal progeny trials.
            
            
              
                
                  Aims
                
              
              Develop the optimal clonal deployment strategy of Norway spruce in Sweden.
            
            
              
                
                  Methods
                
              
              Wood quality and growth traits were measured in all clonal trials and additive and non-additive genetic variances are partitioned.
            
            
              
                
                  Results
                
              
              Additive and non-additive genetic variances were equally important for growth traits while non-additive variance was small or not significant for wood quality trait. The genetic gain predicted for clonal deployment was greater than any of the other four deployment strategies. Selecting the top 1\% of tested clones (clonal forestry) would have 48.4\% and 134.6\% more gain than the gain predicted for the seedling deployment of selected full-sib families and half-sib family (family forestry), respectively, at the same selection intensity.
            
            
              
                
                  Conclusion
                
              
              This study highlights that testing of 30–40 clones per family would maximize the realized genetic gain for different clonal selection scenarios, either selecting the best ten or 20 clones without any co-ancestry restrictions or selecting the best single clone from each of the best ten or 20 families (e.g., co-ancestry restriction). Clonal mean selection and vegetative deployment are the most effective.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Annals of Forest Science},
	author = {Chen, Zhi-Qiang and Hai, Hong Nguyen Thi and Helmersson, Andreas and Liziniewicz, Mateusz and Hallingbäck, Henrik R. and Fries, Anders and Berlin, Mats and Wu, Harry X.},
	month = mar,
	year = {2020},
	pages = {14},
}

Abstract Key message There is considerable genetic gain of tree volume from clonal deployment in Norway spruce ( Picea abies (L.) H. Karst) and clonal deployment will have at least 50% more or double genetic gain than the seedling deployment. Context Genetic parameters and genetic gains for wood quality and growth traits were estimated in six large clonal progeny trials. Aims Develop the optimal clonal deployment strategy of Norway spruce in Sweden. Methods Wood quality and growth traits were measured in all clonal trials and additive and non-additive genetic variances are partitioned. Results Additive and non-additive genetic variances were equally important for growth traits while non-additive variance was small or not significant for wood quality trait. The genetic gain predicted for clonal deployment was greater than any of the other four deployment strategies. Selecting the top 1% of tested clones (clonal forestry) would have 48.4% and 134.6% more gain than the gain predicted for the seedling deployment of selected full-sib families and half-sib family (family forestry), respectively, at the same selection intensity. Conclusion This study highlights that testing of 30–40 clones per family would maximize the realized genetic gain for different clonal selection scenarios, either selecting the best ten or 20 clones without any co-ancestry restrictions or selecting the best single clone from each of the best ten or 20 families (e.g., co-ancestry restriction). Clonal mean selection and vegetative deployment are the most effective.

@article{blasko_impacts_2020,
	title = {Impacts of tree species identity and species mixing on ecosystem carbon and nitrogen stocks in a boreal forest},
	volume = {458},
	issn = {03781127},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0378112719319607},
	doi = {10.1016/j.foreco.2019.117783},
	language = {en},
	urldate = {2021-06-07},
	journal = {Forest Ecology and Management},
	author = {Blaško, Róbert and Forsmark, Benjamin and Gundale, Michael J. and Lundmark, Tomas and Nordin, Annika},
	month = feb,
	year = {2020},
	pages = {117783},
}

@article{boussardon_tissuespecific_2020,
	title = {Tissue‐specific isolation of {Arabidopsis}/plant mitochondria – {IMTACT} (isolation of mitochondria tagged in specific cell types)},
	volume = {103},
	issn = {0960-7412, 1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.14723},
	doi = {10.1111/tpj.14723},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {The Plant Journal},
	author = {Boussardon, Clément and Przybyla‐Toscano, Jonathan and Carrie, Chris and Keech, Olivier},
	month = jul,
	year = {2020},
	pages = {459--473},
}

@article{vayssieres_vernalization_2020,
	title = {Vernalization shapes shoot architecture and ensures the maintenance of dormant buds in the perennial \textit{{Arabis} alpina}},
	volume = {227},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.16470},
	doi = {10.1111/nph.16470},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Vayssières, Alice and Mishra, Priyanka and Roggen, Adrian and Neumann, Ulla and Ljung, Karin and Albani, Maria C.},
	month = jul,
	year = {2020},
	pages = {99--115},
}

@article{kushwah_arabidopsis_2020,
	title = {Arabidopsis \textit{{XTH4}} and \textit{{XTH9}} {Contribute} to {Wood} {Cell} {Expansion} and {Secondary} {Wall} {Formation}},
	volume = {182},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/182/4/1946-1965/6116228},
	doi = {10.1104/pp.19.01529},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Kushwah, Sunita and Banasiak, Alicja and Nishikubo, Nobuyuki and Derba-Maceluch, Marta and Majda, Mateusz and Endo, Satoshi and Kumar, Vikash and Gomez, Leonardo and Gorzsas, Andras and McQueen-Mason, Simon and Braam, Janet and Sundberg, Björn and Mellerowicz, Ewa J.},
	month = apr,
	year = {2020},
	pages = {1946--1965},
}

@article{brunoni_conifers_2020,
	title = {Conifers exhibit a characteristic inactivation of auxin to maintain tissue homeostasis},
	volume = {226},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.16463},
	doi = {10.1111/nph.16463},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Brunoni, Federica and Collani, Silvio and Casanova‐Sáez, Rubén and Šimura, Jan and Karady, Michal and Schmid, Markus and Ljung, Karin and Bellini, Catherine},
	month = jun,
	year = {2020},
	pages = {1753--1765},
}

@article{mishra_natural_2020,
	title = {Natural {Variation} in {Adventitious} {Rooting} in the {Alpine} {Perennial} {Arabis} alpina},
	volume = {9},
	issn = {2223-7747},
	url = {https://www.mdpi.com/2223-7747/9/2/184},
	doi = {10.3390/plants9020184},
	abstract = {Arctic alpine species follow a mixed clonal-sexual reproductive strategy based on the environmental conditions at flowering. Here, we explored the natural variation for adventitious root formation among genotypes of the alpine perennial Arabis alpina that show differences in flowering habit. We scored the presence of adventitious roots on the hypocotyl, main stem and axillary branches on plants growing in a long-day greenhouse. We also assessed natural variation for adventitious rooting in response to foliar auxin spray. In both experimental approaches, we did not detect a correlation between adventitious rooting and flowering habit. In the greenhouse, and without the application of synthetic auxin, the accession Wca showed higher propensity to produce adventitious roots on the main stem compared to the other accessions. The transcript accumulation of the A. alpina homologue of the auxin inducible GH3.3 gene (AaGH3.3) on stems correlated with the adventitious rooting phenotype of Wca. Synthetic auxin, 1-Naphthaleneacetic acid (1-NAA), enhanced the number of plants with adventitious roots on the main stem and axillary branches. A. alpina plants showed an age-, dosage- and genotype-dependent response to 1-NAA. Among the genotypes tested, the accession Dor was insensitive to auxin and Wca responded to auxin on axillary branches.},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Plants},
	author = {Mishra, Priyanka and Roggen, Adrian and Ljung, Karin and Albani, Maria C.},
	month = feb,
	year = {2020},
	pages = {184},
}

Arctic alpine species follow a mixed clonal-sexual reproductive strategy based on the environmental conditions at flowering. Here, we explored the natural variation for adventitious root formation among genotypes of the alpine perennial Arabis alpina that show differences in flowering habit. We scored the presence of adventitious roots on the hypocotyl, main stem and axillary branches on plants growing in a long-day greenhouse. We also assessed natural variation for adventitious rooting in response to foliar auxin spray. In both experimental approaches, we did not detect a correlation between adventitious rooting and flowering habit. In the greenhouse, and without the application of synthetic auxin, the accession Wca showed higher propensity to produce adventitious roots on the main stem compared to the other accessions. The transcript accumulation of the A. alpina homologue of the auxin inducible GH3.3 gene (AaGH3.3) on stems correlated with the adventitious rooting phenotype of Wca. Synthetic auxin, 1-Naphthaleneacetic acid (1-NAA), enhanced the number of plants with adventitious roots on the main stem and axillary branches. A. alpina plants showed an age-, dosage- and genotype-dependent response to 1-NAA. Among the genotypes tested, the accession Dor was insensitive to auxin and Wca responded to auxin on axillary branches.

@article{alonso-serra_elimaki_2020,
	title = {{ELIMÄKI} {Locus} {Is} {Required} for {Vertical} {Proprioceptive} {Response} in {Birch} {Trees}},
	volume = {30},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982219316112},
	doi = {10.1016/j.cub.2019.12.016},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Current Biology},
	author = {Alonso-Serra, Juan and Shi, Xueping and Peaucelle, Alexis and Rastas, Pasi and Bourdon, Matthieu and Immanen, Juha and Takahashi, Junko and Koivula, Hanna and Eswaran, Gugan and Muranen, Sampo and Help, Hanna and Smolander, Olli-Pekka and Su, Chang and Safronov, Omid and Gerber, Lorenz and Salojärvi, Jarkko and Hagqvist, Risto and Mähönen, Ari Pekka and Helariutta, Ykä and Nieminen, Kaisa},
	month = feb,
	year = {2020},
	pages = {589--599.e5},
}

@article{kumar_genome-wide_2020,
	title = {Genome-{Wide} {Identification} of {Populus} {Malectin}/{Malectin}-{Like} {Domain}-{Containing} {Proteins} and {Expression} {Analyses} {Reveal} {Novel} {Candidates} for {Signaling} and {Regulation} of {Wood} {Development}},
	volume = {11},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2020.588846/full},
	doi = {10/gjcxjw},
	abstract = {Malectin domain (MD) is a ligand-binding protein motif of pro- and eukaryotes. It is particularly abundant in Viridiplantae, where it occurs as either a single (MD, PF11721) or tandemly duplicated domain (PF12819) called malectin-like domain (MLD). In herbaceous plants, MD- or MLD-containing proteins (MD proteins) are known to regulate development, reproduction, and resistance to various stresses. However, their functions in woody plants have not yet been studied. To unravel their potential role in wood development, we carried out genome-wide identification of MD proteins in the model tree species black cottonwood (
              Populus trichocarpa
              ), and analyzed their expression and co-expression networks.
              P. trichocarpa
              had 146
              MD
              genes assigned to 14 different clades, two of which were specific to the genus
              Populus
              . 87\% of these genes were located on chromosomes, the rest being associated with scaffolds. Based on their protein domain organization, and in agreement with the exon-intron structures, the
              MD
              genes identified here could be classified into five superclades having the following domains: leucine-rich repeat (LRR)-MD-protein kinase (PK), MLD-LRR-PK, MLD-PK (
              Cr
              RLK1L), MLD-LRR, and MD-Kinesin. Whereas the majority of
              MD
              genes were highly expressed in leaves, particularly under stress conditions, eighteen showed a peak of expression during secondary wall formation in the xylem and their co-expression networks suggested signaling functions in cell wall integrity, pathogen-associated molecular patterns, calcium, ROS, and hormone pathways. Thus,
              P. trichocarpa MD
              genes having different domain organizations comprise many genes with putative foliar defense functions, some of which could be specific to
              Populus
              and related species, as well as genes with potential involvement in signaling pathways in other tissues including developing wood.},
	urldate = {2021-06-03},
	journal = {Frontiers in Plant Science},
	author = {Kumar, Vikash and Donev, Evgeniy N. and Barbut, Félix R. and Kushwah, Sunita and Mannapperuma, Chanaka and Urbancsok, János and Mellerowicz, Ewa J.},
	month = dec,
	year = {2020},
	pages = {588846},
}

Malectin domain (MD) is a ligand-binding protein motif of pro- and eukaryotes. It is particularly abundant in Viridiplantae, where it occurs as either a single (MD, PF11721) or tandemly duplicated domain (PF12819) called malectin-like domain (MLD). In herbaceous plants, MD- or MLD-containing proteins (MD proteins) are known to regulate development, reproduction, and resistance to various stresses. However, their functions in woody plants have not yet been studied. To unravel their potential role in wood development, we carried out genome-wide identification of MD proteins in the model tree species black cottonwood ( Populus trichocarpa ), and analyzed their expression and co-expression networks. P. trichocarpa had 146 MD genes assigned to 14 different clades, two of which were specific to the genus Populus . 87% of these genes were located on chromosomes, the rest being associated with scaffolds. Based on their protein domain organization, and in agreement with the exon-intron structures, the MD genes identified here could be classified into five superclades having the following domains: leucine-rich repeat (LRR)-MD-protein kinase (PK), MLD-LRR-PK, MLD-PK ( Cr RLK1L), MLD-LRR, and MD-Kinesin. Whereas the majority of MD genes were highly expressed in leaves, particularly under stress conditions, eighteen showed a peak of expression during secondary wall formation in the xylem and their co-expression networks suggested signaling functions in cell wall integrity, pathogen-associated molecular patterns, calcium, ROS, and hormone pathways. Thus, P. trichocarpa MD genes having different domain organizations comprise many genes with putative foliar defense functions, some of which could be specific to Populus and related species, as well as genes with potential involvement in signaling pathways in other tissues including developing wood.