Street, Nathaniel - A Systems Genetics Approach to Understanding Natural Variation

@article{sandell_genomic_2024,
	title = {Genomic basis of seed colour in quinoa inferred from variant patterns using extreme gradient boosting},
	volume = {22},
	copyright = {© 2023 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley \& Sons Ltd.},
	issn = {1467-7652},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pbi.14267},
	doi = {10.1111/pbi.14267},
	abstract = {Quinoa is an agriculturally important crop species originally domesticated in the Andes of central South America. One of its most important phenotypic traits is seed colour. Seed colour variation is determined by contrasting abundance of betalains, a class of strong antioxidant and free radicals scavenging colour pigments only found in plants of the order Caryophyllales. However, the genetic basis for these pigments in seeds remains to be identified. Here we demonstrate the application of machine learning (extreme gradient boosting) to identify genetic variants predictive of seed colour. We show that extreme gradient boosting outperforms the classical genome-wide association approach. We provide re-sequencing and phenotypic data for 156 South American quinoa accessions and identify candidate genes potentially controlling betalain content in quinoa seeds. Genes identified include novel cytochrome P450 genes and known members of the betalain synthesis pathway, as well as genes annotated as being involved in seed development. Our work showcases the power of modern machine learning methods to extract biologically meaningful information from large sequencing data sets.},
	language = {en},
	number = {5},
	urldate = {2024-04-19},
	journal = {Plant Biotechnology Journal},
	author = {Sandell, Felix L. and Holzweber, Thomas and Street, Nathaniel R. and Dohm, Juliane C. and Himmelbauer, Heinz},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pbi.14267},
	keywords = {betalain synthesis pathway, genome sequencing, genotype-phenotype relationships, machine learning, quinoa, seed colour},
	pages = {1312--1324},
}

Quinoa is an agriculturally important crop species originally domesticated in the Andes of central South America. One of its most important phenotypic traits is seed colour. Seed colour variation is determined by contrasting abundance of betalains, a class of strong antioxidant and free radicals scavenging colour pigments only found in plants of the order Caryophyllales. However, the genetic basis for these pigments in seeds remains to be identified. Here we demonstrate the application of machine learning (extreme gradient boosting) to identify genetic variants predictive of seed colour. We show that extreme gradient boosting outperforms the classical genome-wide association approach. We provide re-sequencing and phenotypic data for 156 South American quinoa accessions and identify candidate genes potentially controlling betalain content in quinoa seeds. Genes identified include novel cytochrome P450 genes and known members of the betalain synthesis pathway, as well as genes annotated as being involved in seed development. Our work showcases the power of modern machine learning methods to extract biologically meaningful information from large sequencing data sets.

@article{yang_genomic_2024,
	title = {Genomic basis of the distinct biosynthesis of β-glucogallin, a biochemical marker for hydrolyzable tannin production, in three oak species},
	copyright = {© 2024 The Authors. New Phytologist © 2024 New Phytologist Foundation},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.19711},
	doi = {10.1111/nph.19711},
	abstract = {Hydrolyzable tannins (HTs), predominant polyphenols in oaks, are widely used in grape wine aging, feed additives, and human healthcare. However, the limited availability of a high-quality reference genome of oaks greatly hampered the recognition of the mechanism of HT biosynthesis. Here, high-quality reference genomes of three Asian oak species (Quercus variabilis, Quercus aliena, and Quercus dentata) that have different HT contents were generated. Multi-omics studies were carried out to identify key genes regulating HT biosynthesis. In vitro enzyme activity assay was also conducted. Dual-luciferase and yeast one-hybrid assays were used to reveal the transcriptional regulation. Our results revealed that β-glucogallin was a biochemical marker for HT production in the cupules of the three Asian oaks. UGT84A13 was confirmed as the key enzyme for β-glucogallin biosynthesis. The differential expression of UGT84A13, rather than enzyme activity, was the main reason for different β-glucogallin and HT accumulation. Notably, sequence variations in UGT84A13 promoters led to different trans-activating activities of WRKY32/59, explaining the different expression patterns of UGT84A13 among the three species. Our findings provide three high-quality new reference genomes for oak trees and give new insights into different transcriptional regulation for understanding β-glucogallin and HT biosynthesis in closely related oak species.},
	language = {en},
	urldate = {2024-04-02},
	journal = {New Phytologist},
	author = {Yang, Qinsong and Li, Jinjin and Wang, Yan and Wang, Zefu and Pei, Ziqi and Street, Nathaniel R. and Bhalerao, Rishikesh P. and Yu, Zhaowei and Gao, Yuhao and Ni, Junbei and Jiao, Yang and Sun, Minghui and Yang, Xiong and Chen, Yixin and Liu, Puyuan and Wang, Jiaxi and Liu, Yong and Li, Guolei},
	month = mar,
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.19711},
	keywords = {UGT84A13, hydrolyzable tannin, oak, whole-genome sequencing, β-glucogallin},
}

Hydrolyzable tannins (HTs), predominant polyphenols in oaks, are widely used in grape wine aging, feed additives, and human healthcare. However, the limited availability of a high-quality reference genome of oaks greatly hampered the recognition of the mechanism of HT biosynthesis. Here, high-quality reference genomes of three Asian oak species (Quercus variabilis, Quercus aliena, and Quercus dentata) that have different HT contents were generated. Multi-omics studies were carried out to identify key genes regulating HT biosynthesis. In vitro enzyme activity assay was also conducted. Dual-luciferase and yeast one-hybrid assays were used to reveal the transcriptional regulation. Our results revealed that β-glucogallin was a biochemical marker for HT production in the cupules of the three Asian oaks. UGT84A13 was confirmed as the key enzyme for β-glucogallin biosynthesis. The differential expression of UGT84A13, rather than enzyme activity, was the main reason for different β-glucogallin and HT accumulation. Notably, sequence variations in UGT84A13 promoters led to different trans-activating activities of WRKY32/59, explaining the different expression patterns of UGT84A13 among the three species. Our findings provide three high-quality new reference genomes for oak trees and give new insights into different transcriptional regulation for understanding β-glucogallin and HT biosynthesis in closely related oak species.

@article{shi_high-quality_2024,
	title = {High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiae078},
	doi = {10.1093/plphys/kiae078},
	abstract = {Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio High-Fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the two parents of the well-studied F1 hybrid “84K” (Populus alba × P. tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from two small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the two subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77\% accuracy on the training set and 74\% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.},
	urldate = {2024-03-01},
	journal = {Plant Physiology},
	author = {Shi, Tian-Le and Jia, Kai-Hua and Bao, Yu-Tao and Nie, Shuai and Tian, Xue-Chan and Yan, Xue-Mei and Chen, Zhao-Yang and Li, Zhi-Chao and Zhao, Shi-Wei and Ma, Hai-Yao and Zhao, Ye and Li, Xiang and Zhang, Ren-Gang and Guo, Jing and Zhao, Wei and El-Kassaby, Yousry Aly and Müller, Niels and Van de Peer, Yves and Wang, Xiao-Ru and Street, Nathaniel Robert and Porth, Ilga and An, Xinmin and Mao, Jian-Feng},
	month = feb,
	year = {2024},
	pages = {kiae078},
}

Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio High-Fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the two parents of the well-studied F1 hybrid “84K” (Populus alba × P. tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from two small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the two subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77% accuracy on the training set and 74% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.

@article{shi_super-pangenome_2024,
	title = {The super-pangenome of \textit{{Populus}} unveil genomic facets for its adaptation and diversification in widespread forest trees},
	issn = {1674-2052},
	url = {https://www.sciencedirect.com/science/article/pii/S1674205224000820},
	doi = {10.1016/j.molp.2024.03.009},
	abstract = {Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies. Poplars, among the world’s most widely distributed and cultivated trees, exhibit extensive phenotypic diversity and environmental adaptability. In this study, we present a genus-level super-pangenome comprising 19 Populus genomes, revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation. Through the integration of pan-genomes with transcriptomes, methylomes and chromatin accessibility mapping, we unveil that the evolutionary trajectories of pan-genes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures, notably CG methylation in gene-body regions. Further comparative genomic analyses have enabled the identification of 142,202 structural variants (SVs) across species, which intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence. We have experimentally validated a ∼180 bp presence/absence variant impacting the expression of the CUC2 gene, crucial for leaf serration formation. Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome (http://www.populus-superpangenome.com/). Together, the present pioneering super-pangenome resource in forest trees not only aid in the advancement of breeding efforts of this globally important tree genus but also offer valuable insights into potential avenues for comprehending tree biology.},
	urldate = {2024-03-22},
	journal = {Molecular Plant},
	author = {Shi, Tingting and Zhang, Xinxin and Hou, Yukang and Jia, Changfu and Dan, Xuming and Zhang, Yulin and Jiang, Yuanzhong and Lai, Qiang and Feng, Jiajun and Feng, Jianju and Ma, Tao and Wu, Jiali and Liu, Shuyu and Zhang, Lei and Long, Zhiqin and Chen, Liyang and Street, Nathaniel R. and Ingvarsson, Pär K. and Liu, Jianquan and Yin, Tongming and Wang, Jing},
	month = mar,
	year = {2024},
	keywords = {genome evolution, pan-genomes, structural variation, whole genome duplication},
}

Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies. Poplars, among the world’s most widely distributed and cultivated trees, exhibit extensive phenotypic diversity and environmental adaptability. In this study, we present a genus-level super-pangenome comprising 19 Populus genomes, revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation. Through the integration of pan-genomes with transcriptomes, methylomes and chromatin accessibility mapping, we unveil that the evolutionary trajectories of pan-genes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures, notably CG methylation in gene-body regions. Further comparative genomic analyses have enabled the identification of 142,202 structural variants (SVs) across species, which intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence. We have experimentally validated a ∼180 bp presence/absence variant impacting the expression of the CUC2 gene, crucial for leaf serration formation. Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome (http://www.populus-superpangenome.com/). Together, the present pioneering super-pangenome resource in forest trees not only aid in the advancement of breeding efforts of this globally important tree genus but also offer valuable insights into potential avenues for comprehending tree biology.

@article{estravis_barcala_whole-genome_2024,
	title = {Whole-genome resequencing facilitates the development of a {50K} single nucleotide polymorphism genotyping array for {Scots} pine ({Pinus} sylvestris {L}.) and its transferability to other pine species},
	volume = {117},
	copyright = {© 2023 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley \& Sons Ltd.},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.16535},
	doi = {10.1111/tpj.16535},
	abstract = {Scots pine (Pinus sylvestris L.) is one of the most widespread and economically important conifer species in the world. Applications like genomic selection and association studies, which could help accelerate breeding cycles, are challenging in Scots pine because of its large and repetitive genome. For this reason, genotyping tools for conifer species, and in particular for Scots pine, are commonly based on transcribed regions of the genome. In this article, we present the Axiom Psyl50K array, the first single nucleotide polymorphism (SNP) genotyping array for Scots pine based on whole-genome resequencing, that represents both genic and intergenic regions. This array was designed following a two-step procedure: first, 192 trees were sequenced, and a 430K SNP screening array was constructed. Then, 480 samples, including haploid megagametophytes, full-sib family trios, breeding population, and range-wide individuals from across Eurasia were genotyped with the screening array. The best 50K SNPs were selected based on quality, replicability, distribution across the draft genome assembly, balance between genic and intergenic regions, and genotype–environment and genotype–phenotype associations. Of the final 49 877 probes tiled in the array, 20 372 (40.84\%) occur inside gene models, while the rest lie in intergenic regions. We also show that the Psyl50K array can yield enough high-confidence SNPs for genetic studies in pine species from North America and Eurasia. This new genotyping tool will be a valuable resource for high-throughput fundamental and applied research of Scots pine and other pine species.},
	language = {en},
	number = {3},
	urldate = {2024-02-02},
	journal = {The Plant Journal},
	author = {Estravis Barcala, Maximiliano and van der Valk, Tom and Chen, Zhiqiang and Funda, Tomas and Chaudhary, Rajiv and Klingberg, Adam and Fundova, Irena and Suontama, Mari and Hallingbäck, Henrik and Bernhardsson, Carolina and Nystedt, Björn and Ingvarsson, Pär K. and Sherwood, Ellen and Street, Nathaniel and Gyllensten, Ulf and Nilsson, Ove and Wu, Harry X.},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.16535},
	keywords = {Pinus sylvestris, SNP array, genome resequencing, genome-wide association studies, genomic selection, pines},
	pages = {944--955},
}

Scots pine (Pinus sylvestris L.) is one of the most widespread and economically important conifer species in the world. Applications like genomic selection and association studies, which could help accelerate breeding cycles, are challenging in Scots pine because of its large and repetitive genome. For this reason, genotyping tools for conifer species, and in particular for Scots pine, are commonly based on transcribed regions of the genome. In this article, we present the Axiom Psyl50K array, the first single nucleotide polymorphism (SNP) genotyping array for Scots pine based on whole-genome resequencing, that represents both genic and intergenic regions. This array was designed following a two-step procedure: first, 192 trees were sequenced, and a 430K SNP screening array was constructed. Then, 480 samples, including haploid megagametophytes, full-sib family trios, breeding population, and range-wide individuals from across Eurasia were genotyped with the screening array. The best 50K SNPs were selected based on quality, replicability, distribution across the draft genome assembly, balance between genic and intergenic regions, and genotype–environment and genotype–phenotype associations. Of the final 49 877 probes tiled in the array, 20 372 (40.84%) occur inside gene models, while the rest lie in intergenic regions. We also show that the Psyl50K array can yield enough high-confidence SNPs for genetic studies in pine species from North America and Eurasia. This new genotyping tool will be a valuable resource for high-throughput fundamental and applied research of Scots pine and other pine species.

@article{urbancsok_flexure_2023,
	title = {Flexure wood formation via growth reprogramming in hybrid aspen involves jasmonates and polyamines and transcriptional changes resembling tension wood development},
	copyright = {New Phytologist© 2023 The Authors New Phytologist © 2023 New Phytologist Foundation},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.19307},
	doi = {10.1111/nph.19307},
	abstract = {Stem bending in trees induces flexure wood but its properties and development are poorly understood. Here, we investigated the effects of low-intensity multidirectional stem flexing on growth and wood properties of hybrid aspen, and on its transcriptomic and hormonal responses. Glasshouse-grown trees were either kept stationary or subjected to several daily shakes for 5 wk, after which the transcriptomes and hormones were analyzed in the cambial region and developing wood tissues, and the wood properties were analyzed by physical, chemical and microscopy techniques. Shaking increased primary and secondary growth and altered wood differentiation by stimulating gelatinous-fiber formation, reducing secondary wall thickness, changing matrix polysaccharides and increasing cellulose, G- and H-lignin contents, cell wall porosity and saccharification yields. Wood-forming tissues exhibited elevated jasmonate, polyamine, ethylene and brassinosteroids and reduced abscisic acid and gibberellin signaling. Transcriptional responses resembled those during tension wood formation but not opposite wood formation and revealed several thigmomorphogenesis-related genes as well as novel gene networks including FLA and XTH genes encoding plasma membrane-bound proteins. Low-intensity stem flexing stimulates growth and induces wood having improved biorefinery properties through molecular and hormonal pathways similar to thigmomorphogenesis in herbaceous plants and largely overlapping with the tension wood program of hardwoods.},
	language = {en},
	urldate = {2023-10-20},
	journal = {New Phytologist},
	author = {Urbancsok, János and Donev, Evgeniy N. and Sivan, Pramod and van Zalen, Elena and Barbut, Félix R. and Derba-Maceluch, Marta and Šimura, Jan and Yassin, Zakiya and Gandla, Madhavi L. and Karady, Michal and Ljung, Karin and Winestrand, Sandra and Jönsson, Leif J. and Scheepers, Gerhard and Delhomme, Nicolas and Street, Nathaniel R. and Mellerowicz, Ewa J.},
	month = oct,
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.19307},
	keywords = {Populus tremula × tremuloides, flexure wood, jasmonic acid signaling, mechanostimulation, polyamines, saccharification, thigmomorphogenesis, wood development},
}

Stem bending in trees induces flexure wood but its properties and development are poorly understood. Here, we investigated the effects of low-intensity multidirectional stem flexing on growth and wood properties of hybrid aspen, and on its transcriptomic and hormonal responses. Glasshouse-grown trees were either kept stationary or subjected to several daily shakes for 5 wk, after which the transcriptomes and hormones were analyzed in the cambial region and developing wood tissues, and the wood properties were analyzed by physical, chemical and microscopy techniques. Shaking increased primary and secondary growth and altered wood differentiation by stimulating gelatinous-fiber formation, reducing secondary wall thickness, changing matrix polysaccharides and increasing cellulose, G- and H-lignin contents, cell wall porosity and saccharification yields. Wood-forming tissues exhibited elevated jasmonate, polyamine, ethylene and brassinosteroids and reduced abscisic acid and gibberellin signaling. Transcriptional responses resembled those during tension wood formation but not opposite wood formation and revealed several thigmomorphogenesis-related genes as well as novel gene networks including FLA and XTH genes encoding plasma membrane-bound proteins. Low-intensity stem flexing stimulates growth and induces wood having improved biorefinery properties through molecular and hormonal pathways similar to thigmomorphogenesis in herbaceous plants and largely overlapping with the tension wood program of hardwoods.

@article{escamez_genetic_2023,
	title = {Genetic markers and tree properties predicting wood biorefining potential in aspen ({Populus} tremula) bioenergy feedstock},
	volume = {16},
	issn = {2731-3654},
	url = {https://doi.org/10.1186/s13068-023-02315-1},
	doi = {10.1186/s13068-023-02315-1},
	abstract = {Wood represents the majority of the biomass on land and constitutes a renewable source of biofuels and other bioproducts. However, wood is recalcitrant to bioconversion, raising a need for feedstock improvement in production of, for instance, biofuels. We investigated the properties of wood that affect bioconversion, as well as the underlying genetics, to help identify superior tree feedstocks for biorefining.},
	number = {1},
	urldate = {2023-04-14},
	journal = {Biotechnology for Biofuels and Bioproducts},
	author = {Escamez, Sacha and Robinson, Kathryn M. and Luomaranta, Mikko and Gandla, Madhavi Latha and Mähler, Niklas and Yassin, Zakiya and Grahn, Thomas and Scheepers, Gerhard and Stener, Lars-Göran and Jansson, Stefan and Jönsson, Leif J. and Street, Nathaniel R. and Tuominen, Hannele},
	month = apr,
	year = {2023},
	keywords = {Bioenergy, Biomass, Biorefining, Feedstock recalcitrance, Forest feedstocks, Saccharification},
	pages = {65},
}

Wood represents the majority of the biomass on land and constitutes a renewable source of biofuels and other bioproducts. However, wood is recalcitrant to bioconversion, raising a need for feedstock improvement in production of, for instance, biofuels. We investigated the properties of wood that affect bioconversion, as well as the underlying genetics, to help identify superior tree feedstocks for biorefining.

@article{schiffthaler_seir_2023,
	title = {Seiðr: {Efficient} calculation of robust ensemble gene networks},
	volume = {9},
	issn = {2405-8440},
	shorttitle = {Seiðr},
	url = {https://www.sciencedirect.com/science/article/pii/S2405844023040185},
	doi = {10.1016/j.heliyon.2023.e16811},
	abstract = {Gene regulatory and gene co-expression networks are powerful research tools for identifying biological signal within high-dimensional gene expression data. In recent years, research has focused on addressing shortcomings of these techniques with regard to the low signal-to-noise ratio, non-linear interactions and dataset dependent biases of published methods. Furthermore, it has been shown that aggregating networks from multiple methods provides improved results. Despite this, few useable and scalable software tools have been implemented to perform such best-practice analyses. Here, we present Seidr (stylized Seiðr), a software toolkit designed to assist scientists in gene regulatory and gene co-expression network inference. Seidr creates community networks to reduce algorithmic bias and utilizes noise corrected network backboning to prune noisy edges in the networks. Using benchmarks in real-world conditions across three eukaryotic model organisms, Saccharomyces cerevisiae, Drosophila melanogaster, and Arabidopsis thaliana, we show that individual algorithms are biased toward functional evidence for certain gene-gene interactions. We further demonstrate that the community network is less biased, providing robust performance across different standards and comparisons for the model organisms. Finally, we apply Seidr to a network of drought stress in Norway spruce (Picea abies (L.) H. Krast) as an example application in a non-model species. We demonstrate the use of a network inferred using Seidr for identifying key components, communities and suggesting gene function for non-annotated genes.},
	language = {en},
	number = {6},
	urldate = {2023-06-16},
	journal = {Heliyon},
	author = {Schiffthaler, Bastian and van Zalen, Elena and Serrano, Alonso R. and Street, Nathaniel R. and Delhomme, Nicolas},
	month = jun,
	year = {2023},
	keywords = {Functional genomics, Gene co-expression network, Gene network inference, Gene regulatory network, Systems biology},
	pages = {e16811},
}

Gene regulatory and gene co-expression networks are powerful research tools for identifying biological signal within high-dimensional gene expression data. In recent years, research has focused on addressing shortcomings of these techniques with regard to the low signal-to-noise ratio, non-linear interactions and dataset dependent biases of published methods. Furthermore, it has been shown that aggregating networks from multiple methods provides improved results. Despite this, few useable and scalable software tools have been implemented to perform such best-practice analyses. Here, we present Seidr (stylized Seiðr), a software toolkit designed to assist scientists in gene regulatory and gene co-expression network inference. Seidr creates community networks to reduce algorithmic bias and utilizes noise corrected network backboning to prune noisy edges in the networks. Using benchmarks in real-world conditions across three eukaryotic model organisms, Saccharomyces cerevisiae, Drosophila melanogaster, and Arabidopsis thaliana, we show that individual algorithms are biased toward functional evidence for certain gene-gene interactions. We further demonstrate that the community network is less biased, providing robust performance across different standards and comparisons for the model organisms. Finally, we apply Seidr to a network of drought stress in Norway spruce (Picea abies (L.) H. Krast) as an example application in a non-model species. We demonstrate the use of a network inferred using Seidr for identifying key components, communities and suggesting gene function for non-annotated genes.

@article{akhter_cone-setting_2022,
	title = {Cone-setting in spruce is regulated by conserved elements of the age-dependent flowering pathway},
	volume = {236},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18449},
	doi = {10.1111/nph.18449},
	abstract = {Reproductive phase change is well characterized in angiosperm model species, but less studied in gymnosperms. We utilize the early cone-setting acrocona mutant to study reproductive phase change in the conifer Picea abies (Norway spruce), a gymnosperm. The acrocona mutant frequently initiates cone-like structures, called transition shoots, in positions where wild-type P. abies always produces vegetative shoots. We collect acrocona and wild-type samples, and RNA-sequence their messenger RNA (mRNA) and microRNA (miRNA) fractions. We establish gene expression patterns and then use allele-specific transcript assembly to identify mutations in acrocona. We genotype a segregating population of inbred acrocona trees. A member of the SQUAMOSA BINDING PROTEIN-LIKE (SPL) gene family, PaSPL1, is active in reproductive meristems, whereas two putative negative regulators of PaSPL1, miRNA156 and the conifer specific miRNA529, are upregulated in vegetative and transition shoot meristems. We identify a mutation in a putative miRNA156/529 binding site of the acrocona PaSPL1 allele and show that the mutation renders the acrocona allele tolerant to these miRNAs. We show co-segregation between the early cone-setting phenotype and trees homozygous for the acrocona mutation. In conclusion, we demonstrate evolutionary conservation of the age-dependent flowering pathway and involvement of this pathway in regulating reproductive phase change in the conifer P. abies.},
	language = {en},
	number = {5},
	urldate = {2022-11-10},
	journal = {New Phytologist},
	author = {Akhter, Shirin and Westrin, Karl Johan and Zivi, Nathan and Nordal, Veronika and Kretzschmar, Warren W. and Delhomme, Nicolas and Street, Nathaniel R. and Nilsson, Ove and Emanuelsson, Olof and Sundström, Jens F.},
	month = dec,
	year = {2022},
	keywords = {Cone-setting, Flowering, Gymnosperm, Picea abies, Reproductive development, SPL-gene family, Transcriptome, cone-setting, flowering, gymnosperm, reproductive development, transcriptome},
	pages = {1951--1963},
}

Reproductive phase change is well characterized in angiosperm model species, but less studied in gymnosperms. We utilize the early cone-setting acrocona mutant to study reproductive phase change in the conifer Picea abies (Norway spruce), a gymnosperm. The acrocona mutant frequently initiates cone-like structures, called transition shoots, in positions where wild-type P. abies always produces vegetative shoots. We collect acrocona and wild-type samples, and RNA-sequence their messenger RNA (mRNA) and microRNA (miRNA) fractions. We establish gene expression patterns and then use allele-specific transcript assembly to identify mutations in acrocona. We genotype a segregating population of inbred acrocona trees. A member of the SQUAMOSA BINDING PROTEIN-LIKE (SPL) gene family, PaSPL1, is active in reproductive meristems, whereas two putative negative regulators of PaSPL1, miRNA156 and the conifer specific miRNA529, are upregulated in vegetative and transition shoot meristems. We identify a mutation in a putative miRNA156/529 binding site of the acrocona PaSPL1 allele and show that the mutation renders the acrocona allele tolerant to these miRNAs. We show co-segregation between the early cone-setting phenotype and trees homozygous for the acrocona mutation. In conclusion, we demonstrate evolutionary conservation of the age-dependent flowering pathway and involvement of this pathway in regulating reproductive phase change in the conifer P. abies.

@article{liu_demographic_2022,
	title = {Demographic history and natural selection shape patterns of deleterious mutation load and barriers to introgression across {Populus} genome},
	volume = {39},
	issn = {1537-1719},
	url = {https://doi.org/10.1093/molbev/msac008},
	doi = {10/gn9jc6},
	abstract = {Hybridization and resulting introgression are important processes shaping the tree of life and appear to be far more common than previously thought. However, how the genome evolution was shaped by various genetic and evolutionary forces after hybridization remains unresolved. Here we used whole genome resequencing data of 227 individuals from multiple widespread Populus species to characterize their contemporary patterns of hybridization and to quantify genomic signatures of past introgression. We observe a high frequency of contemporary hybridization and confirm that multiple previously ambiguous species are in fact F1 hybrids. Seven species were identified, which experienced different demographic histories that resulted in strikingly varied efficacy of selection and burdens of deleterious mutations. Frequent past introgression has been found to be a pervasive feature throughout the speciation of these Populus species. The retained introgressed regions, more generally, tend to contain reduced genetic load and to be located in regions of high recombination. We also find that in pairs of species with substantial differences in effective population size, introgressed regions are inferred to have undergone selective sweeps at greater than expected frequencies in the species with lower effective population size, suggesting that introgression likely have higher potential to provide beneficial variation for species with small populations. Our results, therefore, illustrate that demography and recombination have interplayed with both positive and negative selection in determining the genomic evolution after hybridization.},
	number = {2},
	urldate = {2022-01-24},
	journal = {Molecular Biology and Evolution},
	author = {Liu, Shuyu and Zhang, Lei and Sang, Yupeng and Lai, Qiang and Zhang, Xinxin and Jia, Changfu and Long, Zhiqin and Wu, Jiali and Ma, Tao and Mao, Kangshan and Street, Nathaniel R and Ingvarsson, Pär K and Liu, Jianquan and Wang, Jing},
	month = jan,
	year = {2022},
	pages = {msac008},
}

Hybridization and resulting introgression are important processes shaping the tree of life and appear to be far more common than previously thought. However, how the genome evolution was shaped by various genetic and evolutionary forces after hybridization remains unresolved. Here we used whole genome resequencing data of 227 individuals from multiple widespread Populus species to characterize their contemporary patterns of hybridization and to quantify genomic signatures of past introgression. We observe a high frequency of contemporary hybridization and confirm that multiple previously ambiguous species are in fact F1 hybrids. Seven species were identified, which experienced different demographic histories that resulted in strikingly varied efficacy of selection and burdens of deleterious mutations. Frequent past introgression has been found to be a pervasive feature throughout the speciation of these Populus species. The retained introgressed regions, more generally, tend to contain reduced genetic load and to be located in regions of high recombination. We also find that in pairs of species with substantial differences in effective population size, introgressed regions are inferred to have undergone selective sweeps at greater than expected frequencies in the species with lower effective population size, suggesting that introgression likely have higher potential to provide beneficial variation for species with small populations. Our results, therefore, illustrate that demography and recombination have interplayed with both positive and negative selection in determining the genomic evolution after hybridization.

@article{curci_identification_2022,
	title = {Identification of growth regulators using cross-species network analysis in plants},
	volume = {190},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiac374},
	doi = {10.1093/plphys/kiac374},
	abstract = {With the need to increase plant productivity, one of the challenges plant scientists are facing is to identify genes that play a role in beneficial plant traits. Moreover, even when such genes are found, it is generally not trivial to transfer this knowledge about gene function across species to identify functional orthologs. Here, we focused on the leaf to study plant growth. First, we built leaf growth transcriptional networks in Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and aspen (Populus tremula). Next, known growth regulators, here defined as genes that when mutated or ectopically expressed alter plant growth, together with cross-species conserved networks, were used as guides to predict novel Arabidopsis growth regulators. Using an in-depth literature screening, 34 out of 100 top predicted growth regulators were confirmed to affect leaf phenotype when mutated or overexpressed and thus represent novel potential growth regulators. Globally, these growth regulators were involved in cell cycle, plant defense responses, gibberellin, auxin, and brassinosteroid signaling. Phenotypic characterization of loss-of-function lines confirmed two predicted growth regulators to be involved in leaf growth (NPF6.4 and LATE MERISTEM IDENTITY2). In conclusion, the presented network approach offers an integrative cross-species strategy to identify genes involved in plant growth and development.},
	number = {4},
	urldate = {2022-12-02},
	journal = {Plant Physiology},
	author = {Curci, Pasquale Luca and Zhang, Jie and Mähler, Niklas and Seyfferth, Carolin and Mannapperuma, Chanaka and Diels, Tim and Van Hautegem, Tom and Jonsen, David and Street, Nathaniel and Hvidsten, Torgeir R and Hertzberg, Magnus and Nilsson, Ove and Inzé, Dirk and Nelissen, Hilde and Vandepoele, Klaas},
	month = dec,
	year = {2022},
	pages = {2350--2365},
}

With the need to increase plant productivity, one of the challenges plant scientists are facing is to identify genes that play a role in beneficial plant traits. Moreover, even when such genes are found, it is generally not trivial to transfer this knowledge about gene function across species to identify functional orthologs. Here, we focused on the leaf to study plant growth. First, we built leaf growth transcriptional networks in Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and aspen (Populus tremula). Next, known growth regulators, here defined as genes that when mutated or ectopically expressed alter plant growth, together with cross-species conserved networks, were used as guides to predict novel Arabidopsis growth regulators. Using an in-depth literature screening, 34 out of 100 top predicted growth regulators were confirmed to affect leaf phenotype when mutated or overexpressed and thus represent novel potential growth regulators. Globally, these growth regulators were involved in cell cycle, plant defense responses, gibberellin, auxin, and brassinosteroid signaling. Phenotypic characterization of loss-of-function lines confirmed two predicted growth regulators to be involved in leaf growth (NPF6.4 and LATE MERISTEM IDENTITY2). In conclusion, the presented network approach offers an integrative cross-species strategy to identify genes involved in plant growth and development.

@article{law_metatranscriptomics_2022,
	title = {Metatranscriptomics captures dynamic shifts in mycorrhizal coordination in boreal forests},
	volume = {119},
	url = {https://www.pnas.org/doi/full/10.1073/pnas.2118852119},
	doi = {10.1073/pnas.2118852119},
	abstract = {Carbon storage and cycling in boreal forests—the largest terrestrial carbon store—is moderated by complex interactions between trees and soil microorganisms. However, existing methods limit our ability to predict how changes in environmental conditions will alter these associations and the essential ecosystem services they provide. To address this, we developed a metatranscriptomic approach to analyze the impact of nutrient enrichment on Norway spruce fine roots and the community structure, function, and tree–microbe coordination of over 350 root-associated fungal species. In response to altered nutrient status, host trees redefined their relationship with the fungal community by reducing sugar efflux carriers and enhancing defense processes. This resulted in a profound restructuring of the fungal community and a collapse in functional coordination between the tree and the dominant Basidiomycete species, and an increase in functional coordination with versatile Ascomycete species. As such, there was a functional shift in community dominance from Basidiomycetes species, with important roles in enzymatically cycling recalcitrant carbon, to Ascomycete species that have melanized cell walls that are highly resistant to degradation. These changes were accompanied by prominent shifts in transcriptional coordination between over 60 predicted fungal effectors, with more than 5,000 Norway spruce transcripts, providing mechanistic insight into the complex molecular dialogue coordinating host trees and their fungal partners. The host–microbe dynamics captured by this study functionally inform how these complex and sensitive biological relationships may mediate the carbon storage potential of boreal soils under changing nutrient conditions.},
	number = {26},
	urldate = {2022-06-22},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Law, Simon R. and Serrano, Alonso R. and Daguerre, Yohann and Sundh, John and Schneider, Andreas N. and Stangl, Zsofia R. and Castro, David and Grabherr, Manfred and Näsholm, Torgny and Street, Nathaniel R. and Hurry, Vaughan},
	month = jun,
	year = {2022},
	pages = {e2118852119},
}

Carbon storage and cycling in boreal forests—the largest terrestrial carbon store—is moderated by complex interactions between trees and soil microorganisms. However, existing methods limit our ability to predict how changes in environmental conditions will alter these associations and the essential ecosystem services they provide. To address this, we developed a metatranscriptomic approach to analyze the impact of nutrient enrichment on Norway spruce fine roots and the community structure, function, and tree–microbe coordination of over 350 root-associated fungal species. In response to altered nutrient status, host trees redefined their relationship with the fungal community by reducing sugar efflux carriers and enhancing defense processes. This resulted in a profound restructuring of the fungal community and a collapse in functional coordination between the tree and the dominant Basidiomycete species, and an increase in functional coordination with versatile Ascomycete species. As such, there was a functional shift in community dominance from Basidiomycetes species, with important roles in enzymatically cycling recalcitrant carbon, to Ascomycete species that have melanized cell walls that are highly resistant to degradation. These changes were accompanied by prominent shifts in transcriptional coordination between over 60 predicted fungal effectors, with more than 5,000 Norway spruce transcripts, providing mechanistic insight into the complex molecular dialogue coordinating host trees and their fungal partners. The host–microbe dynamics captured by this study functionally inform how these complex and sensitive biological relationships may mediate the carbon storage potential of boreal soils under changing nutrient conditions.

@article{ranjan_molecular_2022,
	title = {Molecular basis of differential adventitious rooting competence in poplar genotypes},
	volume = {73},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erac126},
	doi = {10.1093/jxb/erac126},
	abstract = {Recalcitrant adventitious root (AR) development is a major hurdle in propagating commercially important woody plants. Although significant progress has been made to identify genes involved in subsequent steps of AR development, the molecular basis of differences in apparent recalcitrance to form AR between easy-to-root and difficult-to-root genotypes remains unknown. To address this, we generated cambium tissue-specific transcriptomic data from stem cuttings of hybrid aspen, T89 (difficult-to-root) and hybrid poplar OP42 (easy-to-root), and used transgenic approaches to verify the role of several transcription factors in the control of adventitious rooting. Increased peroxidase activity was positively correlated with better rooting. We found differentially expressed genes encoding reactive oxygen species scavenging proteins to be enriched in OP42 compared with T89. A greater number of differentially expressed transcription factors in cambium cells of OP42 compared with T89 was revealed by a more intense transcriptional reprograming in the former. PtMYC2, a potential negative regulator, was less expressed in OP42 compared with T89. Using transgenic approaches, we demonstrated that PttARF17.1 and PttMYC2.1 negatively regulate adventitious rooting. Our results provide insights into the molecular basis of genotypic differences in AR and implicate differential expression of the master regulator MYC2 as a critical player in this process.},
	number = {12},
	urldate = {2022-06-30},
	journal = {Journal of Experimental Botany},
	author = {Ranjan, Alok and Perrone, Irene and Alallaq, Sanaria and Singh, Rajesh and Rigal, Adeline and Brunoni, Federica and Chitarra, Walter and Guinet, Frederic and Kohler, Annegret and Martin, Francis and Street, Nathaniel R and Bhalerao, Rishikesh and Legué, Valérie and Bellini, Catherine},
	month = jun,
	year = {2022},
	pages = {4046--4064},
}

Recalcitrant adventitious root (AR) development is a major hurdle in propagating commercially important woody plants. Although significant progress has been made to identify genes involved in subsequent steps of AR development, the molecular basis of differences in apparent recalcitrance to form AR between easy-to-root and difficult-to-root genotypes remains unknown. To address this, we generated cambium tissue-specific transcriptomic data from stem cuttings of hybrid aspen, T89 (difficult-to-root) and hybrid poplar OP42 (easy-to-root), and used transgenic approaches to verify the role of several transcription factors in the control of adventitious rooting. Increased peroxidase activity was positively correlated with better rooting. We found differentially expressed genes encoding reactive oxygen species scavenging proteins to be enriched in OP42 compared with T89. A greater number of differentially expressed transcription factors in cambium cells of OP42 compared with T89 was revealed by a more intense transcriptional reprograming in the former. PtMYC2, a potential negative regulator, was less expressed in OP42 compared with T89. Using transgenic approaches, we demonstrated that PttARF17.1 and PttMYC2.1 negatively regulate adventitious rooting. Our results provide insights into the molecular basis of genotypic differences in AR and implicate differential expression of the master regulator MYC2 as a critical player in this process.

@article{vergara_norway_2022,
	title = {Norway spruce deploys tissue-specific responses during acclimation to cold},
	volume = {45},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.14241},
	doi = {10.1111/pce.14241},
	abstract = {Climate change in the conifer-dominated boreal forest is expected to lead to warmer but more dynamic winter air temperatures, reducing the depth and duration of snow cover, which in turn results in colder winter soils. To gain insight into the mechanisms that have enabled conifers to dominate when exposed to extremes of long exposure to freezing temperatures, we performed genome-wide RNA-Seq analysis from needles and roots of non-dormant two-year Norway spruce (Picea abies (L.) H. Karst), and contrasted these response to herbaceous model Arabidopsis We show that, relative to Arabidopsis leaves, the main transcriptional response of Norway spruce (Picea abies (L.) H. Karst) needles exposed to cold was delayed, and this delay was associated with slower development of freezing tolerance. However, despite this difference in timing, our results indicate that Norway spruce principally utilizes early response transcription factors (TFs) belonging to the same gene families as used by Arabidopsis, indicating broad evolutionary conservation of cold response networks. However, needles and root of Norway spruce showed contrasting results, in keeping with their different metabolic and developmental states. Regulatory network analysis identified conserved TFs, including a root-specific bHLH101 homolog, and other members of the same TF family with a pervasive role in cold regulation, such as homologs of ICE1 and AKS3, and also homologs of the NAC (anac47 and anac28) and AP2/ERF superfamilies (DREB2 and ERF3), providing new functional insights into cold stress response strategies in Norway spruce. This article is protected by copyright. All rights reserved.},
	language = {en},
	number = {2},
	urldate = {2021-12-09},
	journal = {Plant, Cell \& Environment},
	author = {Vergara, Alexander and Haas, Julia Christa and Aro, Tuuli and Stachula, Paulina and Street, Nathaniel Robert and Hurry, Vaughan},
	month = feb,
	year = {2022},
	keywords = {Norway spruce, cold, transcriptome},
}

Climate change in the conifer-dominated boreal forest is expected to lead to warmer but more dynamic winter air temperatures, reducing the depth and duration of snow cover, which in turn results in colder winter soils. To gain insight into the mechanisms that have enabled conifers to dominate when exposed to extremes of long exposure to freezing temperatures, we performed genome-wide RNA-Seq analysis from needles and roots of non-dormant two-year Norway spruce (Picea abies (L.) H. Karst), and contrasted these response to herbaceous model Arabidopsis We show that, relative to Arabidopsis leaves, the main transcriptional response of Norway spruce (Picea abies (L.) H. Karst) needles exposed to cold was delayed, and this delay was associated with slower development of freezing tolerance. However, despite this difference in timing, our results indicate that Norway spruce principally utilizes early response transcription factors (TFs) belonging to the same gene families as used by Arabidopsis, indicating broad evolutionary conservation of cold response networks. However, needles and root of Norway spruce showed contrasting results, in keeping with their different metabolic and developmental states. Regulatory network analysis identified conserved TFs, including a root-specific bHLH101 homolog, and other members of the same TF family with a pervasive role in cold regulation, such as homologs of ICE1 and AKS3, and also homologs of the NAC (anac47 and anac28) and AP2/ERF superfamilies (DREB2 and ERF3), providing new functional insights into cold stress response strategies in Norway spruce. This article is protected by copyright. All rights reserved.

@article{rendon-anaya_adaptive_2021,
	title = {Adaptive introgression facilitate adaptation to high latitudes in {European} aspen ({Populus} tremula {L}.)},
	volume = {38},
	issn = {1537-1719},
	url = {https://doi.org/10.1093/molbev/msab229},
	doi = {10.1093/molbev/msab229},
	abstract = {Understanding local adaptation has become a key research area given the ongoing climate challenge and the concomitant requirement to conserve genetic resources. Perennial plants, such as forest trees, are good models to study local adaptation given their wide geographic distribution, largely outcrossing mating systems and demographic histories. We evaluated signatures of local adaptation in European aspen (Populus tremula) across Europe by means of whole genome re-sequencing of a collection of 411 individual trees. We dissected admixture patterns between aspen lineages and observed a strong genomic mosaicism in Scandinavian trees, evidencing different colonization trajectories into the peninsula from Russia, Central and Western Europe. As a consequence of the secondary contacts between populations after the last glacial maximum (LGM), we detected an adaptive introgression event in a genome region of ∼500kb in chromosome 10, harboring a large-effect locus that has previously been shown to contribute to adaptation to the short growing seasons characteristic of northern Scandinavia. Demographic simulations and ancestry inference suggest an Eastern origin - probably Russian - of the adaptive Nordic allele which nowadays is present in a homozygous state at the north of Scandinavia. The strength of introgression and positive selection signatures in this region is a unique feature in the genome. Furthermore, we detected signals of balancing selection, shared across regional populations, that highlight the importance of standing variation as a primary source of alleles that facilitate local adaptation. Our results therefore emphasize the importance of migration-selection balance underlying the genetic architecture of key adaptive quantitative traits.},
	language = {eng},
	number = {11},
	journal = {Molecular Biology and Evolution},
	author = {Rendón-Anaya, Martha and Wilson, Jonathan and Sveinsson, Sæmundur and Fedorkov, Aleksey and Cottrell, Joan and Bailey, Mark E. S. and Ruņģis, Dainis and Lexer, Christian and Jansson, Stefan and Robinson, Kathryn M. and Street, Nathaniel R. and Ingvarsson, Pär K.},
	month = jul,
	year = {2021},
	pages = {5034--5050},
}

Understanding local adaptation has become a key research area given the ongoing climate challenge and the concomitant requirement to conserve genetic resources. Perennial plants, such as forest trees, are good models to study local adaptation given their wide geographic distribution, largely outcrossing mating systems and demographic histories. We evaluated signatures of local adaptation in European aspen (Populus tremula) across Europe by means of whole genome re-sequencing of a collection of 411 individual trees. We dissected admixture patterns between aspen lineages and observed a strong genomic mosaicism in Scandinavian trees, evidencing different colonization trajectories into the peninsula from Russia, Central and Western Europe. As a consequence of the secondary contacts between populations after the last glacial maximum (LGM), we detected an adaptive introgression event in a genome region of ∼500kb in chromosome 10, harboring a large-effect locus that has previously been shown to contribute to adaptation to the short growing seasons characteristic of northern Scandinavia. Demographic simulations and ancestry inference suggest an Eastern origin - probably Russian - of the adaptive Nordic allele which nowadays is present in a homozygous state at the north of Scandinavia. The strength of introgression and positive selection signatures in this region is a unique feature in the genome. Furthermore, we detected signals of balancing selection, shared across regional populations, that highlight the importance of standing variation as a primary source of alleles that facilitate local adaptation. Our results therefore emphasize the importance of migration-selection balance underlying the genetic architecture of key adaptive quantitative traits.

@article{haas_candidate_2021,
	title = {Candidate regulators and target genes of drought stress in needles and roots of {Norway} spruce},
	volume = {41},
	issn = {1758-4469},
	url = {https://doi.org/10.1093/treephys/tpaa178},
	doi = {10.1093/treephys/tpaa178},
	abstract = {Drought stress impacts seedling establishment, survival and whole-plant productivity. Molecular responses to drought stress have been most extensively studied in herbaceous species, mostly considering only aboveground tissues. Coniferous tree species dominate boreal forests, which are predicted to be exposed to more frequent and acute drought as a result of ongoing climate change. The associated impact at all stages of the forest tree life cycle is expected to have large-scale ecological and economic impacts. However, the molecular response to drought has not been comprehensively profiled for coniferous species. We assayed the physiological and transcriptional response of Picea abies (L.) H. Karst seedling needles and roots after exposure to mild and severe drought. Shoots and needles showed an extensive reversible plasticity for physiological measures indicative of drought-response mechanisms, including changes in stomatal conductance (gs), shoot water potential and abscisic acid (ABA). In both tissues, the most commonly observed expression profiles in response to drought were highly correlated with the ABA levels. Still, root and needle transcriptional responses contrasted, with extensive root-specific down-regulation of growth. Comparison between previously characterized Arabidopsis thaliana L. drought-response genes and P. abies revealed both conservation and divergence of transcriptional response to drought. In P. abies, transcription factors belonging to the ABA responsive element(ABRE) binding/ABRE binding factors ABA-dependent pathway had a more limited role. These results highlight the importance of profiling both above- and belowground tissues, and provide a comprehensive framework to advance the understanding of the drought response of P. abies. The results demonstrate that a short-term, severe drought induces severe physiological responses coupled to extensive transcriptome modulation and highlight the susceptibility of Norway spruce seedlings to such drought events.},
	number = {7},
	urldate = {2021-11-04},
	journal = {Tree Physiology},
	author = {Haas, Julia C and Vergara, Alexander and Serrano, Alonso R and Mishra, Sanatkumar and Hurry, Vaughan and Street, Nathaniel R},
	month = jul,
	year = {2021},
	pages = {1230--1246},
}

Drought stress impacts seedling establishment, survival and whole-plant productivity. Molecular responses to drought stress have been most extensively studied in herbaceous species, mostly considering only aboveground tissues. Coniferous tree species dominate boreal forests, which are predicted to be exposed to more frequent and acute drought as a result of ongoing climate change. The associated impact at all stages of the forest tree life cycle is expected to have large-scale ecological and economic impacts. However, the molecular response to drought has not been comprehensively profiled for coniferous species. We assayed the physiological and transcriptional response of Picea abies (L.) H. Karst seedling needles and roots after exposure to mild and severe drought. Shoots and needles showed an extensive reversible plasticity for physiological measures indicative of drought-response mechanisms, including changes in stomatal conductance (gs), shoot water potential and abscisic acid (ABA). In both tissues, the most commonly observed expression profiles in response to drought were highly correlated with the ABA levels. Still, root and needle transcriptional responses contrasted, with extensive root-specific down-regulation of growth. Comparison between previously characterized Arabidopsis thaliana L. drought-response genes and P. abies revealed both conservation and divergence of transcriptional response to drought. In P. abies, transcription factors belonging to the ABA responsive element(ABRE) binding/ABRE binding factors ABA-dependent pathway had a more limited role. These results highlight the importance of profiling both above- and belowground tissues, and provide a comprehensive framework to advance the understanding of the drought response of P. abies. The results demonstrate that a short-term, severe drought induces severe physiological responses coupled to extensive transcriptome modulation and highlight the susceptibility of Norway spruce seedlings to such drought events.

@article{liu_centromere-specific_2021,
	title = {Centromere-{Specific} {Retrotransposons} and {Very}-{Long}-{Chain} {Fatty} {Acid} {Biosynthesis} in the {Genome} of {Yellowhorn} ({Xanthoceras} sorbifolium, {Sapindaceae}), an {Oil}-{Producing} {Tree} {With} {Significant} {Drought} {Resistance}},
	volume = {12},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2021.766389},
	doi = {10/gnsqvv},
	abstract = {In-depth genome characterization is still lacking for most of biofuel crops, especially for centromeres, which play a fundamental role during nuclear division and in the maintenance of genome stability. This study applied long-read sequencing technologies to assemble a highly contiguous genome for yellowhorn (Xanthoceras sorbifolium), an oil-producing tree, and conducted extensive comparative analyses to understand centromere structure and evolution, and fatty acid biosynthesis. We produced a reference-level genome of yellowhorn, ∼470 Mb in length with ∼95\% of contigs anchored onto 15 chromosomes. Genome annotation identified 22,049 protein-coding genes and 65.7\% of the genome sequence as repetitive elements. Long terminal repeat retrotransposons (LTR-RTs) account for ∼30\% of the yellowhorn genome, which is maintained by a moderate birth rate and a low removal rate. We identified the centromeric regions on each chromosome and found enrichment of centromere-specific retrotransposons of LINE1 and Gypsy in these regions, which have evolved recently (∼0.7 MYA). We compared the genomes of three cultivars and found frequent inversions. We analyzed the transcriptomes from different tissues and identified the candidate genes involved in very-long-chain fatty acid biosynthesis and their expression profiles. Collinear block analysis showed that yellowhorn shared the gamma (γ) hexaploidy event with Vitis vinifera but did not undergo any further whole-genome duplication. This study provides excellent genomic resources for understanding centromere structure and evolution and for functional studies in this important oil-producing plant.},
	urldate = {2021-12-16},
	journal = {Frontiers in Plant Science},
	author = {Liu, Hui and Yan, Xue-Mei and Wang, Xin-rui and Zhang, Dong-Xu and Zhou, Qingyuan and Shi, Tian-Le and Jia, Kai-Hua and Tian, Xue-Chan and Zhou, Shan-Shan and Zhang, Ren-Gang and Yun, Quan-Zheng and Wang, Qing and Xiang, Qiuhong and Mannapperuma, Chanaka and Van Zalen, Elena and Street, Nathaniel R. and Porth, Ilga and El-Kassaby, Yousry A. and Zhao, Wei and Wang, Xiao-Ru and Guan, Wenbin and Mao, Jian-Feng},
	year = {2021},
	pages = {2546},
}

In-depth genome characterization is still lacking for most of biofuel crops, especially for centromeres, which play a fundamental role during nuclear division and in the maintenance of genome stability. This study applied long-read sequencing technologies to assemble a highly contiguous genome for yellowhorn (Xanthoceras sorbifolium), an oil-producing tree, and conducted extensive comparative analyses to understand centromere structure and evolution, and fatty acid biosynthesis. We produced a reference-level genome of yellowhorn, ∼470 Mb in length with ∼95% of contigs anchored onto 15 chromosomes. Genome annotation identified 22,049 protein-coding genes and 65.7% of the genome sequence as repetitive elements. Long terminal repeat retrotransposons (LTR-RTs) account for ∼30% of the yellowhorn genome, which is maintained by a moderate birth rate and a low removal rate. We identified the centromeric regions on each chromosome and found enrichment of centromere-specific retrotransposons of LINE1 and Gypsy in these regions, which have evolved recently (∼0.7 MYA). We compared the genomes of three cultivars and found frequent inversions. We analyzed the transcriptomes from different tissues and identified the candidate genes involved in very-long-chain fatty acid biosynthesis and their expression profiles. Collinear block analysis showed that yellowhorn shared the gamma (γ) hexaploidy event with Vitis vinifera but did not undergo any further whole-genome duplication. This study provides excellent genomic resources for understanding centromere structure and evolution and for functional studies in this important oil-producing plant.

@article{schneider_comparative_2021,
	title = {Comparative {Fungal} {Community} {Analyses} {Using} {Metatranscriptomics} and {Internal} {Transcribed} {Spacer} {Amplicon} {Sequencing} from {Norway} {Spruce}},
	volume = {6},
	issn = {2379-5077},
	url = {https://journals.asm.org/doi/10.1128/mSystems.00884-20},
	doi = {10/gjnmqq},
	abstract = {A deeper understanding of microbial communities associated with plants is revealing their importance for plant health and productivity. RNA extracted from plant field samples represents the host and other organisms present.
          , 
            ABSTRACT
            
              The health, growth, and fitness of boreal forest trees are impacted and improved by their associated microbiomes. Microbial gene expression and functional activity can be assayed with RNA sequencing (RNA-Seq) data from host samples. In contrast, phylogenetic marker gene amplicon sequencing data are used to assess taxonomic composition and community structure of the microbiome. Few studies have considered how much of this structural and taxonomic information is included in transcriptomic data from matched samples. Here, we described fungal communities using both host-derived RNA-Seq and fungal ITS1 DNA amplicon sequencing to compare the outcomes between the methods. We used a panel of root and needle samples from the coniferous tree species
              Picea abies
              (Norway spruce) growing in untreated (nutrient-deficient) and nutrient-enriched plots at the Flakaliden forest research site in boreal northern Sweden. We show that the relationship between samples and alpha and beta diversity indicated by the fungal transcriptome is in agreement with that generated by the ITS data, while also identifying a lack of taxonomic overlap due to limitations imposed by current database coverage. Furthermore, we demonstrate how metatranscriptomics data additionally provide biologically informative functional insights. At the community level, there were changes in starch and sucrose metabolism, biosynthesis of amino acids, and pentose and glucuronate interconversions, while processing of organic macromolecules, including aromatic and heterocyclic compounds, was enriched in transcripts assigned to the genus
              Cortinarius
              .
            
            
              IMPORTANCE
              A deeper understanding of microbial communities associated with plants is revealing their importance for plant health and productivity. RNA extracted from plant field samples represents the host and other organisms present. Typically, gene expression studies focus on the plant component or, in a limited number of studies, expression in one or more associated organisms. However, metatranscriptomic data are rarely used for taxonomic profiling, which is currently performed using amplicon approaches. We created an assembly-based, reproducible, and hardware-agnostic workflow to taxonomically and functionally annotate fungal RNA-Seq data obtained from Norway spruce roots, which we compared to matching ITS amplicon sequencing data. While we identified some limitations and caveats, we show that functional, taxonomic, and compositional insights can all be obtained from RNA-Seq data. These findings highlight the potential of metatranscriptomics to advance our understanding of interaction, response, and effect between host plants and their associated microbial communities.},
	language = {en},
	number = {1},
	urldate = {2021-06-03},
	journal = {mSystems},
	author = {Schneider, Andreas N. and Sundh, John and Sundström, Görel and Richau, Kerstin and Delhomme, Nicolas and Grabherr, Manfred and Hurry, Vaughan and Street, Nathaniel R.},
	editor = {McClure, Ryan},
	month = feb,
	year = {2021},
}

A deeper understanding of microbial communities associated with plants is revealing their importance for plant health and productivity. RNA extracted from plant field samples represents the host and other organisms present. , ABSTRACT The health, growth, and fitness of boreal forest trees are impacted and improved by their associated microbiomes. Microbial gene expression and functional activity can be assayed with RNA sequencing (RNA-Seq) data from host samples. In contrast, phylogenetic marker gene amplicon sequencing data are used to assess taxonomic composition and community structure of the microbiome. Few studies have considered how much of this structural and taxonomic information is included in transcriptomic data from matched samples. Here, we described fungal communities using both host-derived RNA-Seq and fungal ITS1 DNA amplicon sequencing to compare the outcomes between the methods. We used a panel of root and needle samples from the coniferous tree species Picea abies (Norway spruce) growing in untreated (nutrient-deficient) and nutrient-enriched plots at the Flakaliden forest research site in boreal northern Sweden. We show that the relationship between samples and alpha and beta diversity indicated by the fungal transcriptome is in agreement with that generated by the ITS data, while also identifying a lack of taxonomic overlap due to limitations imposed by current database coverage. Furthermore, we demonstrate how metatranscriptomics data additionally provide biologically informative functional insights. At the community level, there were changes in starch and sucrose metabolism, biosynthesis of amino acids, and pentose and glucuronate interconversions, while processing of organic macromolecules, including aromatic and heterocyclic compounds, was enriched in transcripts assigned to the genus Cortinarius . IMPORTANCE A deeper understanding of microbial communities associated with plants is revealing their importance for plant health and productivity. RNA extracted from plant field samples represents the host and other organisms present. Typically, gene expression studies focus on the plant component or, in a limited number of studies, expression in one or more associated organisms. However, metatranscriptomic data are rarely used for taxonomic profiling, which is currently performed using amplicon approaches. We created an assembly-based, reproducible, and hardware-agnostic workflow to taxonomically and functionally annotate fungal RNA-Seq data obtained from Norway spruce roots, which we compared to matching ITS amplicon sequencing data. While we identified some limitations and caveats, we show that functional, taxonomic, and compositional insights can all be obtained from RNA-Seq data. These findings highlight the potential of metatranscriptomics to advance our understanding of interaction, response, and effect between host plants and their associated microbial communities.

@article{castro_effects_2021,
	title = {Effects of {Early}, {Small}-{Scale} {Nitrogen} {Addition} on {Germination} and {Early} {Growth} of {Scots} {Pine} ({Pinus} sylvestris) {Seedlings} and on the {Recruitment} of the {Root}-{Associated} {Fungal} {Community}},
	volume = {12},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	url = {https://www.mdpi.com/1999-4907/12/11/1589},
	doi = {10/gnr3sf},
	abstract = {Scots pine (Pinus sylvestris L.) is one of the most economically important species to the Swedish forest industry, and cost-efficient planting methods are needed to ensure successful reestablishment after harvesting forest stands. While the majority of clear-cuts are replanted with pre-grown seedlings, direct seeding can be a viable option on poorer sites. Organic fertilizer has been shown to improve planted seedling establishment, but the effect on direct seeding is less well known. Therefore, at a scarified (disc trencher harrowed) clear-cut site in northern Sweden, we evaluated the effect of early, small-scale nitrogen addition on establishment and early recruitment of fungi from the disturbed soil community by site-planted Scots pine seeds. Individual seeds were planted using a moisture retaining germination matrix containing 10 mg nitrogen in the form of either arginine phosphate or ammonium nitrate. After one growing season, we collected seedlings and assessed the fungal community of seedling roots and the surrounding soil. Our results demonstrate that early, small-scale N addition increases seedling survival and needle carbon content, that there is rapid recruitment of ectomycorrhizal fungi to the roots and rhizosphere of the young seedlings and that this rapid recruitment was modified but not prevented by N addition.},
	language = {en},
	number = {11},
	urldate = {2021-12-16},
	journal = {Forests},
	author = {Castro, David and Schneider, Andreas N. and Holmlund, Mattias and Näsholm, Torgny and Street, Nathaniel R. and Hurry, Vaughan},
	month = nov,
	year = {2021},
	keywords = {Scots pine, boreal forest, clear-cut, ectomycorrhiza, fungal community composition, mycobiome, nitrogen addition},
	pages = {1589},
}

Scots pine (Pinus sylvestris L.) is one of the most economically important species to the Swedish forest industry, and cost-efficient planting methods are needed to ensure successful reestablishment after harvesting forest stands. While the majority of clear-cuts are replanted with pre-grown seedlings, direct seeding can be a viable option on poorer sites. Organic fertilizer has been shown to improve planted seedling establishment, but the effect on direct seeding is less well known. Therefore, at a scarified (disc trencher harrowed) clear-cut site in northern Sweden, we evaluated the effect of early, small-scale nitrogen addition on establishment and early recruitment of fungi from the disturbed soil community by site-planted Scots pine seeds. Individual seeds were planted using a moisture retaining germination matrix containing 10 mg nitrogen in the form of either arginine phosphate or ammonium nitrate. After one growing season, we collected seedlings and assessed the fungal community of seedling roots and the surrounding soil. Our results demonstrate that early, small-scale N addition increases seedling survival and needle carbon content, that there is rapid recruitment of ectomycorrhizal fungi to the roots and rhizosphere of the young seedlings and that this rapid recruitment was modified but not prevented by N addition.

@article{shen_boptype_2021,
	title = {The {BOP}‐type co‐transcriptional regulator {NODULE} {ROOT1} promotes stem secondary growth of the tropical {Cannabaceae} tree {Parasponia} andersonii},
	issn = {0960-7412, 1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/tpj.15242},
	doi = {10/gjs436},
	language = {en},
	urldate = {2021-06-03},
	journal = {The Plant Journal},
	author = {Shen, Defeng and Holmer, Rens and Kulikova, Olga and Mannapperuma, Chanaka and Street, Nathaniel R. and Yan, Zhichun and Maden, Thomas and Bu, Fengjiao and Zhang, Yuanyuan and Geurts, Rene and Magne, Kévin},
	month = apr,
	year = {2021},
	pages = {tpj.15242},
}

@article{christie_qtlxplorer_2021,
	title = {{qtlXplorer}: an online systems genetics browser in the {Eucalyptus} {Genome} {Integrative} {Explorer} ({EucGenIE})},
	volume = {22},
	issn = {1471-2105},
	shorttitle = {{qtlXplorer}},
	url = {https://doi.org/10.1186/s12859-021-04514-9},
	doi = {10/gnxfq5},
	abstract = {Affordable high-throughput DNA and RNA sequencing technologies are allowing genomic analysis of plant and animal populations and as a result empowering new systems genetics approaches to study complex traits. The availability of intuitive tools to browse and analyze the resulting large-scale genetic and genomic datasets remain a significant challenge. Furthermore, these integrative genomics approaches require innovative methods to dissect the flow and interconnectedness of biological information underlying complex trait variation. The Plant Genome Integrative Explorer (PlantGenIE.org) is a multi-species database and domain that houses online tools for model and woody plant species including Eucalyptus. Since the Eucalyptus Genome Integrative Explorer (EucGenIE) is integrated within PlantGenIE, it shares genome and expression analysis tools previously implemented within the various subdomains (ConGenIE, PopGenIE and AtGenIE). Despite the success in setting up integrative genomics databases, online tools for systems genetics modelling and high-resolution dissection of complex trait variation in plant populations have been lacking.},
	number = {1},
	urldate = {2021-12-29},
	journal = {BMC Bioinformatics},
	author = {Christie, Nanette and Mannapperuma, Chanaka and Ployet, Raphael and van der Merwe, Karen and Mähler, Niklas and Delhomme, Nicolas and Naidoo, Sanushka and Mizrachi, Eshchar and Street, Nathaniel R. and Myburg, Alexander A.},
	month = dec,
	year = {2021},
	keywords = {Co-expression, Database, EucGenIE, Eucalyptus, Genome browser, Online resource, Systems genetics, eQTL, qtlXplorer, ‘Omics integration},
	pages = {595},
}

Affordable high-throughput DNA and RNA sequencing technologies are allowing genomic analysis of plant and animal populations and as a result empowering new systems genetics approaches to study complex traits. The availability of intuitive tools to browse and analyze the resulting large-scale genetic and genomic datasets remain a significant challenge. Furthermore, these integrative genomics approaches require innovative methods to dissect the flow and interconnectedness of biological information underlying complex trait variation. The Plant Genome Integrative Explorer (PlantGenIE.org) is a multi-species database and domain that houses online tools for model and woody plant species including Eucalyptus. Since the Eucalyptus Genome Integrative Explorer (EucGenIE) is integrated within PlantGenIE, it shares genome and expression analysis tools previously implemented within the various subdomains (ConGenIE, PopGenIE and AtGenIE). Despite the success in setting up integrative genomics databases, online tools for systems genetics modelling and high-resolution dissection of complex trait variation in plant populations have been lacking.

@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{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{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{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{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{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{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{bernhardsson_ultra-dense_2019,
	title = {An {Ultra}-{Dense} {Haploid} {Genetic} {Map} for {Evaluating} the {Highly} {Fragmented} {Genome} {Assembly} of {Norway} {Spruce} ({Picea} abies )},
	volume = {9},
	issn = {2160-1836},
	url = {https://academic.oup.com/g3journal/article/9/5/1623/6026441},
	doi = {10/gjcr63},
	abstract = {Abstract
            Norway spruce (Picea abies (L.) Karst.) is a conifer species of substanital economic and ecological importance. In common with most conifers, the P. abies genome is very large (∼20 Gbp) and contains a high fraction of repetitive DNA. The current P. abies genome assembly (v1.0) covers approximately 60\% of the total genome size but is highly fragmented, consisting of \>10 million scaffolds. The genome annotation contains 66,632 gene models that are at least partially validated (www.congenie.org), however, the fragmented nature of the assembly means that there is currently little information available on how these genes are physically distributed over the 12 P. abies chromosomes. By creating an ultra-dense genetic linkage map, we anchored and ordered scaffolds into linkage groups, which complements the fine-scale information available in assembly contigs. Our ultra-dense haploid consensus genetic map consists of 21,056 markers derived from 14,336 scaffolds that contain 17,079 gene models (25.6\% of the validated gene models) that we have anchored to the 12 linkage groups. We used data from three independent component maps, as well as comparisons with previously published Picea maps to evaluate the accuracy and marker ordering of the linkage groups. We demonstrate that approximately 3.8\% of the anchored scaffolds and 1.6\% of the gene models covered by the consensus map have likely assembly errors as they contain genetic markers that map to different regions within or between linkage groups. We further evaluate the utility of the genetic map for the conifer research community by using an independent data set of unrelated individuals to assess genome-wide variation in genetic diversity using the genomic regions anchored to linkage groups. The results show that our map is sufficiently dense to enable detailed evolutionary analyses across the P. abies genome.},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {G3 Genes{\textbar}Genomes{\textbar}Genetics},
	author = {Bernhardsson, Carolina and Vidalis, Amaryllis and Wang, Xi and Scofield, Douglas G and Schiffthaler, Bastian and Baison, John and Street, Nathaniel R and García-Gil, M Rosario and Ingvarsson, Pär K},
	month = may,
	year = {2019},
	pages = {1623--1632},
}

Abstract Norway spruce (Picea abies (L.) Karst.) is a conifer species of substanital economic and ecological importance. In common with most conifers, the P. abies genome is very large (∼20 Gbp) and contains a high fraction of repetitive DNA. The current P. abies genome assembly (v1.0) covers approximately 60% of the total genome size but is highly fragmented, consisting of >10 million scaffolds. The genome annotation contains 66,632 gene models that are at least partially validated (www.congenie.org), however, the fragmented nature of the assembly means that there is currently little information available on how these genes are physically distributed over the 12 P. abies chromosomes. By creating an ultra-dense genetic linkage map, we anchored and ordered scaffolds into linkage groups, which complements the fine-scale information available in assembly contigs. Our ultra-dense haploid consensus genetic map consists of 21,056 markers derived from 14,336 scaffolds that contain 17,079 gene models (25.6% of the validated gene models) that we have anchored to the 12 linkage groups. We used data from three independent component maps, as well as comparisons with previously published Picea maps to evaluate the accuracy and marker ordering of the linkage groups. We demonstrate that approximately 3.8% of the anchored scaffolds and 1.6% of the gene models covered by the consensus map have likely assembly errors as they contain genetic markers that map to different regions within or between linkage groups. We further evaluate the utility of the genetic map for the conifer research community by using an independent data set of unrelated individuals to assess genome-wide variation in genetic diversity using the genomic regions anchored to linkage groups. The results show that our map is sufficiently dense to enable detailed evolutionary analyses across the P. abies genome.

@article{wegrzyn_cyberinfrastructure_2019,
	title = {Cyberinfrastructure to {Improve} {Forest} {Health} and {Productivity}: {The} {Role} of {Tree} {Databases} in {Connecting} {Genomes}, {Phenomes}, and the {Environment}},
	volume = {10},
	issn = {1664-462X},
	shorttitle = {Cyberinfrastructure to {Improve} {Forest} {Health} and {Productivity}},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2019.00813/full},
	doi = {10/ghpwhz},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Wegrzyn, Jill L. and Staton, Margaret A. and Street, Nathaniel R. and Main, Dorrie and Grau, Emily and Herndon, Nic and Buehler, Sean and Falk, Taylor and Zaman, Sumaira and Ramnath, Risharde and Richter, Peter and Sun, Lang and Condon, Bradford and Almsaeed, Abdullah and Chen, Ming and Mannapperuma, Chanaka and Jung, Sook and Ficklin, Stephen},
	month = jun,
	year = {2019},
	pages = {813},
}

@incollection{street_genomics_2019,
	title = {Genomics of forest trees},
	volume = {89},
	isbn = {978-0-12-815465-6},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0065229618300867},
	language = {en},
	urldate = {2021-06-07},
	booktitle = {Advances in {Botanical} {Research}},
	publisher = {Elsevier},
	author = {Street, Nathaniel Robert},
	year = {2019},
	doi = {10.1016/bs.abr.2018.11.001},
	pages = {1--37},
}

@incollection{giacomello_high_2019,
	title = {High {Spatial} {Resolution} {Profiling} in {Tree} {Species}},
	isbn = {978-1-119-31299-4},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/9781119312994.apr0688},
	abstract = {Until recently, the majority of genomics assays have been performed on bulk tissue samples containing multiple cell types. Tissues such as the wood formation zone in trees contain a complex mix of cell types organised in three-dimensional space. Moreover, cells within the wood formation zone represent a continual developmental progression from meristematic cambial initials through to cell death. This spatiotemporal developmental gradient and cell type information are not assayed by bulk samples. New and improved sampling methods coupled to next-generation sequencing assays are enabling the generation of high spatial resolution and single-cell transcriptomics data, offering unprecedented insight into the biology of unique cell types and cell developmental programs. We overview the application of these approaches to the study of wood development, in particular, and highlight challenges associated with the analysis of such data.},
	language = {en},
	urldate = {2021-10-20},
	booktitle = {Annual {Plant} {Reviews} online},
	publisher = {American Cancer Society},
	author = {Giacomello, Stefania and Delhomme, Nicolas and Niittylä, Totte and Tuominen, Hannele and Street, Nathaniel R.},
	year = {2019},
	doi = {10.1002/9781119312994.apr0688},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/9781119312994.apr0688},
	keywords = {RNA sequencing, cell type, single cell, spatial resolution, transcriptome, wood formation, xylem},
	pages = {329--360},
}

Until recently, the majority of genomics assays have been performed on bulk tissue samples containing multiple cell types. Tissues such as the wood formation zone in trees contain a complex mix of cell types organised in three-dimensional space. Moreover, cells within the wood formation zone represent a continual developmental progression from meristematic cambial initials through to cell death. This spatiotemporal developmental gradient and cell type information are not assayed by bulk samples. New and improved sampling methods coupled to next-generation sequencing assays are enabling the generation of high spatial resolution and single-cell transcriptomics data, offering unprecedented insight into the biology of unique cell types and cell developmental programs. We overview the application of these approaches to the study of wood development, in particular, and highlight challenges associated with the analysis of such data.

@article{kumar_poplar_2019,
	title = {Poplar carbohydrate‐active enzymes: whole‐genome annotation and functional analyses based on {RNA} expression data},
	volume = {99},
	issn = {0960-7412, 1365-313X},
	shorttitle = {Poplar carbohydrate‐active enzymes},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.14417},
	doi = {10.1111/tpj.14417},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {The Plant Journal},
	author = {Kumar, Vikash and Hainaut, Matthieu and Delhomme, Nicolas and Mannapperuma, Chanaka and Immerzeel, Peter and Street, Nathaniel R. and Henrissat, Bernard and Mellerowicz, Ewa J.},
	month = aug,
	year = {2019},
	pages = {589--609},
}

@article{blokhina_ray_2019,
	title = {Ray {Parenchymal} {Cells} {Contribute} to {Lignification} of {Tracheids} in {Developing} {Xylem} of {Norway} {Spruce}},
	volume = {181},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/181/4/1552-1572/6000532},
	doi = {10.1104/pp.19.00743},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Blokhina, Olga and Laitinen, Teresa and Hatakeyama, Yuto and Delhomme, Nicolas and Paasela, Tanja and Zhao, Lei and Street, Nathaniel R. and Wada, Hiroshi and Kärkönen, Anna and Fagerstedt, Kurt},
	month = dec,
	year = {2019},
	pages = {1552--1572},
}

@article{myburg_systems_2019,
	title = {Systems and {Synthetic} {Biology} of {Forest} {Trees}: {A} {Bioengineering} {Paradigm} for {Woody} {Biomass} {Feedstocks}},
	volume = {10},
	issn = {1664-462X},
	shorttitle = {Systems and {Synthetic} {Biology} of {Forest} {Trees}},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2019.00775/full},
	doi = {10/gjdzht},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Myburg, Alexander A. and Hussey, Steven G. and Wang, Jack P. and Street, Nathaniel R. and Mizrachi, Eshchar},
	month = jun,
	year = {2019},
	pages = {775},
}

@article{bonner_why_2019,
	title = {Why does nitrogen addition to forest soils inhibit decomposition?},
	volume = {137},
	issn = {00380717},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0038071719302342},
	doi = {10.1016/j.soilbio.2019.107570},
	language = {en},
	urldate = {2021-06-07},
	journal = {Soil Biology and Biochemistry},
	author = {Bonner, Mark TL. and Castro, David and Schneider, Andreas N. and Sundström, Görel and Hurry, Vaughan and Street, Nathaniel R. and Näsholm, Torgny},
	month = oct,
	year = {2019},
	pages = {107570},
}

@article{wang_major_2018,
	title = {A major locus controls local adaptation and adaptive life history variation in a perennial plant},
	volume = {19},
	issn = {1474-760X},
	url = {https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1444-y},
	doi = {10.1186/s13059-018-1444-y},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Genome Biology},
	author = {Wang, Jing and Ding, Jihua and Tan, Biyue and Robinson, Kathryn M. and Michelson, Ingrid H. and Johansson, Anna and Nystedt, Björn and Scofield, Douglas G. and Nilsson, Ove and Jansson, Stefan and Street, Nathaniel R. and Ingvarsson, Pär K.},
	month = dec,
	year = {2018},
	pages = {72},
}

@article{ratke_downregulating_2018,
	title = {Downregulating aspen xylan biosynthetic {GT43} genes in developing wood stimulates growth via reprograming of the transcriptome},
	volume = {219},
	issn = {0028646X},
	url = {http://doi.wiley.com/10.1111/nph.15160},
	doi = {10/gdmzzr},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Ratke, Christine and Terebieniec, Barbara K. and Winestrand, Sandra and Derba-Maceluch, Marta and Grahn, Thomas and Schiffthaler, Bastian and Ulvcrona, Thomas and Özparpucu, Merve and Rüggeberg, Markus and Lundqvist, Sven-Olof and Street, Nathaniel R. and Jönsson, Leif J. and Mellerowicz, Ewa J.},
	month = jul,
	year = {2018},
	pages = {230--245},
}

@article{lin_functional_2018,
	title = {Functional and evolutionary genomic inferences in \textit{{Populus}} through genome and population sequencing of {American} and {European} aspen},
	volume = {115},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1801437115},
	doi = {10.1073/pnas.1801437115},
	abstract = {The
              Populus
              genus is one of the major plant model systems, but genomic resources have thus far primarily been available for poplar species, and primarily
              Populus trichocarpa
              (Torr. \& Gray), which was the first tree with a whole-genome assembly. To further advance evolutionary and functional genomic analyses in
              Populus
              , we produced genome assemblies and population genetics resources of two aspen species,
              Populus tremula
              L. and
              Populus tremuloides
              Michx. The two aspen species have distributions spanning the Northern Hemisphere, where they are keystone species supporting a wide variety of dependent communities and produce a diverse array of secondary metabolites. Our analyses show that the two aspens share a similar genome structure and a highly conserved gene content with
              P. trichocarpa
              but display substantially higher levels of heterozygosity. Based on population resequencing data, we observed widespread positive and negative selection acting on both coding and noncoding regions. Furthermore, patterns of genetic diversity and molecular evolution in aspen are influenced by a number of features, such as expression level, coexpression network connectivity, and regulatory variation. To maximize the community utility of these resources, we have integrated all presented data within the PopGenIE web resource (
              PopGenIE.org
              ).},
	language = {en},
	number = {46},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Lin, Yao-Cheng and Wang, Jing and Delhomme, Nicolas and Schiffthaler, Bastian and Sundström, Görel and Zuccolo, Andrea and Nystedt, Björn and Hvidsten, Torgeir R. and de la Torre, Amanda and Cossu, Rosa M. and Hoeppner, Marc P. and Lantz, Henrik and Scofield, Douglas G. and Zamani, Neda and Johansson, Anna and Mannapperuma, Chanaka and Robinson, Kathryn M. and Mähler, Niklas and Leitch, Ilia J. and Pellicer, Jaume and Park, Eung-Jun and Van Montagu, Marc and Van de Peer, Yves and Grabherr, Manfred and Jansson, Stefan and Ingvarsson, Pär K. and Street, Nathaniel R.},
	month = nov,
	year = {2018},
	pages = {E10970--E10978},
}

The Populus genus is one of the major plant model systems, but genomic resources have thus far primarily been available for poplar species, and primarily Populus trichocarpa (Torr. & Gray), which was the first tree with a whole-genome assembly. To further advance evolutionary and functional genomic analyses in Populus , we produced genome assemblies and population genetics resources of two aspen species, Populus tremula L. and Populus tremuloides Michx. The two aspen species have distributions spanning the Northern Hemisphere, where they are keystone species supporting a wide variety of dependent communities and produce a diverse array of secondary metabolites. Our analyses show that the two aspens share a similar genome structure and a highly conserved gene content with P. trichocarpa but display substantially higher levels of heterozygosity. Based on population resequencing data, we observed widespread positive and negative selection acting on both coding and noncoding regions. Furthermore, patterns of genetic diversity and molecular evolution in aspen are influenced by a number of features, such as expression level, coexpression network connectivity, and regulatory variation. To maximize the community utility of these resources, we have integrated all presented data within the PopGenIE web resource ( PopGenIE.org ).

@article{akhter_integrative_2018,
	title = {Integrative {Analysis} of {Three} {RNA} {Sequencing} {Methods} {Identifies} {Mutually} {Exclusive} {Exons} of {MADS}-{Box} {Isoforms} {During} {Early} {Bud} {Development} in {Picea} abies},
	volume = {9},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2018.01625/full},
	doi = {10/gh967n},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Akhter, Shirin and Kretzschmar, Warren W. and Nordal, Veronika and Delhomme, Nicolas and Street, Nathaniel R. and Nilsson, Ove and Emanuelsson, Olof and Sundström, Jens F.},
	month = nov,
	year = {2018},
	pages = {1625},
}

@article{haas_microbial_2018,
	title = {Microbial community response to growing season and plant nutrient optimisation in a boreal {Norway} spruce forest},
	volume = {125},
	issn = {00380717},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0038071718302335},
	doi = {10.1016/j.soilbio.2018.07.005},
	language = {en},
	urldate = {2021-06-07},
	journal = {Soil Biology and Biochemistry},
	author = {Haas, Julia C. and Street, Nathaniel R. and Sjödin, Andreas and Lee, Natuschka M. and Högberg, Mona N. and Näsholm, Torgny and Hurry, Vaughan},
	month = oct,
	year = {2018},
	pages = {197--209},
}

@article{grimberg_storage_2018,
	title = {Storage lipid accumulation is controlled by photoperiodic signal acting via regulators of growth cessation and dormancy in hybrid aspen},
	volume = {219},
	issn = {0028646X},
	url = {http://doi.wiley.com/10.1111/nph.15197},
	doi = {10.1111/nph.15197},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Grimberg, Åsa and Lager, Ida and Street, Nathaniel R. and Robinson, Kathryn M. and Marttila, Salla and Mähler, Niklas and Ingvarsson, Pär K. and Bhalerao, Rishikesh P.},
	month = jul,
	year = {2018},
	pages = {619--630},
}

@article{jokipii-lukkari_transcriptional_2018,
	title = {Transcriptional {Roadmap} to {Seasonal} {Variation} in {Wood} {Formation} of {Norway} {Spruce}},
	volume = {176},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/176/4/2851-2870/6117009},
	doi = {10.1104/pp.17.01590},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Jokipii-Lukkari, Soile and Delhomme, Nicolas and Schiffthaler, Bastian and Mannapperuma, Chanaka and Prestele, Jakob and Nilsson, Ove and Street, Nathaniel R. and Tuominen, Hannele},
	month = apr,
	year = {2018},
	pages = {2851--2870},
}

@article{reza_transcriptome_2018,
	title = {Transcriptome analysis of embryonic domains in {Norway} spruce reveals potential regulators of suspensor cell death},
	volume = {13},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0192945},
	doi = {10/gc8wb4},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {PLOS ONE},
	author = {Reza, Salim H. and Delhomme, Nicolas and Street, Nathaniel R. and Ramachandran, Prashanth and Dalman, Kerstin and Nilsson, Ove and Minina, Elena A. and Bozhkov, Peter V.},
	editor = {Sun, Meng-xiang},
	month = mar,
	year = {2018},
	pages = {e0192945},
}

@article{laitinen_key_2017,
	title = {A {Key} {Role} for {Apoplastic} {H2O2} in {Norway} {Spruce} {Phenolic} {Metabolism}},
	volume = {174},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/174/3/1449-1475/6117375},
	doi = {10/gbkxvh},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Laitinen, Teresa and Morreel, Kris and Delhomme, Nicolas and Gauthier, Adrien and Schiffthaler, Bastian and Nickolov, Kaloian and Brader, Günter and Lim, Kean-Jin and Teeri, Teemu H. and Street, Nathaniel R. and Boerjan, Wout and Kärkönen, Anna},
	month = jul,
	year = {2017},
	pages = {1449--1475},
}

@article{sundell_aspwood_2017,
	title = {{AspWood}: {High}-{Spatial}-{Resolution} {Transcriptome} {Profiles} {Reveal} {Uncharacterized} {Modularity} of {Wood} {Formation} in {Populus} tremula},
	volume = {29},
	issn = {1040-4651, 1532-298X},
	shorttitle = {{AspWood}},
	url = {https://academic.oup.com/plcell/article/29/7/1585-1604/6099151},
	doi = {10/gbshnb},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {The Plant Cell},
	author = {Sundell, David and Street, Nathaniel R. and Kumar, Manoj and Mellerowicz, Ewa J. and Kucukoglu, Melis and Johnsson, Christoffer and Kumar, Vikash and Mannapperuma, Chanaka and Delhomme, Nicolas and Nilsson, Ove and Tuominen, Hannele and Pesquet, Edouard and Fischer, Urs and Niittylä, Totte and Sundberg, Björn and Hvidsten, Torgeir R.},
	month = jul,
	year = {2017},
	pages = {1585--1604},
}

@article{schiffthaler_batchmap_2017,
	title = {{BatchMap}: {A} parallel implementation of the {OneMap} {R} package for fast computation of {F1} linkage maps in outcrossing species},
	volume = {12},
	issn = {1932-6203},
	shorttitle = {{BatchMap}},
	url = {https://dx.plos.org/10.1371/journal.pone.0189256},
	doi = {10.1371/journal.pone.0189256},
	language = {en},
	number = {12},
	urldate = {2021-06-07},
	journal = {PLOS ONE},
	author = {Schiffthaler, Bastian and Bernhardsson, Carolina and Ingvarsson, Pär K. and Street, Nathaniel R.},
	editor = {Candela, Hector},
	month = dec,
	year = {2017},
	pages = {e0189256},
}

@article{mahler_gene_2017,
	title = {Gene co-expression network connectivity is an important determinant of selective constraint},
	volume = {13},
	issn = {1553-7404},
	url = {https://dx.plos.org/10.1371/journal.pgen.1006402},
	doi = {10.1371/journal.pgen.1006402},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {PLOS Genetics},
	author = {Mähler, Niklas and Wang, Jing and Terebieniec, Barbara K. and Ingvarsson, Pär K. and Street, Nathaniel R. and Hvidsten, Torgeir R.},
	editor = {Springer, Nathan M.},
	month = apr,
	year = {2017},
	pages = {e1006402},
}

@article{sullivan_interspecific_2017,
	title = {Interspecific {Plastome} {Recombination} {Reflects} {Ancient} {Reticulate} {Evolution} in {Picea} ({Pinaceae})},
	volume = {34},
	issn = {0737-4038, 1537-1719},
	url = {https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msx111},
	doi = {10.1093/molbev/msx111},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {Molecular Biology and Evolution},
	author = {Sullivan, Alexis R. and Schiffthaler, Bastian and Thompson, Stacey Lee and Street, Nathaniel R. and Wang, Xiao-Ru},
	month = jul,
	year = {2017},
	pages = {1689--1701},
}

@article{norman_landscape_2017,
	title = {Landscape relatedness: detecting contemporary fine-scale spatial structure in wild populations},
	volume = {32},
	issn = {0921-2973, 1572-9761},
	shorttitle = {Landscape relatedness},
	url = {http://link.springer.com/10.1007/s10980-016-0434-2},
	doi = {10.1007/s10980-016-0434-2},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Landscape Ecology},
	author = {Norman, Anita J. and Stronen, Astrid V. and Fuglstad, Geir-Arne and Ruiz-Gonzalez, Aritz and Kindberg, Jonas and Street, Nathaniel R. and Spong, Göran},
	month = jan,
	year = {2017},
	pages = {181--194},
}

@article{jokipiilukkari_norwood_2017,
	title = {{NorWood}: a gene expression resource for evo‐devo studies of conifer wood development},
	volume = {216},
	issn = {0028-646X, 1469-8137},
	shorttitle = {{NorWood}},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.14458},
	doi = {10.1111/nph.14458},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Jokipii‐Lukkari, Soile and Sundell, David and Nilsson, Ove and Hvidsten, Torgeir R. and Street, Nathaniel R. and Tuominen, Hannele},
	month = oct,
	year = {2017},
	pages = {482--494},
}

@article{giacomello_spatially_2017,
	title = {Spatially resolved transcriptome profiling in model plant species},
	volume = {3},
	issn = {2055-0278},
	url = {http://www.nature.com/articles/nplants201761},
	doi = {10.1038/nplants.2017.61},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Nature Plants},
	author = {Giacomello, Stefania and Salmén, Fredrik and Terebieniec, Barbara K. and Vickovic, Sanja and Navarro, José Fernandez and Alexeyenko, Andrey and Reimegård, Johan and McKee, Lauren S. and Mannapperuma, Chanaka and Bulone, Vincent and Ståhl, Patrik L. and Sundström, Jens F. and Street, Nathaniel R. and Lundeberg, Joakim},
	month = jun,
	year = {2017},
	pages = {17061},
}

@article{immanen_cytokinin_2016,
	title = {Cytokinin and {Auxin} {Display} {Distinct} but {Interconnected} {Distribution} and {Signaling} {Profiles} to {Stimulate} {Cambial} {Activity}},
	volume = {26},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982216305504},
	doi = {10/f82nd5},
	language = {en},
	number = {15},
	urldate = {2021-06-07},
	journal = {Current Biology},
	author = {Immanen, Juha and Nieminen, Kaisa and Smolander, Olli-Pekka and Kojima, Mikiko and Alonso Serra, Juan and Koskinen, Patrik and Zhang, Jing and Elo, Annakaisa and Mähönen, Ari Pekka and Street, Nathaniel and Bhalerao, Rishikesh P. and Paulin, Lars and Auvinen, Petri and Sakakibara, Hitoshi and Helariutta, Ykä},
	month = aug,
	year = {2016},
	pages = {1990--1997},
}

@article{ausin_dna_2016,
	title = {{DNA} methylome of the 20-gigabase {Norway} spruce genome},
	volume = {113},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1618019113},
	doi = {10.1073/pnas.1618019113},
	abstract = {DNA methylation plays important roles in many biological processes, such as silencing of transposable elements, imprinting, and regulating gene expression. Many studies of DNA methylation have shown its essential roles in angiosperms (flowering plants). However, few studies have examined the roles and patterns of DNA methylation in gymnosperms. Here, we present genome-wide high coverage single-base resolution methylation maps of Norway spruce (
              Picea abies
              ) from both needles and somatic embryogenesis culture cells via whole genome bisulfite sequencing. On average, DNA methylation levels of CG and CHG of Norway spruce were higher than most other plants studied. CHH methylation was found at a relatively low level; however, at least one copy of most of the RNA-directed DNA methylation pathway genes was found in Norway spruce, and CHH methylation was correlated with levels of siRNAs. In comparison with needles, somatic embryogenesis culture cells that are used for clonally propagating spruce trees showed lower levels of CG and CHG methylation but higher level of CHH methylation, suggesting that like in other species, these culture cells show abnormal methylation patterns.},
	language = {en},
	number = {50},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Ausin, Israel and Feng, Suhua and Yu, Chaowei and Liu, Wanlu and Kuo, Hsuan Yu and Jacobsen, Elise L. and Zhai, Jixian and Gallego-Bartolome, Javier and Wang, Lin and Egertsdotter, Ulrika and Street, Nathaniel R. and Jacobsen, Steven E. and Wang, Haifeng},
	month = dec,
	year = {2016},
	pages = {E8106--E8113},
}

DNA methylation plays important roles in many biological processes, such as silencing of transposable elements, imprinting, and regulating gene expression. Many studies of DNA methylation have shown its essential roles in angiosperms (flowering plants). However, few studies have examined the roles and patterns of DNA methylation in gymnosperms. Here, we present genome-wide high coverage single-base resolution methylation maps of Norway spruce ( Picea abies ) from both needles and somatic embryogenesis culture cells via whole genome bisulfite sequencing. On average, DNA methylation levels of CG and CHG of Norway spruce were higher than most other plants studied. CHH methylation was found at a relatively low level; however, at least one copy of most of the RNA-directed DNA methylation pathway genes was found in Norway spruce, and CHH methylation was correlated with levels of siRNAs. In comparison with needles, somatic embryogenesis culture cells that are used for clonally propagating spruce trees showed lower levels of CG and CHG methylation but higher level of CHH methylation, suggesting that like in other species, these culture cells show abnormal methylation patterns.

@article{wang_natural_2016,
	title = {Natural {Selection} and {Recombination} {Rate} {Variation} {Shape} {Nucleotide} {Polymorphism} {Across} the {Genomes} of {Three} {Related} {Populus} {Species}},
	volume = {202},
	issn = {1943-2631},
	url = {https://academic.oup.com/genetics/article/202/3/1185/5930198},
	doi = {10.1534/genetics.115.183152},
	abstract = {Abstract
            A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome resequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, and population-scaled recombination rates in three species of Populus: Populus tremula, P. tremuloides, and P. trichocarpa. We find that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies, and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, due to both purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. The present work provides the first phylogenetic comparative study on a genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species.},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Genetics},
	author = {Wang, Jing and Street, Nathaniel R and Scofield, Douglas G and Ingvarsson, Pär K},
	month = mar,
	year = {2016},
	pages = {1185--1200},
}

Abstract A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome resequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, and population-scaled recombination rates in three species of Populus: Populus tremula, P. tremuloides, and P. trichocarpa. We find that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies, and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, due to both purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. The present work provides the first phylogenetic comparative study on a genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species.

@article{ingvarsson_towards_2016,
	title = {Towards integration of population and comparative genomics in forest trees},
	volume = {212},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.14153},
	doi = {10/f3tpmx},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Ingvarsson, Pär K. and Hvidsten, Torgeir R. and Street, Nathaniel R.},
	month = oct,
	year = {2016},
	pages = {338--344},
}

@article{liu_resource_2015,
	title = {A resource for characterizing genome-wide binding and putative target genes of transcription factors expressed during secondary growth and wood formation in {Populus}},
	volume = {82},
	issn = {1365-313X (Electronic) 0960-7412 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25903933},
	doi = {10.1111/tpj.12850},
	abstract = {Identifying transcription factor target genes is essential for modeling the transcriptional networks underlying developmental processes. Here we report a chromatin immunoprecipitation sequencing (ChIP-seq) resource consisting of genome-wide binding regions and associated putative target genes for four Populus homeodomain transcription factors expressed during secondary growth and wood formation. Software code (programs and scripts) for processing the Populus ChIP-seq data are provided within a publically available iPlant image, including tools for ChIP-seq data quality control and evaluation adapted from the human Encyclopedia of DNA Elements (ENCODE) project. Basic information for each transcription factor (including members of Class I KNOX, Class III HD ZIP, BEL1-like families) binding are summarized, including the number and location of binding regions, distribution of binding regions relative to gene features, associated putative target genes, and enriched functional categories of putative target genes. These ChIP-seq data have been integrated within the Populus Genome Integrative Explorer (PopGenIE) where they can be analyzed using a variety of web-based tools. We present an example analysis that shows preferential binding of transcription factor ARBORKNOX1 to the nearest neighbor genes in a pre-calculated co-expression network module, and enrichment for meristem-related genes within this module including multiple orthologs of Arabidopsis KNOTTED-like Arabidopsis 2/6.},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Plant J},
	author = {Liu, L. and Ramsay, T. and Zinkgraf, M. and Sundell, D. and Street, N. R. and Filkov, V. and Groover, A.},
	month = jun,
	year = {2015},
	note = {Edition: 2015/04/24},
	keywords = {Amino Acid Sequence, Binding Sites, Chromatin Immunoprecipitation, Gene Expression Profiling/methods, Gene Expression Regulation, Plant, Gene Regulatory Networks, Genome, Plant, Image Processing, Computer-Assisted, Molecular Sequence Data, Plant Proteins/*genetics/metabolism, Populus trichocarpa, Populus/*genetics/growth \& development, Transcription Factors/genetics/*metabolism, Wood/genetics/*growth \& development, Workflow, cambium, chromatin immunoprecipitation sequencing, secondary growth, transcription factor, wood formation},
	pages = {887--98},
}

Identifying transcription factor target genes is essential for modeling the transcriptional networks underlying developmental processes. Here we report a chromatin immunoprecipitation sequencing (ChIP-seq) resource consisting of genome-wide binding regions and associated putative target genes for four Populus homeodomain transcription factors expressed during secondary growth and wood formation. Software code (programs and scripts) for processing the Populus ChIP-seq data are provided within a publically available iPlant image, including tools for ChIP-seq data quality control and evaluation adapted from the human Encyclopedia of DNA Elements (ENCODE) project. Basic information for each transcription factor (including members of Class I KNOX, Class III HD ZIP, BEL1-like families) binding are summarized, including the number and location of binding regions, distribution of binding regions relative to gene features, associated putative target genes, and enriched functional categories of putative target genes. These ChIP-seq data have been integrated within the Populus Genome Integrative Explorer (PopGenIE) where they can be analyzed using a variety of web-based tools. We present an example analysis that shows preferential binding of transcription factor ARBORKNOX1 to the nearest neighbor genes in a pre-calculated co-expression network module, and enrichment for meristem-related genes within this module including multiple orthologs of Arabidopsis KNOTTED-like Arabidopsis 2/6.

@article{soolanayakanahally_comparative_2015,
	title = {Comparative physiology of allopatric {Populus} species: geographic clines in photosynthesis, height growth, and carbon isotope discrimination in common gardens},
	volume = {6},
	issn = {1664-462X (Print) 1664-462X (Linking)},
	shorttitle = {Comparative physiology of allopatric {Populus} species},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26236324},
	doi = {10.3389/fpls.2015.00528},
	abstract = {Populus species with wide geographic ranges display strong adaptation to local environments. We studied the clinal patterns in phenology and ecophysiology in allopatric Populus species adapted to similar environments on different continents under common garden settings. As a result of climatic adaptation, both Populus tremula L. and Populus balsamifera L. display latitudinal clines in photosynthetic rates (A), whereby high-latitude trees of P. tremula had higher A compared to low-latitude trees and nearly so in P. balsamifera (p = 0.06). Stomatal conductance (g s) and chlorophyll content index (CCI) follow similar latitudinal trends. However, foliar nitrogen was positively correlated with latitude in P. balsamifera and negatively correlated in P. tremula. No significant trends in carbon isotope composition of the leaf tissue (delta(13)C) were observed for both species; but, intrinsic water-use efficiency (WUEi) was negatively correlated with the latitude of origin in P. balsamifera. In spite of intrinsically higher A, high-latitude trees in both common gardens accomplished less height gain as a result of early bud set. Thus, shoot biomass was determined by height elongation duration (HED), which was well approximated by the number of days available for free growth between bud flush and bud set. We highlight the shortcoming of unreplicated outdoor common gardens for tree improvement and the crucial role of photoperiod in limiting height growth, further complicating interpretation of other secondary effects.},
	language = {English},
	urldate = {2021-06-07},
	journal = {Front Plant Sci},
	author = {Soolanayakanahally, R. Y. and Guy, R. D. and Street, N. R. and Robinson, K. M. and Silim, S. N. and Albrectsen, B. R. and Jansson, S.},
	year = {2015},
	note = {Edition: 2015/08/04},
	keywords = {Photosynthesis, bud set, carbon isotope discrimination, common garden, comparative physiology, latitude, photosynthesis, poplar, water-use efficiency},
	pages = {528},
}

Populus species with wide geographic ranges display strong adaptation to local environments. We studied the clinal patterns in phenology and ecophysiology in allopatric Populus species adapted to similar environments on different continents under common garden settings. As a result of climatic adaptation, both Populus tremula L. and Populus balsamifera L. display latitudinal clines in photosynthetic rates (A), whereby high-latitude trees of P. tremula had higher A compared to low-latitude trees and nearly so in P. balsamifera (p = 0.06). Stomatal conductance (g s) and chlorophyll content index (CCI) follow similar latitudinal trends. However, foliar nitrogen was positively correlated with latitude in P. balsamifera and negatively correlated in P. tremula. No significant trends in carbon isotope composition of the leaf tissue (delta(13)C) were observed for both species; but, intrinsic water-use efficiency (WUEi) was negatively correlated with the latitude of origin in P. balsamifera. In spite of intrinsically higher A, high-latitude trees in both common gardens accomplished less height gain as a result of early bud set. Thus, shoot biomass was determined by height elongation duration (HED), which was well approximated by the number of days available for free growth between bud flush and bud set. We highlight the shortcoming of unreplicated outdoor common gardens for tree improvement and the crucial role of photoperiod in limiting height growth, further complicating interpretation of other secondary effects.

@article{delhomme_serendipitous_2015,
	title = {Serendipitous {Meta}-{Transcriptomics}: {The} {Fungal} {Community} of {Norway} {Spruce} ({Picea} abies)},
	volume = {10},
	issn = {1932-6203 (Electronic) 1932-6203 (Linking)},
	shorttitle = {Serendipitous {Meta}-{Transcriptomics}},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26413905},
	doi = {10/f3m8d5},
	abstract = {After performing de novo transcript assembly of {\textgreater}1 billion RNA-Sequencing reads obtained from 22 samples of different Norway spruce (Picea abies) tissues that were not surface sterilized, we found that assembled sequences captured a mix of plant, lichen, and fungal transcripts. The latter were likely expressed by endophytic and epiphytic symbionts, indicating that these organisms were present, alive, and metabolically active. Here, we show that these serendipitously sequenced transcripts need not be considered merely as contamination, as is common, but that they provide insight into the plant's phyllosphere. Notably, we could classify these transcripts as originating predominantly from Dothideomycetes and Leotiomycetes species, with functional annotation of gene families indicating active growth and metabolism, with particular regards to glucose intake and processing, as well as gene regulation.},
	language = {en},
	number = {9},
	urldate = {2021-06-07},
	journal = {PLoS One},
	author = {Delhomme, N. and Sundstrom, G. and Zamani, N. and Lantz, H. and Lin, Y. C. and Hvidsten, T. R. and Hoppner, M. P. and Jern, P. and Van de Peer, Y. and Lundeberg, J. and Grabherr, M. G. and Street, N. R.},
	month = sep,
	year = {2015},
	note = {Edition: 2015/09/29},
	keywords = {Base Composition/genetics, Fungi/*genetics, Gene Expression Regulation, Fungal, Gene Expression Regulation, Plant, Picea/*genetics/*microbiology, RNA, Messenger/genetics/metabolism, Transcriptome/*genetics},
	pages = {e0139080},
}

After performing de novo transcript assembly of \textgreater1 billion RNA-Sequencing reads obtained from 22 samples of different Norway spruce (Picea abies) tissues that were not surface sterilized, we found that assembled sequences captured a mix of plant, lichen, and fungal transcripts. The latter were likely expressed by endophytic and epiphytic symbionts, indicating that these organisms were present, alive, and metabolically active. Here, we show that these serendipitously sequenced transcripts need not be considered merely as contamination, as is common, but that they provide insight into the plant's phyllosphere. Notably, we could classify these transcripts as originating predominantly from Dothideomycetes and Leotiomycetes species, with functional annotation of gene families indicating active growth and metabolism, with particular regards to glucose intake and processing, as well as gene regulation.

@article{sundell_plant_2015,
	title = {The {Plant} {Genome} {Integrative} {Explorer} {Resource}: {PlantGenIE}.org},
	volume = {208},
	issn = {1469-8137 (Electronic) 0028-646X (Linking)},
	shorttitle = {The {Plant} {Genome} {Integrative} {Explorer} {Resource}},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26192091},
	doi = {10.1111/nph.13557},
	abstract = {Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training. We present the integrated PlantGenIE.org platform for exploration of Populus, conifer and Arabidopsis genomics data, which includes expression networks and associated visualization tools. Standard features of a model organism database are provided, including genome browsers, gene list annotation, Blast homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo. We have produced an RNA-sequencing (RNA-Seq) expression atlas for Populus tremula and have integrated these data within the expression tools. An updated version of the ComPlEx resource for performing comparative plant expression analyses of gene coexpression network conservation between species has also been integrated. The PlantGenIE.org platform provides intuitive access to large-scale and genome-wide genomics data from model forest tree species, facilitating both community contributions to annotation improvement and tools supporting use of the included data resources to inform biological insight.},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {New Phytol},
	author = {Sundell, D. and Mannapperuma, C. and Netotea, S. and Delhomme, N. and Lin, Y. C. and Sjodin, A. and Van de Peer, Y. and Jansson, S. and Hvidsten, T. R. and Street, N. R.},
	month = dec,
	year = {2015},
	note = {Edition: 2015/07/21},
	keywords = {*Databases, Factual, *Genes, Plant, *Genome, Plant, Arabidopsis/*genetics, Computational Biology, Forests, Gene Expression, Genomics/methods, Internet, Models, Biological, Populus, Populus/*genetics, RNA, Plant, Sequence Analysis, DNA, Tracheophyta/*genetics, Trees/*genetics, annotation, coexpression, conifer, database, genome browser, transcriptomics, web resource},
	pages = {1149--56},
}

Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training. We present the integrated PlantGenIE.org platform for exploration of Populus, conifer and Arabidopsis genomics data, which includes expression networks and associated visualization tools. Standard features of a model organism database are provided, including genome browsers, gene list annotation, Blast homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo. We have produced an RNA-sequencing (RNA-Seq) expression atlas for Populus tremula and have integrated these data within the expression tools. An updated version of the ComPlEx resource for performing comparative plant expression analyses of gene coexpression network conservation between species has also been integrated. The PlantGenIE.org platform provides intuitive access to large-scale and genome-wide genomics data from model forest tree species, facilitating both community contributions to annotation improvement and tools supporting use of the included data resources to inform biological insight.

@techreport{wang_variation_2015,
	type = {preprint},
	title = {Variation in linked selection and recombination drive genomic divergence during allopatric speciation of {European} and {American} aspens},
	url = {http://biorxiv.org/lookup/doi/10.1101/029561},
	abstract = {Abstract
          
            Despite the global economic and ecological importance of forest trees, the genomic basis of differential adaptation and speciation in tree species is still poorly understood.
            Populus tremula
            and
            P. tremuloides
            are two of the most widespread tree species in the Northern Hemisphere. Using whole-genome re-sequencing data of 24
            P. tremula
            and 22
            P. tremuloides
            individuals, we find that the two species diverged ∼2.2-3.1 million years ago, coinciding with the severing of the Bering land bridge and the onset of dramatic climatic oscillations during the Pleistocene. Both species have experienced substantial population expansions following long-term declines after species divergence. We detect widespread and heterogeneous genomic differentiation between species, and in accordance with the expectation of allopatric speciation, coalescent simulations suggest that neutral evolutionary processes can account for most of the observed patterns of genomic differentiation. However, there is an excess of regions exhibiting extreme differentiation relative to those expected under demographic simulations, which is indicative of the action of natural selection. Overall genetic differentiation is negatively associated with recombination rate in both species, providing strong support for a role of linked selection in generating the heterogeneous genomic landscape of differentiation between species. Finally, we identify a number of candidate regions and genes that may have been subject to positive and/or balancing selection during the speciation process.},
	language = {en},
	urldate = {2021-06-07},
	institution = {Evolutionary Biology},
	author = {Wang, Jing and Street, Nathaniel R. and Scofield, Douglas G. and Ingvarsson, Pär K.},
	month = oct,
	year = {2015},
	doi = {10.1101/029561},
}

Abstract Despite the global economic and ecological importance of forest trees, the genomic basis of differential adaptation and speciation in tree species is still poorly understood. Populus tremula and P. tremuloides are two of the most widespread tree species in the Northern Hemisphere. Using whole-genome re-sequencing data of 24 P. tremula and 22 P. tremuloides individuals, we find that the two species diverged ∼2.2-3.1 million years ago, coinciding with the severing of the Bering land bridge and the onset of dramatic climatic oscillations during the Pleistocene. Both species have experienced substantial population expansions following long-term declines after species divergence. We detect widespread and heterogeneous genomic differentiation between species, and in accordance with the expectation of allopatric speciation, coalescent simulations suggest that neutral evolutionary processes can account for most of the observed patterns of genomic differentiation. However, there is an excess of regions exhibiting extreme differentiation relative to those expected under demographic simulations, which is indicative of the action of natural selection. Overall genetic differentiation is negatively associated with recombination rate in both species, providing strong support for a role of linked selection in generating the heterogeneous genomic landscape of differentiation between species. Finally, we identify a number of candidate regions and genes that may have been subject to positive and/or balancing selection during the speciation process.

@article{netotea_complex_2014,
	title = {{ComPlEx}: conservation and divergence of co-expression networks in {A}. thaliana, {Populus} and {O}. sativa},
	volume = {15},
	issn = {1471-2164},
	shorttitle = {{ComPlEx}},
	url = {http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-106},
	doi = {10/f23r6f},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Genomics},
	author = {Netotea, Sergiu and Sundell, David and Street, Nathaniel R and Hvidsten, Torgeir R},
	year = {2014},
	pages = {106},
}

@article{de_la_torre_insights_2014,
	title = {Insights into {Conifer} {Giga}-{Genomes}},
	volume = {166},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/166/4/1724-1732/6113514},
	doi = {10/f25hfn},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {De La Torre, Amanda R. and Birol, Inanc and Bousquet, Jean and Ingvarsson, Pär K. and Jansson, Stefan and Jones, Steven J.M. and Keeling, Christopher I. and MacKay, John and Nilsson, Ove and Ritland, Kermit and Street, Nathaniel and Yanchuk, Alvin and Zerbe, Philipp and Bohlmann, Jörg},
	month = dec,
	year = {2014},
	pages = {1724--1732},
}

@article{robinson_populus_2014,
	title = {Populus tremula ({European} aspen) shows no evidence of sexual dimorphism},
	volume = {14},
	issn = {1471-2229},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-014-0276-5},
	doi = {10/f25brv},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Plant Biology},
	author = {Robinson, Kathryn M and Delhomme, Nicolas and Mähler, Niklas and Schiffthaler, Bastian and Önskog, Jenny and Albrectsen, Benedicte R and Ingvarsson, Pär K and Hvidsten, Torgeir R and Jansson, Stefan and Street, Nathaniel R},
	month = dec,
	year = {2014},
	pages = {276},
}

@article{norman_novo_2013,
	title = {De {Novo} {SNP} {Discovery} in the {Scandinavian} {Brown} {Bear} ({Ursus} arctos)},
	volume = {8},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0081012},
	doi = {10/f23hc8},
	language = {en},
	number = {11},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Norman, Anita J. and Street, Nathaniel R. and Spong, Göran},
	editor = {Caramelli, David},
	month = nov,
	year = {2013},
	pages = {e81012},
}

@article{lafonplacette_methylome_2013,
	title = {Methylome of {DNase} {I} sensitive chromatin in {Populus} trichocarpa shoot apical meristematic cells: a simplified approach revealing characteristics of gene-body {DNA} methylation in open chromatin state},
	volume = {197},
	issn = {0028-646X, 1469-8137},
	shorttitle = {Methylome of {\textless}span style="font-variant},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.12026},
	doi = {10/f22v74},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Lafon‐Placette, Clément and Faivre‐Rampant, Patricia and Delaunay, Alain and Street, Nathaniel and Brignolas, Franck and Maury, Stéphane},
	month = jan,
	year = {2013},
	pages = {416--430},
}

@article{nystedt_norway_2013,
	title = {The {Norway} spruce genome sequence and conifer genome evolution},
	volume = {497},
	issn = {0028-0836, 1476-4687},
	url = {http://www.nature.com/articles/nature12211},
	doi = {10/f2zsx6},
	language = {en},
	number = {7451},
	urldate = {2021-06-08},
	journal = {Nature},
	author = {Nystedt, Björn and Street, Nathaniel R. and Wetterbom, Anna and Zuccolo, Andrea and Lin, Yao-Cheng and Scofield, Douglas G. and Vezzi, Francesco and Delhomme, Nicolas and Giacomello, Stefania and Alexeyenko, Andrey and Vicedomini, Riccardo and Sahlin, Kristoffer and Sherwood, Ellen and Elfstrand, Malin and Gramzow, Lydia and Holmberg, Kristina and Hällman, Jimmie and Keech, Olivier and Klasson, Lisa and Koriabine, Maxim and Kucukoglu, Melis and Käller, Max and Luthman, Johannes and Lysholm, Fredrik and Niittylä, Totte and Olson, Åke and Rilakovic, Nemanja and Ritland, Carol and Rosselló, Josep A. and Sena, Juliana and Svensson, Thomas and Talavera-López, Carlos and Theißen, Günter and Tuominen, Hannele and Vanneste, Kevin and Wu, Zhi-Qiang and Zhang, Bo and Zerbe, Philipp and Arvestad, Lars and Bhalerao, Rishikesh P. and Bohlmann, Joerg and Bousquet, Jean and Garcia Gil, Rosario and Hvidsten, Torgeir R. and de Jong, Pieter and MacKay, John and Morgante, Michele and Ritland, Kermit and Sundberg, Björn and Lee Thompson, Stacey and Van de Peer, Yves and Andersson, Björn and Nilsson, Ove and Ingvarsson, Pär K. and Lundeberg, Joakim and Jansson, Stefan},
	month = may,
	year = {2013},
	pages = {579--584},
}

@article{pacurar_collection_2012,
	title = {A collection of {INDEL} markers for map-based cloning in seven {Arabidopsis} accessions},
	volume = {63},
	issn = {1460-2431, 0022-0957},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/err422},
	doi = {10/fxrh28},
	language = {en},
	number = {7},
	urldate = {2021-06-08},
	journal = {Journal of Experimental Botany},
	author = {Păcurar, Daniel Ioan and Păcurar, Monica Lăcrămioara and Street, Nathaniel and Bussell, John Desmond and Pop, Tiberia Ioana and Gutierrez, Laurent and Bellini, Catherine},
	month = apr,
	year = {2012},
	pages = {2491--2501},
}

@article{sahlin_improved_2012,
	title = {Improved gap size estimation for scaffolding algorithms},
	volume = {28},
	issn = {1460-2059, 1367-4803},
	url = {https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/bts441},
	doi = {10/f2zsch},
	language = {en},
	number = {17},
	urldate = {2021-06-08},
	journal = {Bioinformatics},
	author = {Sahlin, Kristoffer and Street, Nathaniel and Lundeberg, Joakim and Arvestad, Lars},
	month = sep,
	year = {2012},
	pages = {2215--2222},
}

@article{xue_paramutation-like_2012,
	title = {Paramutation-{Like} {Interaction} of {T}-{DNA} {Loci} in {Arabidopsis}},
	volume = {7},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0051651},
	doi = {10/f22djh},
	language = {en},
	number = {12},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Xue, Weiya and Ruprecht, Colin and Street, Nathaniel and Hematy, Kian and Chang, Christine and Frommer, Wolf B. and Persson, Staffan and Niittylä, Totte},
	editor = {Schiefelbein, John},
	month = dec,
	year = {2012},
	pages = {e51651},
}

@article{tuskan_obscure_2012,
	title = {The obscure events contributing to the evolution of an incipient sex chromosome in {Populus}: a retrospective working hypothesis},
	volume = {8},
	issn = {1614-2950},
	shorttitle = {The obscure events contributing to the evolution of an incipient sex chromosome in {Populus}},
	url = {https://doi.org/10.1007/s11295-012-0495-6},
	doi = {10/f24dvz},
	abstract = {Genetic determination of gender is a fundamental developmental and evolutionary process in plants. Although it appears that dioecy in Populus is genetically controlled, the precise gender-determining systems remain unclear. The recently released second draft assembly and annotated gene set of the Populus genome provided an opportunity to revisit this topic. We hypothesized that over evolutionary time, selective pressure has reformed the genome structure and gene composition in the peritelomeric region of the chromosome XIX, which has resulted in a distinctive genome structure and cluster of genes contributing to gender determination in Populus trichocarpa. Multiple lines of evidence support this working hypothesis. First, the peritelomeric region of the chromosome XIX contains significantly fewer single nucleotide polymorphisms than the rest of Populus genome and has a distinct evolutionary history. Second, the peritelomeric end of chromosome XIX contains the largest cluster of the nucleotide-binding site–leucine-rich repeat (NBS–LRR) class of disease resistance genes in the entire Populus genome. Third, there is a high occurrence of small microRNAs on chromosome XIX, which is coincident to the region containing the putative gender-determining locus and the major cluster of NBS–LRR genes. Further, by analyzing the metabolomic profiles of floral bud in male and female Populus trees using a gas chromatography-mass spectrometry, we found that there are gender-specific accumulations of phenolic glycosides. Taken together, these findings led to the hypothesis that resistance to and regulation of a floral pathogen and gender determination coevolved, and that these events triggered the emergence of a nascent sex chromosome. Further studies of chromosome XIX will provide new insights into the genetic control of gender determination in Populus.},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Tree Genetics \& Genomes},
	author = {Tuskan, Gerald A. and DiFazio, Steve and Faivre-Rampant, Patricia and Gaudet, Muriel and Harfouche, Antoine and Jorge, Véronique and Labbé, Jessy L. and Ranjan, Priya and Sabatti, Maurizio and Slavov, Gancho and Street, Nathaniel and Tschaplinski, Timothy J. and Yin, Tongming},
	month = jun,
	year = {2012},
	pages = {559--571},
}

Genetic determination of gender is a fundamental developmental and evolutionary process in plants. Although it appears that dioecy in Populus is genetically controlled, the precise gender-determining systems remain unclear. The recently released second draft assembly and annotated gene set of the Populus genome provided an opportunity to revisit this topic. We hypothesized that over evolutionary time, selective pressure has reformed the genome structure and gene composition in the peritelomeric region of the chromosome XIX, which has resulted in a distinctive genome structure and cluster of genes contributing to gender determination in Populus trichocarpa. Multiple lines of evidence support this working hypothesis. First, the peritelomeric region of the chromosome XIX contains significantly fewer single nucleotide polymorphisms than the rest of Populus genome and has a distinct evolutionary history. Second, the peritelomeric end of chromosome XIX contains the largest cluster of the nucleotide-binding site–leucine-rich repeat (NBS–LRR) class of disease resistance genes in the entire Populus genome. Third, there is a high occurrence of small microRNAs on chromosome XIX, which is coincident to the region containing the putative gender-determining locus and the major cluster of NBS–LRR genes. Further, by analyzing the metabolomic profiles of floral bud in male and female Populus trees using a gas chromatography-mass spectrometry, we found that there are gender-specific accumulations of phenolic glycosides. Taken together, these findings led to the hypothesis that resistance to and regulation of a floral pathogen and gender determination coevolved, and that these events triggered the emergence of a nascent sex chromosome. Further studies of chromosome XIX will provide new insights into the genetic control of gender determination in Populus.

@article{street_systems_2011,
	title = {A systems biology model of the regulatory network in {Populusleaves} reveals interacting regulators and conserved regulation},
	volume = {11},
	issn = {1471-2229},
	url = {https://doi.org/10.1186/1471-2229-11-13},
	doi = {10/dkhmhb},
	abstract = {Green plant leaves have always fascinated biologists as hosts for photosynthesis and providers of basic energy to many food webs. Today, comprehensive databases of gene expression data enable us to apply increasingly more advanced computational methods for reverse-engineering the regulatory network of leaves, and to begin to understand the gene interactions underlying complex emergent properties related to stress-response and development. These new systems biology methods are now also being applied to organisms such as Populus, a woody perennial tree, in order to understand the specific characteristics of these species.},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Plant Biology},
	author = {Street, Nathaniel Robert and Jansson, Stefan and Hvidsten, Torgeir R.},
	month = jan,
	year = {2011},
	keywords = {Biotic Infection, Drought Stress, Nucleosome Assembly, System Biology Model, Transcriptional Module},
	pages = {13},
}

Green plant leaves have always fascinated biologists as hosts for photosynthesis and providers of basic energy to many food webs. Today, comprehensive databases of gene expression data enable us to apply increasingly more advanced computational methods for reverse-engineering the regulatory network of leaves, and to begin to understand the gene interactions underlying complex emergent properties related to stress-response and development. These new systems biology methods are now also being applied to organisms such as Populus, a woody perennial tree, in order to understand the specific characteristics of these species.

@article{ingvarsson_association_2011,
	title = {Association genetics of complex traits in plants},
	volume = {189},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2010.03593.x},
	doi = {10/c2w6s3},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Ingvarsson, Pär K. and Street, Nathaniel R.},
	month = mar,
	year = {2011},
	pages = {909--922},
}

@article{rae_five_2009,
	title = {Five {QTL} hotspots for yield in short rotation coppice bioenergy poplar: {The} {Poplar} {Biomass} {Loci}},
	volume = {9},
	copyright = {2009 Rae et al; licensee BioMed Central Ltd.},
	issn = {1471-2229},
	shorttitle = {Five {QTL} hotspots for yield in short rotation coppice bioenergy poplar},
	url = {https://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-9-23},
	doi = {10/dj94rg},
	abstract = {Concern over land use for non-food bioenergy crops requires breeding programmes that focus on producing biomass on the minimum amount of land that is economically-viable. To achieve this, the maximum potential yield per hectare is a key target for improvement. For long lived tree species, such as poplar, this requires an understanding of the traits that contribute to biomass production and their genetic control. An important aspect of this for long lived plants is an understanding of genetic interactions at different developmental stages, i.e. how genes or genetic regions impact on yield over time. QTL mapping identified regions of genetic control for biomass yield. We mapped consistent QTL across multiple coppice cycles and identified five robust QTL hotspots on linkage groups III, IV, X, XIV and XIX, calling these 'Poplar Biomass Loci' (PBL 1–5). In total 20\% of the variation in final harvest biomass yield was explained by mapped QTL. We also investigated the genetic correlations between yield related traits to identify 'early diagnostic' indicators of yield showing that early biomass was a reasonable predictor of coppice yield and that leaf size, cell number and stem and sylleptic branch number were also valuable traits. These findings provide insight into the genetic control of biomass production and correlation to 'early diagnostic' traits determining yield in poplar SRC for bioenergy. QTL hotspots serve as useful targets for directed breeding for improved biomass productivity that may also be relevant across additional poplar hybrids.},
	language = {en},
	number = {1},
	urldate = {2021-08-20},
	journal = {BMC Plant Biology},
	author = {Rae, Anne M. and Street, Nathaniel Robert and Robinson, Kathryn Megan and Harris, Nicole and Taylor, Gail},
	month = dec,
	year = {2009},
	note = {Number: 1
Publisher: BioMed Central},
	keywords = {Biomass Yield, Linkage Group VIIIa, Short Rotation Coppice, Stem Number, Sylleptic Branch},
	pages = {1--13},
}

Concern over land use for non-food bioenergy crops requires breeding programmes that focus on producing biomass on the minimum amount of land that is economically-viable. To achieve this, the maximum potential yield per hectare is a key target for improvement. For long lived tree species, such as poplar, this requires an understanding of the traits that contribute to biomass production and their genetic control. An important aspect of this for long lived plants is an understanding of genetic interactions at different developmental stages, i.e. how genes or genetic regions impact on yield over time. QTL mapping identified regions of genetic control for biomass yield. We mapped consistent QTL across multiple coppice cycles and identified five robust QTL hotspots on linkage groups III, IV, X, XIV and XIX, calling these 'Poplar Biomass Loci' (PBL 1–5). In total 20% of the variation in final harvest biomass yield was explained by mapped QTL. We also investigated the genetic correlations between yield related traits to identify 'early diagnostic' indicators of yield showing that early biomass was a reasonable predictor of coppice yield and that leaf size, cell number and stem and sylleptic branch number were also valuable traits. These findings provide insight into the genetic control of biomass production and correlation to 'early diagnostic' traits determining yield in poplar SRC for bioenergy. QTL hotspots serve as useful targets for directed breeding for improved biomass productivity that may also be relevant across additional poplar hybrids.

@article{klevebring_genome-wide_2009,
	title = {Genome-wide profiling of populus small {RNAs}},
	volume = {10},
	issn = {1471-2164},
	doi = {10/d7t35k},
	abstract = {BACKGROUND: Short RNAs, and in particular microRNAs, are important regulators of gene expression both within defined regulatory pathways and at the epigenetic scale. We investigated the short RNA (sRNA) population (18-24 nt) of the transcriptome of green leaves from the sequenced Populus trichocarpa using a concatenation strategy in combination with 454 sequencing.
RESULTS: The most abundant size class of sRNAs were 24 nt. Long Terminal Repeats were particularly associated with 24 nt sRNAs. Additionally, some repetitive elements were associated with 22 nt sRNAs. We identified an sRNA hot-spot on chromosome 19, overlapping a region containing both the proposed sex-determining locus and a major cluster of NBS-LRR genes. A number of phased siRNA loci were identified, a subset of which are predicted to target PPR and NBS-LRR disease resistance genes, classes of genes that have been significantly expanded in Populus. Additional loci enriched for sRNA production were identified and characterised. We identified 15 novel predicted microRNAs (miRNAs), including miRNA*sequences, and identified a novel locus that may encode a dual miRNA or a miRNA and short interfering RNAs (siRNAs).
CONCLUSIONS: The short RNA population of P. trichocarpa is at least as complex as that of Arabidopsis thaliana. We provide a first genome-wide view of short RNA production for P. trichocarpa and identify new, non-conserved miRNAs.},
	language = {eng},
	journal = {BMC genomics},
	author = {Klevebring, Daniel and Street, Nathaniel R. and Fahlgren, Noah and Kasschau, Kristin D. and Carrington, James C. and Lundeberg, Joakim and Jansson, Stefan},
	month = dec,
	year = {2009},
	pmid = {20021695},
	pmcid = {PMC2811130},
	keywords = {Chromosomes, Plant, Genome, Plant, Genome-Wide Association Study, MicroRNAs, Plant Leaves, Populus, RNA, Plant, RNA, Small Interfering},
	pages = {620},
}

BACKGROUND: Short RNAs, and in particular microRNAs, are important regulators of gene expression both within defined regulatory pathways and at the epigenetic scale. We investigated the short RNA (sRNA) population (18-24 nt) of the transcriptome of green leaves from the sequenced Populus trichocarpa using a concatenation strategy in combination with 454 sequencing. RESULTS: The most abundant size class of sRNAs were 24 nt. Long Terminal Repeats were particularly associated with 24 nt sRNAs. Additionally, some repetitive elements were associated with 22 nt sRNAs. We identified an sRNA hot-spot on chromosome 19, overlapping a region containing both the proposed sex-determining locus and a major cluster of NBS-LRR genes. A number of phased siRNA loci were identified, a subset of which are predicted to target PPR and NBS-LRR disease resistance genes, classes of genes that have been significantly expanded in Populus. Additional loci enriched for sRNA production were identified and characterised. We identified 15 novel predicted microRNAs (miRNAs), including miRNA*sequences, and identified a novel locus that may encode a dual miRNA or a miRNA and short interfering RNAs (siRNAs). CONCLUSIONS: The short RNA population of P. trichocarpa is at least as complex as that of Arabidopsis thaliana. We provide a first genome-wide view of short RNA production for P. trichocarpa and identify new, non-conserved miRNAs.

@article{sjodin_populus_2009,
	title = {The \textit{{Populus}} {Genome} {Integrative} {Explorer} ({PopGenIE}): a new resource for exploring the \textit{{Populus}} genome},
	volume = {182},
	issn = {0028-646X, 1469-8137},
	shorttitle = {The \textit{{Populus}} {Genome} {Integrative} {Explorer} ({PopGenIE})},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2009.02807.x},
	doi = {10/bwmrwk},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Sjödin, Andreas and Street, Nathaniel Robert and Sandberg, Göran and Gustafsson, Petter and Jansson, Stefan},
	month = jun,
	year = {2009},
	pages = {1013--1025},
}

@article{street_cross-species_2008,
	title = {A cross-species transcriptomics approach to identify genes involved in leaf development},
	volume = {9},
	issn = {1471-2164},
	url = {http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-9-589},
	doi = {10/d5c8qb},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {BMC Genomics},
	author = {Street, Nathaniel and Sjödin, Andreas and Bylesjö, Max and Gustafsson, Petter and Trygg, Johan and Jansson, Stefan},
	year = {2008},
	pages = {589},
}

@article{bylesjo_lamina_2008,
	title = {{LAMINA}: a tool for rapid quantification of leaf size and shape parameters},
	volume = {8},
	issn = {1471-2229},
	shorttitle = {{LAMINA}},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-8-82},
	doi = {10/dg9gsg},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {BMC Plant Biology},
	author = {Bylesjö, Max and Segura, Vincent and Soolanayakanahally, Raju Y and Rae, Anne M and Trygg, Johan and Gustafsson, Petter and Jansson, Stefan and Street, Nathaniel R},
	year = {2008},
	pages = {82},
}

@article{street_genetics_2006,
	title = {The genetics and genomics of the drought response in {Populus}},
	volume = {48},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-313X.2006.02864.x},
	doi = {10/fj53r5},
	abstract = {The genetic nature of tree adaptation to drought stress was examined by utilizing variation in the drought response of a full-sib second generation (F2) mapping population from a cross between Populus trichocarpa (93-968) and P. deltoides Bart (ILL-129) and known to be highly divergent for a vast range of phenotypic traits. We combined phenotyping, quantitative trait loci (QTL) analysis and microarray experiments to demonstrate that ‘genetical genomics’ can be used to provide information on adaptation at the species level. The grandparents and F2 population were subjected to soil drying, and contrasting responses to drought across genotypes, including leaf coloration, expansion and abscission, were observed, and QTL for these traits mapped. A subset of extreme genotypes exhibiting extreme sensitivity and insensitivity to drought on the basis of leaf abscission were defined, and microarray experiments conducted on these genotypes and the grandparent species. The extreme genotype groups induced a different set of genes: 215 and 125 genes differed in their expression response between groups in control and drought, respectively, suggesting species adaptation at the gene expression level. Co-location of differentially expressed genes with drought-specific and drought-responsive QTLs was examined, and these may represent candidate genes contributing to the variation in drought response.},
	language = {en},
	number = {3},
	urldate = {2021-06-11},
	journal = {The Plant Journal},
	author = {Street, Nathaniel Robert and Skogström, Oskar and Sjödin, Andreas and Tucker, James and Rodríguez-Acosta, Maricela and Nilsson, Peter and Jansson, Stefan and Taylor, Gail},
	year = {2006},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2006.02864.x},
	keywords = {QTL, drought, microarray, poplar, transcriptome},
	pages = {321--341},
}

The genetic nature of tree adaptation to drought stress was examined by utilizing variation in the drought response of a full-sib second generation (F2) mapping population from a cross between Populus trichocarpa (93-968) and P. deltoides Bart (ILL-129) and known to be highly divergent for a vast range of phenotypic traits. We combined phenotyping, quantitative trait loci (QTL) analysis and microarray experiments to demonstrate that ‘genetical genomics’ can be used to provide information on adaptation at the species level. The grandparents and F2 population were subjected to soil drying, and contrasting responses to drought across genotypes, including leaf coloration, expansion and abscission, were observed, and QTL for these traits mapped. A subset of extreme genotypes exhibiting extreme sensitivity and insensitivity to drought on the basis of leaf abscission were defined, and microarray experiments conducted on these genotypes and the grandparent species. The extreme genotype groups induced a different set of genes: 215 and 125 genes differed in their expression response between groups in control and drought, respectively, suggesting species adaptation at the gene expression level. Co-location of differentially expressed genes with drought-specific and drought-responsive QTLs was examined, and these may represent candidate genes contributing to the variation in drought response.

@article{taylor_transcriptome_2005,
	title = {The transcriptome of {Populus} in elevated {CO2}},
	volume = {167},
	issn = {1469-8137},
	url = {https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/j.1469-8137.2005.01450.x},
	doi = {10/d7g7mz},
	abstract = {• The consequences of increasing atmospheric carbon dioxide for long-term adaptation of forest ecosystems remain uncertain, with virtually no studies undertaken at the genetic level. A global analysis using cDNA microarrays was conducted following 6 yr exposure of Populus × euramericana (clone I-214) to elevated [CO2] in a FACE (free-air CO2 enrichment) experiment. • Gene expression was sensitive to elevated [CO2] but the response depended on the developmental age of the leaves, and {\textless} 50 transcripts differed significantly between different CO2 environments. For young leaves most differentially expressed genes were upregulated in elevated [CO2], while in semimature leaves most were downregulated in elevated [CO2]. • For transcripts related only to the small subunit of Rubisco, upregulation in LPI 3 and downregulation in LPI 6 leaves in elevated CO2 was confirmed by anova. Similar patterns of gene expression for young leaves were also confirmed independently across year 3 and year 6 microarray data, and using real-time RT–PCR. • This study provides the first clues to the long-term genetic expression changes that may occur during long-term plant response to elevated CO2.},
	language = {en},
	number = {1},
	urldate = {2021-06-11},
	journal = {New Phytologist},
	author = {Taylor, Gail and Street, Nathaniel R. and Tricker, Penny J. and Sjödin, Andreas and Graham, Laura and Skogström, Oskar and Calfapietra, Carlo and Scarascia-Mugnozza, Giuseppe and Jansson, Stefan},
	year = {2005},
	note = {\_eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-8137.2005.01450.x},
	keywords = {FACE (free-air CO2 enrichment), Populus, elevated CO2, gene expression, leaf development, microarray},
	pages = {143--154},
}

• The consequences of increasing atmospheric carbon dioxide for long-term adaptation of forest ecosystems remain uncertain, with virtually no studies undertaken at the genetic level. A global analysis using cDNA microarrays was conducted following 6 yr exposure of Populus × euramericana (clone I-214) to elevated [CO2] in a FACE (free-air CO2 enrichment) experiment. • Gene expression was sensitive to elevated [CO2] but the response depended on the developmental age of the leaves, and \textless 50 transcripts differed significantly between different CO2 environments. For young leaves most differentially expressed genes were upregulated in elevated [CO2], while in semimature leaves most were downregulated in elevated [CO2]. • For transcripts related only to the small subunit of Rubisco, upregulation in LPI 3 and downregulation in LPI 6 leaves in elevated CO2 was confirmed by anova. Similar patterns of gene expression for young leaves were also confirmed independently across year 3 and year 6 microarray data, and using real-time RT–PCR. • This study provides the first clues to the long-term genetic expression changes that may occur during long-term plant response to elevated CO2.

@article{rae_morphological_2004,
	title = {Morphological and physiological traits influencing biomass productivity in short-rotation coppice poplar},
	volume = {34},
	issn = {0045-5067},
	url = {https://cdnsciencepub.com/doi/10.1139/x04-033},
	doi = {10/d4fjbn},
	number = {7},
	urldate = {2021-08-23},
	journal = {Canadian Journal of Forest Research},
	author = {Rae, A M and Robinson, K M and Street, N R and Taylor, G},
	month = jul,
	year = {2004},
	note = {Publisher: NRC Research Press},
	pages = {1488--1498},
}