Jansson, Stefan - How do trees survive the winter?

@article{robinson_improved_2024,
	title = {An {Improved} {Chromosome}-scale {Genome} {Assembly} and {Population} {Genetics} resource for {Populus} tremula.},
	volume = {176},
	copyright = {© 2024 The Author(s). Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.14511},
	doi = {10.1111/ppl.14511},
	abstract = {Aspen (Populus tremula L.) is a keystone species and a model system for forest tree genomics. We present an updated resource comprising a chromosome-scale assembly, population genetics and genomics data. Using the resource, we explore the genetic basis of natural variation in leaf size and shape, traits with complex genetic architecture. We generated the genome assembly using long-read sequencing, optical and high-density genetic maps. We conducted whole-genome resequencing of the Umeå Aspen (UmAsp) collection. Using the assembly and re-sequencing data from the UmAsp, Swedish Aspen (SwAsp) and Scottish Aspen (ScotAsp) collections we performed genome-wide association analyses (GWAS) using Single Nucleotide Polymorphisms (SNPs) for 26 leaf physiognomy phenotypes. We conducted Assay of Transposase Accessible Chromatin sequencing (ATAC-Seq), identified genomic regions of accessible chromatin, and subset SNPs to these regions, improving the GWAS detection rate. We identified candidate long non-coding RNAs in leaf samples, quantified their expression in an updated co-expression network, and used this to explore the functions of candidate genes identified from the GWAS. A GWAS found SNP associations for seven traits. The associated SNPs were in or near genes annotated with developmental functions, which represent candidates for further study. Of particular interest was a 177-kbp region harbouring associations with several leaf phenotypes in ScotAsp. We have incorporated the assembly, population genetics, genomics, and GWAS data into the PlantGenIE.org web resource, including updating existing genomics data to the new genome version, to enable easy exploration and visualisation. We provide all raw and processed data to facilitate reuse in future studies.},
	language = {en},
	number = {5},
	urldate = {2024-09-19},
	journal = {Physiologia Plantarum},
	author = {Robinson, Kathryn M. and Schiffthaler, Bastian and Liu, Hui and Rydman, Sara M. and Rendón-Anaya, Martha and Kalman, Teitur Ahlgren and Kumar, Vikash and Canovi, Camilla and Bernhardsson, Carolina and Delhomme, Nicolas and Jenkins, Jerry and Wang, Jing and Mähler, Niklas and Richau, Kerstin H. and Stokes, Victoria and A'Hara, Stuart and Cottrell, Joan and Coeck, Kizi and Diels, Tim and Vandepoele, Klaas and Mannapperuma, Chanaka and Park, Eung-Jun and Plaisance, Stephane and Jansson, Stefan and Ingvarsson, Pär K. and Street, Nathaniel R.},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.14511},
	keywords = {ATAC-Seq, GWAS, Populus, aspen, co-expression, genetic architecture, genome assembly, leaf physiognomy, leaf shape, leaf size, lncRNA, natural selection, population genetics},
	pages = {e14511},
}

Aspen (Populus tremula L.) is a keystone species and a model system for forest tree genomics. We present an updated resource comprising a chromosome-scale assembly, population genetics and genomics data. Using the resource, we explore the genetic basis of natural variation in leaf size and shape, traits with complex genetic architecture. We generated the genome assembly using long-read sequencing, optical and high-density genetic maps. We conducted whole-genome resequencing of the Umeå Aspen (UmAsp) collection. Using the assembly and re-sequencing data from the UmAsp, Swedish Aspen (SwAsp) and Scottish Aspen (ScotAsp) collections we performed genome-wide association analyses (GWAS) using Single Nucleotide Polymorphisms (SNPs) for 26 leaf physiognomy phenotypes. We conducted Assay of Transposase Accessible Chromatin sequencing (ATAC-Seq), identified genomic regions of accessible chromatin, and subset SNPs to these regions, improving the GWAS detection rate. We identified candidate long non-coding RNAs in leaf samples, quantified their expression in an updated co-expression network, and used this to explore the functions of candidate genes identified from the GWAS. A GWAS found SNP associations for seven traits. The associated SNPs were in or near genes annotated with developmental functions, which represent candidates for further study. Of particular interest was a 177-kbp region harbouring associations with several leaf phenotypes in ScotAsp. We have incorporated the assembly, population genetics, genomics, and GWAS data into the PlantGenIE.org web resource, including updating existing genomics data to the new genome version, to enable easy exploration and visualisation. We provide all raw and processed data to facilitate reuse in future studies.

@article{nanda_chlorospec_2024,
	title = {{ChloroSpec}: {A} new in vivo chlorophyll fluorescence spectrometer for simultaneous wavelength- and time-resolved detection},
	volume = {176},
	copyright = {© 2024 The Authors. Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.14306},
	doi = {10.1111/ppl.14306},
	abstract = {Chlorophyll fluorescence is a ubiquitous tool in basic and applied plant science research. Various standard commercial instruments are available for characterization of photosynthetic material like leaves or microalgae, most of which integrate the overall fluorescence signals above a certain cut-off wavelength. However, wavelength-resolved (fluorescence signals appearing at different wavelengths having different time dependent decay) signals contain vast information required to decompose complex signals and processes into their underlying components that can untangle the photo-physiological process of photosynthesis. Hence, to address this we describe an advanced chlorophyll fluorescence spectrometer - ChloroSpec - allowing three-dimensional simultaneous detection of fluorescence intensities at different wavelengths in a time-resolved manner. We demonstrate for a variety of typical examples that most of the generally used fluorescence parameters are strongly wavelength dependent. This indicates a pronounced heterogeneity and a highly dynamic nature of the thylakoid and the photosynthetic apparatus under actinic illumination. Furthermore, we provide examples of advanced global analysis procedures integrating this three-dimensional signal and relevant information extracted from them that relate to the physiological properties of the organism. This conveniently obtained broad range of data can make ChloroSpec a new standard tool in photosynthesis research.},
	language = {en},
	number = {2},
	urldate = {2024-09-04},
	journal = {Physiologia Plantarum},
	author = {Nanda, Sanchali and Shutova, Tatyana and Cainzos, Maximiliano and Hu, Chen and Sasbrink, Bart and Bag, Pushan and Blanken, Tristian den and Buijs, Ronald and Gracht, Lex van der and Hendriks, Frans and Lambrev, Petar and Limburg, Rob and Mascoli, Vincenzo and Nawrocki, Wojciech J and Reus, Michael and Parmessar, Ramon and Singerling, Björn and Stokkum, Ivo H M and Jansson, Stefan and Holzwarth, Alfred R.},
	month = aug,
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.14306},
	pages = {e14306},
}

Chlorophyll fluorescence is a ubiquitous tool in basic and applied plant science research. Various standard commercial instruments are available for characterization of photosynthetic material like leaves or microalgae, most of which integrate the overall fluorescence signals above a certain cut-off wavelength. However, wavelength-resolved (fluorescence signals appearing at different wavelengths having different time dependent decay) signals contain vast information required to decompose complex signals and processes into their underlying components that can untangle the photo-physiological process of photosynthesis. Hence, to address this we describe an advanced chlorophyll fluorescence spectrometer - ChloroSpec - allowing three-dimensional simultaneous detection of fluorescence intensities at different wavelengths in a time-resolved manner. We demonstrate for a variety of typical examples that most of the generally used fluorescence parameters are strongly wavelength dependent. This indicates a pronounced heterogeneity and a highly dynamic nature of the thylakoid and the photosynthetic apparatus under actinic illumination. Furthermore, we provide examples of advanced global analysis procedures integrating this three-dimensional signal and relevant information extracted from them that relate to the physiological properties of the organism. This conveniently obtained broad range of data can make ChloroSpec a new standard tool in photosynthesis research.

@article{bag_flavodiiron-mediated_2023,
	title = {Flavodiiron-mediated {O2} photoreduction at photosystem {I} acceptor-side provides photoprotection to conifer thylakoids in early spring},
	volume = {14},
	copyright = {2023 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-023-38938-z},
	doi = {10.1038/s41467-023-38938-z},
	abstract = {Green organisms evolve oxygen (O2) via photosynthesis and consume it by respiration. Generally, net O2 consumption only becomes dominant when photosynthesis is suppressed at night. Here, we show that green thylakoid membranes of Scots pine (Pinus sylvestris L) and Norway spruce (Picea abies) needles display strong O2 consumption even in the presence of light when extremely low temperatures coincide with high solar irradiation during early spring (ES). By employing different electron transport chain inhibitors, we show that this unusual light-induced O2 consumption occurs around photosystem (PS) I and correlates with higher abundance of flavodiiron (Flv) A protein in ES thylakoids. With P700 absorption changes, we demonstrate that electron scavenging from the acceptor-side of PSI via O2 photoreduction is a major alternative pathway in ES. This photoprotection mechanism in vascular plants indicates that conifers have developed an adaptative evolution trajectory for growing in harsh environments.},
	language = {en},
	number = {1},
	urldate = {2023-06-09},
	journal = {Nature Communications},
	author = {Bag, Pushan and Shutova, Tatyana and Shevela, Dmitry and Lihavainen, Jenna and Nanda, Sanchali and Ivanov, Alexander G. and Messinger, Johannes and Jansson, Stefan},
	month = jun,
	year = {2023},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Abiotic, Light responses, Photosystem I},
	pages = {3210},
}

Green organisms evolve oxygen (O2) via photosynthesis and consume it by respiration. Generally, net O2 consumption only becomes dominant when photosynthesis is suppressed at night. Here, we show that green thylakoid membranes of Scots pine (Pinus sylvestris L) and Norway spruce (Picea abies) needles display strong O2 consumption even in the presence of light when extremely low temperatures coincide with high solar irradiation during early spring (ES). By employing different electron transport chain inhibitors, we show that this unusual light-induced O2 consumption occurs around photosystem (PS) I and correlates with higher abundance of flavodiiron (Flv) A protein in ES thylakoids. With P700 absorption changes, we demonstrate that electron scavenging from the acceptor-side of PSI via O2 photoreduction is a major alternative pathway in ES. This photoprotection mechanism in vascular plants indicates that conifers have developed an adaptative evolution trajectory for growing in harsh environments.

@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{lihavainen_salicylic_2023,
	title = {Salicylic acid metabolism and signalling coordinate senescence initiation in aspen in nature},
	volume = {14},
	copyright = {2023 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-023-39564-5},
	doi = {10.1038/s41467-023-39564-5},
	abstract = {Deciduous trees exhibit a spectacular phenomenon of autumn senescence driven by the seasonality of their growth environment, yet there is no consensus which external or internal cues trigger it. Senescence starts at different times in European aspen (Populus tremula L.) genotypes grown in same location. By integrating omics studies, we demonstrate that aspen genotypes utilize similar transcriptional cascades and metabolic cues to initiate senescence, but at different times during autumn. The timing of autumn senescence initiation appeared to be controlled by two consecutive “switches”; 1) first the environmental variation induced the rewiring of the transcriptional network, stress signalling pathways and metabolic perturbations and 2) the start of senescence process was defined by the ability of the genotype to activate and sustain stress tolerance mechanisms mediated by salicylic acid. We propose that salicylic acid represses the onset of leaf senescence in stressful natural conditions, rather than promoting it as often observed in annual plants.},
	language = {en},
	number = {1},
	urldate = {2023-07-21},
	journal = {Nature Communications},
	author = {Lihavainen, Jenna and Šimura, Jan and Bag, Pushan and Fataftah, Nazeer and Robinson, Kathryn Megan and Delhomme, Nicolas and Novák, Ondřej and Ljung, Karin and Jansson, Stefan},
	month = jul,
	year = {2023},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Metabolomics, Plant physiology, Regulatory networks, Senescence},
	pages = {4288},
}

Deciduous trees exhibit a spectacular phenomenon of autumn senescence driven by the seasonality of their growth environment, yet there is no consensus which external or internal cues trigger it. Senescence starts at different times in European aspen (Populus tremula L.) genotypes grown in same location. By integrating omics studies, we demonstrate that aspen genotypes utilize similar transcriptional cascades and metabolic cues to initiate senescence, but at different times during autumn. The timing of autumn senescence initiation appeared to be controlled by two consecutive “switches”; 1) first the environmental variation induced the rewiring of the transcriptional network, stress signalling pathways and metabolic perturbations and 2) the start of senescence process was defined by the ability of the genotype to activate and sustain stress tolerance mechanisms mediated by salicylic acid. We propose that salicylic acid represses the onset of leaf senescence in stressful natural conditions, rather than promoting it as often observed in annual plants.

@article{arshad_kaleidoscope_2022,
	title = {A kaleidoscope of photosynthetic antenna proteins and their emerging roles},
	volume = {189},
	issn = {1532-2548},
	doi = {10.1093/plphys/kiac175},
	abstract = {Photosynthetic light-harvesting antennae are pigment-binding proteins that perform one of the most fundamental tasks on Earth, capturing light and transferring energy that enables life in our biosphere. Adaptation to different light environments led to the evolution of an astonishing diversity of light-harvesting systems. At the same time, several strategies have been developed to optimize the light energy input into photosynthetic membranes in response to fluctuating conditions. The basic feature of these prompt responses is the dynamic nature of antenna complexes, whose function readily adapts to the light available. High-resolution microscopy and spectroscopic studies on membrane dynamics demonstrate the crosstalk between antennae and other thylakoid membrane components. With the increased understanding of light-harvesting mechanisms and their regulation, efforts are focusing on the development of sustainable processes for effective conversion of sunlight into functional bio-products. The major challenge in this approach lies in the application of fundamental discoveries in light-harvesting systems for the improvement of plant or algal photosynthesis. Here, we underline some of the latest fundamental discoveries on the molecular mechanisms and regulation of light harvesting that can potentially be exploited for the optimization of photosynthesis.},
	language = {eng},
	number = {3},
	journal = {Plant Physiology},
	author = {Arshad, Rameez and Saccon, Francesco and Bag, Pushan and Biswas, Avratanu and Calvaruso, Claudio and Bhatti, Ahmad Farhan and Grebe, Steffen and Mascoli, Vincenzo and Mahbub, Moontaha and Muzzopappa, Fernando and Polyzois, Alexandros and Schiphorst, Christo and Sorrentino, Mirella and Streckaité, Simona and van Amerongen, Herbert and Aro, Eva-Mari and Bassi, Roberto and Boekema, Egbert J. and Croce, Roberta and Dekker, Jan and van Grondelle, Rienk and Jansson, Stefan and Kirilovsky, Diana and Kouřil, Roman and Michel, Sylvie and Mullineaux, Conrad W. and Panzarová, Klára and Robert, Bruno and Ruban, Alexander V. and van Stokkum, Ivo and Wientjes, Emilie and Büchel, Claudia},
	month = jun,
	year = {2022},
	pmid = {35512089},
	keywords = {Adaptation, Physiological, Light-Harvesting Protein Complexes, Photosynthesis, Plants, Thylakoids},
	pages = {1204--1219},
}

Photosynthetic light-harvesting antennae are pigment-binding proteins that perform one of the most fundamental tasks on Earth, capturing light and transferring energy that enables life in our biosphere. Adaptation to different light environments led to the evolution of an astonishing diversity of light-harvesting systems. At the same time, several strategies have been developed to optimize the light energy input into photosynthetic membranes in response to fluctuating conditions. The basic feature of these prompt responses is the dynamic nature of antenna complexes, whose function readily adapts to the light available. High-resolution microscopy and spectroscopic studies on membrane dynamics demonstrate the crosstalk between antennae and other thylakoid membrane components. With the increased understanding of light-harvesting mechanisms and their regulation, efforts are focusing on the development of sustainable processes for effective conversion of sunlight into functional bio-products. The major challenge in this approach lies in the application of fundamental discoveries in light-harvesting systems for the improvement of plant or algal photosynthesis. Here, we underline some of the latest fundamental discoveries on the molecular mechanisms and regulation of light harvesting that can potentially be exploited for the optimization of photosynthesis.

@article{fataftah_nitrate_2022,
	title = {Nitrate fertilization may delay autumn leaf senescence, while amino acid treatments do not},
	volume = {174},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.13690},
	doi = {10.1111/ppl.13690},
	abstract = {Fertilization with nitrogen (N)-rich compounds leads to increased growth but may compromise phenology and winter survival of trees in boreal regions. During autumn, N is remobilized from senescing leaves and stored in other parts of the tree to be used in the next growing season. However, the mechanism behind the N fertilization effect on winter survival is not well understood, and it is unclear how N levels or forms modulate autumn senescence. We performed fertilization experiments and showed that treating Populus saplings with inorganic nitrogen resulted in a delay in senescence. In addition, by using precise delivery of solutes into the xylem stream of Populus trees in their natural environment, we found that delay of autumn senescence was dependent on the form of N administered: inorganic N (NO3−) delayed senescence, but amino acids (Arg, Glu, Gln, and Leu) did not. Metabolite profiling of leaves showed that the levels of tricarboxylic acids, arginine catabolites (ammonium, ornithine), glycine, glycine-serine ratio and overall carbon-to-nitrogen (C/N) ratio were affected differently by the way of applying NO3− and Arg treatments. In addition, the onset of senescence did not coincide with soluble sugar accumulation in control trees or in any of the treatments. We propose that different regulation of C and N status through direct molecular signaling of NO3− and/or different allocation of N between tree parts depending on N forms could account for the contrasting effects of NO3− and tested here amino acids (Arg, Glu, Gln, and Leu) on autumn senescence.},
	language = {en},
	number = {3},
	urldate = {2022-06-30},
	journal = {Physiologia Plantarum},
	author = {Fataftah, Nazeer and Edlund, Erik and Lihavainen, Jenna and Bag, Pushan and Björkén, Lars and Näsholm, Torgny and Jansson, Stefan},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.13690},
	pages = {e13690},
}

Fertilization with nitrogen (N)-rich compounds leads to increased growth but may compromise phenology and winter survival of trees in boreal regions. During autumn, N is remobilized from senescing leaves and stored in other parts of the tree to be used in the next growing season. However, the mechanism behind the N fertilization effect on winter survival is not well understood, and it is unclear how N levels or forms modulate autumn senescence. We performed fertilization experiments and showed that treating Populus saplings with inorganic nitrogen resulted in a delay in senescence. In addition, by using precise delivery of solutes into the xylem stream of Populus trees in their natural environment, we found that delay of autumn senescence was dependent on the form of N administered: inorganic N (NO3−) delayed senescence, but amino acids (Arg, Glu, Gln, and Leu) did not. Metabolite profiling of leaves showed that the levels of tricarboxylic acids, arginine catabolites (ammonium, ornithine), glycine, glycine-serine ratio and overall carbon-to-nitrogen (C/N) ratio were affected differently by the way of applying NO3− and Arg treatments. In addition, the onset of senescence did not coincide with soluble sugar accumulation in control trees or in any of the treatments. We propose that different regulation of C and N status through direct molecular signaling of NO3− and/or different allocation of N between tree parts depending on N forms could account for the contrasting effects of NO3− and tested here amino acids (Arg, Glu, Gln, and Leu) on autumn senescence.

@article{boussardon_rpn12a_2022,
	title = {The {RPN12a} proteasome subunit is essential for the multiple hormonal homeostasis controlling the progression of leaf senescence},
	volume = {5},
	copyright = {2022 The Author(s)},
	issn = {2399-3642},
	url = {https://www.nature.com/articles/s42003-022-03998-2},
	doi = {10.1038/s42003-022-03998-2},
	abstract = {The 26S proteasome is a conserved multi-subunit machinery in eukaryotes. It selectively degrades ubiquitinated proteins, which in turn provides an efficient molecular mechanism to regulate numerous cellular functions and developmental processes. Here, we studied a new loss-of-function allele of RPN12a, a plant ortholog of the yeast and human structural component of the 19S proteasome RPN12. Combining a set of biochemical and molecular approaches, we confirmed that a rpn12a knock-out had exacerbated 20S and impaired 26S activities. The altered proteasomal activity led to a pleiotropic phenotype affecting both the vegetative growth and reproductive phase of the plant, including a striking repression of leaf senescence associate cell-death. Further investigation demonstrated that RPN12a is involved in the regulation of several conjugates associated with the auxin, cytokinin, ethylene and jasmonic acid homeostasis. Such enhanced aptitude of plant cells for survival in rpn12a contrasts with reports on animals, where 26S proteasome mutants generally show an accelerated cell death phenotype.},
	language = {en},
	number = {1},
	urldate = {2022-10-03},
	journal = {Communications Biology},
	author = {Boussardon, Clément and Bag, Pushan and Juvany, Marta and Šimura, Jan and Ljung, Karin and Jansson, Stefan and Keech, Olivier},
	month = sep,
	year = {2022},
	keywords = {Leaf development, Senescence},
	pages = {1--14},
}

The 26S proteasome is a conserved multi-subunit machinery in eukaryotes. It selectively degrades ubiquitinated proteins, which in turn provides an efficient molecular mechanism to regulate numerous cellular functions and developmental processes. Here, we studied a new loss-of-function allele of RPN12a, a plant ortholog of the yeast and human structural component of the 19S proteasome RPN12. Combining a set of biochemical and molecular approaches, we confirmed that a rpn12a knock-out had exacerbated 20S and impaired 26S activities. The altered proteasomal activity led to a pleiotropic phenotype affecting both the vegetative growth and reproductive phase of the plant, including a striking repression of leaf senescence associate cell-death. Further investigation demonstrated that RPN12a is involved in the regulation of several conjugates associated with the auxin, cytokinin, ethylene and jasmonic acid homeostasis. Such enhanced aptitude of plant cells for survival in rpn12a contrasts with reports on animals, where 26S proteasome mutants generally show an accelerated cell death phenotype.

@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{bag_atlas_2021,
	title = {An atlas of the {Norway} spruce needle seasonal transcriptome},
	volume = {108},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.15530},
	doi = {10.1111/tpj.15530},
	abstract = {Boreal conifers possess a tremendous ability to survive and remain evergreen during harsh winter conditions and resume growth during summer. This is enabled by coordinated regulation of major cellular functions at the level of gene expression, metabolism, and physiology. Here we present a comprehensive characterization of the annual changes in the global transcriptome of Norway spruce (Picea abies) needles as a resource to understand needle development and acclimation processes throughout the year. In young, growing needles (May 15 until June 30), cell walls, organelles, etc., were formed, and this developmental program heavily influenced the transcriptome, explained by over-represented Gene Ontology (GO) categories. Later changes in gene expression were smaller but four phases were recognized: summer (July–August), autumn (September–October), winter (November–February), and spring (March–April), where over-represented GO categories demonstrated how the needles acclimated to the various seasons. Changes in the seasonal global transcriptome profile were accompanied by differential expression of members of the major transcription factor families. We present a tentative model of how cellular activities are regulated over the year in needles of Norway spruce, which demonstrates the value of mining this dataset, accessible in ConGenIE together with advanced visualization tools.},
	language = {en},
	number = {6},
	urldate = {2021-11-04},
	journal = {The Plant Journal},
	author = {Bag, Pushan and Lihavainen, Jenna and Delhomme, Nicolas and Riquelme, Thomas and Robinson, Kathryn M and Jansson, Stefan},
	month = oct,
	year = {2021},
	keywords = {Conifers, Norway spruce, Seasonal adaptation, Transcriptomics, conifers, resource, seasonal adaptation, transcriptomics},
}

Boreal conifers possess a tremendous ability to survive and remain evergreen during harsh winter conditions and resume growth during summer. This is enabled by coordinated regulation of major cellular functions at the level of gene expression, metabolism, and physiology. Here we present a comprehensive characterization of the annual changes in the global transcriptome of Norway spruce (Picea abies) needles as a resource to understand needle development and acclimation processes throughout the year. In young, growing needles (May 15 until June 30), cell walls, organelles, etc., were formed, and this developmental program heavily influenced the transcriptome, explained by over-represented Gene Ontology (GO) categories. Later changes in gene expression were smaller but four phases were recognized: summer (July–August), autumn (September–October), winter (November–February), and spring (March–April), where over-represented GO categories demonstrated how the needles acclimated to the various seasons. Changes in the seasonal global transcriptome profile were accompanied by differential expression of members of the major transcription factor families. We present a tentative model of how cellular activities are regulated over the year in needles of Norway spruce, which demonstrates the value of mining this dataset, accessible in ConGenIE together with advanced visualization tools.

@article{fataftah_gigantea_2021,
	title = {{GIGANTEA} influences leaf senescence in trees in two different ways},
	volume = {187},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiab439},
	doi = {10/gnxfqw},
	abstract = {GIGANTEA (GI) genes have a central role in plant development and influence several processes. Hybrid aspen T89 (Populus tremula x tremuloides) trees with low GI expression engineered through RNAi show severely compromised growth. To study the effect of reduced GI expression on leaf traits with special emphasis on leaf senescence, we grafted GI-RNAi scions onto wild-type rootstocks and successfully restored growth of the scions. The RNAi line had a distorted leaf shape and reduced photosynthesis, probably caused by modulation of phloem or stomatal function, increased starch accumulation, a higher carbon-to-nitrogen ratio, and reduced capacity to withstand moderate light stress. GI-RNAi also induced senescence under long day (LD) and moderate light conditions. Furthermore, the GI-RNAi lines were affected in their capacity to respond to “autumn environmental cues” inducing senescence, a type of leaf senescence that has physiological and biochemical characteristics that differ from those of senescence induced directly by stress under LD conditions. Overexpression of GI delayed senescence under simulated autumn conditions. The two different effects on leaf senescence under LD or simulated autumn conditions were not affected by the expression of FLOWERING LOCUS T. GI expression regulated leaf senescence locally—the phenotype followed the genotype of the branch, independent of its position on the tree—and trees with modified gene expression were affected in a similar way when grown in the field as under controlled conditions. Taken together, GI plays a central role in sensing environmental changes during autumn and determining the appropriate timing for leaf senescence in Populus.},
	number = {4},
	urldate = {2021-10-15},
	journal = {Plant Physiology},
	author = {Fataftah, Nazeer and Bag, Pushan and André, Domenique and Lihavainen, Jenna and Zhang, Bo and Ingvarsson, Pär K and Nilsson, Ove and Jansson, Stefan},
	month = sep,
	year = {2021},
	pages = {2435--2450},
}

GIGANTEA (GI) genes have a central role in plant development and influence several processes. Hybrid aspen T89 (Populus tremula x tremuloides) trees with low GI expression engineered through RNAi show severely compromised growth. To study the effect of reduced GI expression on leaf traits with special emphasis on leaf senescence, we grafted GI-RNAi scions onto wild-type rootstocks and successfully restored growth of the scions. The RNAi line had a distorted leaf shape and reduced photosynthesis, probably caused by modulation of phloem or stomatal function, increased starch accumulation, a higher carbon-to-nitrogen ratio, and reduced capacity to withstand moderate light stress. GI-RNAi also induced senescence under long day (LD) and moderate light conditions. Furthermore, the GI-RNAi lines were affected in their capacity to respond to “autumn environmental cues” inducing senescence, a type of leaf senescence that has physiological and biochemical characteristics that differ from those of senescence induced directly by stress under LD conditions. Overexpression of GI delayed senescence under simulated autumn conditions. The two different effects on leaf senescence under LD or simulated autumn conditions were not affected by the expression of FLOWERING LOCUS T. GI expression regulated leaf senescence locally—the phenotype followed the genotype of the branch, independent of its position on the tree—and trees with modified gene expression were affected in a similar way when grown in the field as under controlled conditions. Taken together, GI plays a central role in sensing environmental changes during autumn and determining the appropriate timing for leaf senescence in Populus.

@article{bag_solubilization_2021,
	title = {Solubilization {Method} for {Isolation} of {Photosynthetic} {Mega}- and {Super}-complexes from {Conifer} {Thylakoids}},
	volume = {11},
	url = {https://bio-protocol.org/e4144},
	abstract = {Photosynthesis is the main process by which sunlight is harvested and converted into chemical energy and has been a focal point of fundamental research in plant biology for decades. In higher plants, the process takes place in the thylakoid membranes where the two photosystems (PSI and PSII) are located. In the past few decades, the evolution of biophysical and biochemical techniques allowed detailed studies of the thylakoid organization and the interaction between protein complexes and cofactors. These studies have mainly focused on model plants, such as Arabidopsis, pea, spinach, and tobacco, which are grown in climate chambers even though significant differences between indoor and outdoor growth conditions are present. In this manuscript, we present a new mild-solubilization procedure for use with \“fragile\” samples such as thylakoids from conifers growing outdoors. Here, the solubilization protocol is optimized with two detergents in two species, namely Norway spruce (Picea abies) and Scots pine (Pinus sylvestris). We have optimized the isolation and characterization of PSI and PSII multimeric mega- and super-complexes in a close-to-native condition by Blue-Native gel electrophoresis. Eventually, our protocol will not only help in the characterization of photosynthetic complexes from conifers but also in understanding winter adaptation.},
	number = {17},
	urldate = {2021-10-05},
	journal = {Bio-protocol},
	author = {Bag, Pushan and Schröder, Wolfgang P. and Jansson, Stefan and Farci, Domenica},
	month = sep,
	year = {2021},
	pages = {e4144--e4144},
}

Photosynthesis is the main process by which sunlight is harvested and converted into chemical energy and has been a focal point of fundamental research in plant biology for decades. In higher plants, the process takes place in the thylakoid membranes where the two photosystems (PSI and PSII) are located. In the past few decades, the evolution of biophysical and biochemical techniques allowed detailed studies of the thylakoid organization and the interaction between protein complexes and cofactors. These studies have mainly focused on model plants, such as Arabidopsis, pea, spinach, and tobacco, which are grown in climate chambers even though significant differences between indoor and outdoor growth conditions are present. In this manuscript, we present a new mild-solubilization procedure for use with “fragile” samples such as thylakoids from conifers growing outdoors. Here, the solubilization protocol is optimized with two detergents in two species, namely Norway spruce (Picea abies) and Scots pine (Pinus sylvestris). We have optimized the isolation and characterization of PSI and PSII multimeric mega- and super-complexes in a close-to-native condition by Blue-Native gel electrophoresis. Eventually, our protocol will not only help in the characterization of photosynthetic complexes from conifers but also in understanding winter adaptation.

@article{lihavainen_stem_2021,
	title = {Stem girdling affects the onset of autumn senescence in aspen in interaction with metabolic signals},
	volume = {172},
	issn = {0031-9317, 1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/ppl.13319},
	doi = {10.1111/ppl.13319},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Lihavainen, Jenna and Edlund, Erik and Björkén, Lars and Bag, Pushan and Robinson, Kathryn M. and Jansson, Stefan},
	month = may,
	year = {2021},
	pages = {201--217},
}

@article{robinson_variation_2021,
	title = {Variation in non-target traits in genetically modified hybrid aspens does not exceed natural variation},
	volume = {64},
	issn = {1871-6784},
	url = {https://www.sciencedirect.com/science/article/pii/S1871678421000625},
	doi = {10.1016/j.nbt.2021.05.005},
	abstract = {Genetically modified hybrid aspens (Populus tremula L. x P. tremuloides Michx.), selected for increased growth under controlled conditions, have been grown in highly replicated field trials to evaluate how the target trait (growth) translated to natural conditions. Moreover, the variation was compared among genotypes of ecologically important non-target traits: number of shoots, bud set, pathogen infection, amount of insect herbivory, composition of the insect herbivore community and flower bud induction. This variation was compared with the variation in a population of randomly selected natural accessions of P. tremula grown in common garden trials, to estimate how the “unintended variation” present in transgenic trees, which in the future may be commercialized, compares with natural variation. The natural variation in the traits was found to be typically significantly greater. The data suggest that when authorities evaluate the potential risks associated with a field experiment or commercial introduction of transgenic trees, risk evaluation should focus on target traits and that unintentional variation in non-target traits is of less concern.},
	language = {en},
	urldate = {2021-09-21},
	journal = {New Biotechnology},
	author = {Robinson, Kathryn M. and Möller, Linus and Bhalerao, Rishikesh P. and Hertzberg, Magnus and Nilsson, Ove and Jansson, Stefan},
	month = sep,
	year = {2021},
	keywords = {European aspen, Field experiment, Genetically modified, Hybrid aspen, Natural variation, Non-target traits},
	pages = {27--36},
}

Genetically modified hybrid aspens (Populus tremula L. x P. tremuloides Michx.), selected for increased growth under controlled conditions, have been grown in highly replicated field trials to evaluate how the target trait (growth) translated to natural conditions. Moreover, the variation was compared among genotypes of ecologically important non-target traits: number of shoots, bud set, pathogen infection, amount of insect herbivory, composition of the insect herbivore community and flower bud induction. This variation was compared with the variation in a population of randomly selected natural accessions of P. tremula grown in common garden trials, to estimate how the “unintended variation” present in transgenic trees, which in the future may be commercialized, compares with natural variation. The natural variation in the traits was found to be typically significantly greater. The data suggest that when authorities evaluate the potential risks associated with a field experiment or commercial introduction of transgenic trees, risk evaluation should focus on target traits and that unintentional variation in non-target traits is of less concern.

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

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

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

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

@article{grebe_unique_2019,
	title = {The unique photosynthetic apparatus of {Pinaceae}: analysis of photosynthetic complexes in {Picea} abies},
	volume = {70},
	issn = {0022-0957, 1460-2431},
	shorttitle = {The unique photosynthetic apparatus of {Pinaceae}},
	url = {https://academic.oup.com/jxb/article/70/12/3211/5425460},
	doi = {10/gjdz35},
	abstract = {Abstract
            Pinaceae are the predominant photosynthetic species in boreal forests, but so far no detailed description of the protein components of the photosynthetic apparatus of these gymnosperms has been available. In this study we report a detailed characterization of the thylakoid photosynthetic machinery of Norway spruce (Picea abies (L.) Karst). We first customized a spruce thylakoid protein database from translated transcript sequences combined with existing protein sequences derived from gene models, which enabled reliable tandem mass spectrometry identification of P. abies thylakoid proteins from two-dimensional large pore blue-native/SDS-PAGE. This allowed a direct comparison of the two-dimensional protein map of thylakoid protein complexes from P. abies with the model angiosperm Arabidopsis thaliana. Although the subunit composition of P. abies core PSI and PSII complexes is largely similar to that of Arabidopsis, there was a high abundance of a smaller PSI subcomplex, closely resembling the assembly intermediate PSI* complex. In addition, the evolutionary distribution of light-harvesting complex (LHC) family members of Pinaceae was compared in silico with other land plants, revealing that P. abies and other Pinaceae (also Gnetaceae and Welwitschiaceae) have lost LHCB4, but retained LHCB8 (formerly called LHCB4.3). The findings reported here show the composition of the photosynthetic apparatus of P. abies and other Pinaceae members to be unique among land plants.},
	language = {en},
	number = {12},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Grebe, Steffen and Trotta, Andrea and Bajwa, Azfar A and Suorsa, Marjaana and Gollan, Peter J and Jansson, Stefan and Tikkanen, Mikko and Aro, Eva-Mari},
	month = jun,
	year = {2019},
	pages = {3211--3225},
}

Abstract Pinaceae are the predominant photosynthetic species in boreal forests, but so far no detailed description of the protein components of the photosynthetic apparatus of these gymnosperms has been available. In this study we report a detailed characterization of the thylakoid photosynthetic machinery of Norway spruce (Picea abies (L.) Karst). We first customized a spruce thylakoid protein database from translated transcript sequences combined with existing protein sequences derived from gene models, which enabled reliable tandem mass spectrometry identification of P. abies thylakoid proteins from two-dimensional large pore blue-native/SDS-PAGE. This allowed a direct comparison of the two-dimensional protein map of thylakoid protein complexes from P. abies with the model angiosperm Arabidopsis thaliana. Although the subunit composition of P. abies core PSI and PSII complexes is largely similar to that of Arabidopsis, there was a high abundance of a smaller PSI subcomplex, closely resembling the assembly intermediate PSI* complex. In addition, the evolutionary distribution of light-harvesting complex (LHC) family members of Pinaceae was compared in silico with other land plants, revealing that P. abies and other Pinaceae (also Gnetaceae and Welwitschiaceae) have lost LHCB4, but retained LHCB8 (formerly called LHCB4.3). The findings reported here show the composition of the photosynthetic apparatus of P. abies and other Pinaceae members to be unique among land plants.

@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{michelson_autumn_2018,
	title = {Autumn senescence in aspen is not triggered by day length},
	volume = {162},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/ppl.12593},
	doi = {10.1111/ppl.12593},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Michelson, Ingrid H. and Ingvarsson, Pär K. and Robinson, Kathryn M. and Edlund, Erik and Eriksson, Maria E. and Nilsson, Ove and Jansson, Stefan},
	month = jan,
	year = {2018},
	pages = {123--134},
}

@article{law_darkened_2018,
	title = {Darkened {Leaves} {Use} {Different} {Metabolic} {Strategies} for {Senescence} and {Survival}},
	volume = {177},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/177/1/132-150/6116945},
	doi = {10.1104/pp.18.00062},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Law, Simon R. and Chrobok, Daria and Juvany, Marta and Delhomme, Nicolas and Lindén, Pernilla and Brouwer, Bastiaan and Ahad, Abdul and Moritz, Thomas and Jansson, Stefan and Gardeström, Per and Keech, Olivier},
	month = may,
	year = {2018},
	pages = {132--150},
}

@article{pribil_fine-tuning_2018,
	title = {Fine-{Tuning} of {Photosynthesis} {Requires} {CURVATURE} {THYLAKOID1}-{Mediated} {Thylakoid} {Plasticity}},
	volume = {176},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/176/3/2351-2364/6117159},
	doi = {10.1104/pp.17.00863},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Pribil, Mathias and Sandoval-Ibáñez, Omar and Xu, Wenteng and Sharma, Anurag and Labs, Mathias and Liu, Qiuping and Galgenmüller, Carolina and Schneider, Trang and Wessels, Malgorzata and Matsubara, Shizue and Jansson, Stefan and Wanner, Gerhard and Leister, Dario},
	month = mar,
	year = {2018},
	pages = {2351--2364},
}

@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{jansson_gene-edited_2018,
	title = {Gene-edited plants on the plate: the ‘{CRISPR} cabbage story’},
	volume = {164},
	issn = {00319317},
	shorttitle = {Gene-edited plants on the plate},
	url = {http://doi.wiley.com/10.1111/ppl.12754},
	doi = {10.1111/ppl.12754},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Jansson, Stefan},
	month = dec,
	year = {2018},
	pages = {396--405},
}

@article{jansson_gene-edited_2018,
	title = {Gene-edited plants: {What} is happening now?},
	volume = {164},
	issn = {00319317},
	shorttitle = {Gene-edited plants},
	url = {http://doi.wiley.com/10.1111/ppl.12853},
	doi = {10.1111/ppl.12853},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Jansson, Stefan},
	month = dec,
	year = {2018},
	pages = {370--371},
}

@article{myouga_stable_2018,
	title = {Stable {Accumulation} of {Photosystem} {II} {Requires} {ONE}-{HELIX} {PROTEIN1} ({OHP1}) of the {Light} {Harvesting}-{Like} {Family}},
	volume = {176},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/176/3/2277-2291/6117119},
	doi = {10.1104/pp.17.01782},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Myouga, Fumiyoshi and Takahashi, Kaori and Tanaka, Ryoichi and Nagata, Noriko and Kiss, Anett Z. and Funk, Christiane and Nomura, Yuko and Nakagami, Hirofumi and Jansson, Stefan and Shinozaki, Kazuo},
	month = mar,
	year = {2018},
	pages = {2277--2291},
}

@article{mishra_active-site_2017,
	title = {Active-site plasticity revealed in the asymmetric dimer of {AnPrx6} the 1-{Cys} peroxiredoxin and molecular chaperone from {Anabaena} sp. {PCC} 7120},
	volume = {7},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/s41598-017-17044-3},
	doi = {10/gc2fwt},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	author = {Mishra, Yogesh and Hall, Michael and Locmelis, Roland and Nam, Kwangho and Söderberg, Christopher A. G. and Storm, Patrik and Chaurasia, Neha and Rai, Lal Chand and Jansson, Stefan and Schröder, Wolfgang P. and Sauer, Uwe H.},
	month = dec,
	year = {2017},
	pages = {17151},
}

@article{edlund_contrasting_2017,
	title = {Contrasting patterns of cytokinins between years in senescing aspen leaves},
	volume = {40},
	issn = {0140-7791, 1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.12899},
	doi = {10.1111/pce.12899},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Plant, Cell \& Environment},
	author = {Edlund, Erik and Novak, Ondrej and Karady, Michal and Ljung, Karin and Jansson, Stefan},
	month = may,
	year = {2017},
	pages = {622--634},
}

@article{zas_genetic_2017,
	title = {Genetic variation in resistance of {Norway} spruce seedlings to damage by the pine weevil {Hylobius} abietis},
	volume = {13},
	issn = {1614-2942, 1614-2950},
	url = {http://link.springer.com/10.1007/s11295-017-1193-1},
	doi = {10/gcps32},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Tree Genetics \& Genomes},
	author = {Zas, Rafael and Björklund, Niklas and Sampedro, Luis and Hellqvist, Claes and Karlsson, Bo and Jansson, Stefan and Nordlander, Göran},
	month = oct,
	year = {2017},
	pages = {111},
}

@article{ricroch_challenges_2016,
	title = {Challenges facing {European} agriculture and possible biotechnological solutions},
	volume = {36},
	issn = {0738-8551, 1549-7801},
	url = {https://www.tandfonline.com/doi/full/10.3109/07388551.2015.1055707},
	doi = {10.3109/07388551.2015.1055707},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Critical Reviews in Biotechnology},
	author = {Ricroch, Agnès and Harwood, Wendy and Svobodová, Zdeňka and Sági, László and Hundleby, Penelope and Badea, Elena Marcela and Rosca, Ioan and Cruz, Gabriela and Salema Fevereiro, Manuel Pedro and Marfà Riera, Victoria and Jansson, Stefan and Morandini, Piero and Bojinov, Bojin and Cetiner, Selim and Custers, René and Schrader, Uwe and Jacobsen, Hans-Joerg and Martin-Laffon, Jacqueline and Boisron, Audrey and Kuntz, Marcel},
	month = sep,
	year = {2016},
	pages = {875--883},
}

@article{zulfugarov_enhanced_2016,
	title = {Enhanced resistance of {PsbS}-deficient rice ({Oryza} sativa {L}.) to fungal and bacterial pathogens},
	volume = {59},
	issn = {1226-9239, 1867-0725},
	url = {http://link.springer.com/10.1007/s12374-016-0068-6},
	doi = {10.1007/s12374-016-0068-6},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Journal of Plant Biology},
	author = {Zulfugarov, Ismayil S. and Tovuu, Altanzaya and Kim, Chi-Yeol and Xuan Vo, Kieu Thi and Ko, Soo Yeon and Hall, Michael and Seok, Hye-Yeon and Kim, Yeon-Ki and Skogstrom, Oscar and Moon, Yong-Hwan and Jansson, Stefan and Jeon, Jong-Seong and Lee, Choon-Hwan},
	month = dec,
	year = {2016},
	pages = {616--626},
}

@article{benson_intact_2015,
	title = {An intact light harvesting complex {I} antenna system is required for complete state transitions in {Arabidopsis}},
	volume = {1},
	issn = {2055-0278 (Electronic) 2055-0278 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/27251716},
	doi = {10.1038/nplants.2015.176},
	abstract = {Efficient photosynthesis depends on maintaining balance between the rate of light-driven electron transport occurring in photosystem I (PSI) and photosystem II (PSII), located in the chloroplast thylakoid membranes. Balance is achieved through a process of 'state transitions' that increases energy transfer towards PSI when PSII is overexcited (state II), and towards PSII when PSI is overexcited (state I). This is achieved through redox control of the phosphorylation state of light-harvesting antenna complex II (LHCII). PSI is served by both LHCII and four light-harvesting antenna complex I (LHCI) subunits, Lhca1, 2, 3 and 4. Here we demonstrate that despite unchanged levels of LHCII phosphorylation, absence of specific Lhca subunits reduces state transitions in Arabidopsis. The severest phenotype-observed in a mutant lacking Lhca4 (DeltaLhca4)-displayed a 69\% reduction compared with the wild type. Yet, surprisingly, the amounts of the PSI-LHCI-LHCII supercomplex isolated by blue native polyacrylamide gel electrophoresis (BN-PAGE) from digitonin-solubilized thylakoids were similar in the wild type and DeltaLhca mutants. Fluorescence excitation spectroscopy revealed that in the wild type this PSI-LHCI-LHCII supercomplex is supplemented by energy transfer from additional LHCII trimers in state II, whose binding is sensitive to digitonin, and which are absent in DeltaLhca4. The grana margins of the thylakoid membrane were found to be the primary site of interaction between this 'extra' LHCII and the PSI-LHCI-LHCII supercomplex in state II. The results suggest that the LHCI complexes mediate energetic interactions between LHCII and PSI in the intact membrane.},
	language = {en},
	number = {12},
	urldate = {2021-06-07},
	journal = {Nat Plants},
	author = {Benson, S. L. and Maheswaran, P. and Ware, M. A. and Hunter, C. N. and Horton, P. and Jansson, S. and Ruban, A. V. and Johnson, M. P.},
	month = nov,
	year = {2015},
	note = {Edition: 2015/01/01},
	pages = {15176},
}

Efficient photosynthesis depends on maintaining balance between the rate of light-driven electron transport occurring in photosystem I (PSI) and photosystem II (PSII), located in the chloroplast thylakoid membranes. Balance is achieved through a process of 'state transitions' that increases energy transfer towards PSI when PSII is overexcited (state II), and towards PSII when PSI is overexcited (state I). This is achieved through redox control of the phosphorylation state of light-harvesting antenna complex II (LHCII). PSI is served by both LHCII and four light-harvesting antenna complex I (LHCI) subunits, Lhca1, 2, 3 and 4. Here we demonstrate that despite unchanged levels of LHCII phosphorylation, absence of specific Lhca subunits reduces state transitions in Arabidopsis. The severest phenotype-observed in a mutant lacking Lhca4 (DeltaLhca4)-displayed a 69% reduction compared with the wild type. Yet, surprisingly, the amounts of the PSI-LHCI-LHCII supercomplex isolated by blue native polyacrylamide gel electrophoresis (BN-PAGE) from digitonin-solubilized thylakoids were similar in the wild type and DeltaLhca mutants. Fluorescence excitation spectroscopy revealed that in the wild type this PSI-LHCI-LHCII supercomplex is supplemented by energy transfer from additional LHCII trimers in state II, whose binding is sensitive to digitonin, and which are absent in DeltaLhca4. The grana margins of the thylakoid membrane were found to be the primary site of interaction between this 'extra' LHCII and the PSI-LHCI-LHCII supercomplex in state II. The results suggest that the LHCI complexes mediate energetic interactions between LHCII and PSI in the intact membrane.

@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{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.

@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{keefover-ring_no_2014,
	title = {No {Evidence} of {Geographical} {Structure} of {Salicinoid} {Chemotypes} within {Populus} {Tremula}},
	volume = {9},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0107189},
	doi = {10/f25fhm},
	language = {en},
	number = {10},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Keefover-Ring, Ken and Ahnlund, Maria and Abreu, Ilka Nacif and Jansson, Stefan and Moritz, Thomas and Albrectsen, Benedicte Riber},
	editor = {Yin, Tongming},
	month = oct,
	year = {2014},
	pages = {e107189},
}

@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{zulfugarov_production_2014,
	title = {Production of superoxide from {Photosystem} {II} in a rice ({Oryza} {sativaL}.) mutant lacking {PsbS}},
	volume = {14},
	issn = {1471-2229},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-014-0242-2},
	doi = {10/f3m3zb},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Plant Biology},
	author = {Zulfugarov, Ismayil S and Tovuu, Altanzaya and Eu, Young-Jae and Dogsom, Bolormaa and Poudyal, Roshan Sharma and Nath, Krishna and Hall, Michael and Banerjee, Mainak and Yoon, Ung Chan and Moon, Yong-Hwan and An, Gynheung and Jansson, Stefan and Lee, Choon-Hwan},
	month = dec,
	year = {2014},
	pages = {242},
}

@article{pietrzykowska_light-harvesting_2014,
	title = {The {Light}-{Harvesting} {Chlorophyll} a/b {Binding} {Proteins} {Lhcb1} and {Lhcb2} {Play} {Complementary} {Roles} during {State} {Transitions} in {Arabidopsis}},
	volume = {26},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/26/9/3646-3660/6100356},
	doi = {10/f25cg8},
	language = {en},
	number = {9},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Pietrzykowska, M. and Suorsa, M. and Semchonok, D. A. and Tikkanen, M. and Boekema, E. J. and Aro, E.-M. and Jansson, S.},
	month = sep,
	year = {2014},
	pages = {3646--3660},
}

@article{bernhardsson_geographic_2013,
	title = {Geographic structure in metabolome and herbivore community co-occurs with genetic structure in plant defence genes},
	volume = {16},
	issn = {1461023X},
	url = {http://doi.wiley.com/10.1111/ele.12114},
	doi = {10/f25rz6},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Ecology Letters},
	author = {Bernhardsson, Carolina and Robinson, Kathryn M. and Abreu, Ilka N. and Jansson, Stefan and Albrectsen, Benedicte R. and Ingvarsson, Pär K.},
	editor = {Eubanks, Micky},
	month = jun,
	year = {2013},
	pages = {791--798},
}

@article{johansson_jankanpaa_non-photochemical_2013,
	title = {Non-{Photochemical} {Quenching} {Capacity} in {Arabidopsis} thaliana {Affects} {Herbivore} {Behaviour}},
	volume = {8},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0053232},
	doi = {10/f22s4s},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Johansson Jänkänpää, Hanna and Frenkel, Martin and Zulfugarov, Ismayil and Reichelt, Michael and Krieger-Liszkay, Anja and Mishra, Yogesh and Gershenzon, Jonathan and Moen, Jon and Lee, Choon-Hwan and Jansson, Stefan},
	editor = {Tran, Lam-Son Phan},
	month = jan,
	year = {2013},
	pages = {e53232},
}

@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{leoni_very_2013,
	title = {Very rapid phosphorylation kinetics suggest a unique role for {Lhcb2} during state transitions in {Arabidopsis}},
	volume = {76},
	issn = {0960-7412, 1365-313X},
	shorttitle = {Very rapid phosphorylation kinetics suggest a unique role for {\textless}span style="font-variant},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/tpj.12297},
	doi = {10/f23mzn},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Leoni, Claudia and Pietrzykowska, Malgorzata and Kiss, Anett Z. and Suorsa, Marjaana and Ceci, Luigi R. and Aro, Eva‐Mari and Jansson, Stefan},
	month = oct,
	year = {2013},
	pages = {236--246},
}

@article{mishra_arabidopsis_2012,
	title = {Arabidopsis plants grown in the field and climate chambers significantly differ in leaf morphology and photosystem components},
	volume = {12},
	issn = {1471-2229},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-12-6},
	doi = {10/fx7f9h},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Plant Biology},
	author = {Mishra, Yogesh and Johansson Jänkänpää, Hanna and Kiss, Anett Z and Funk, Christiane and Schröder, Wolfgang P and Jansson, Stefan},
	year = {2012},
	pages = {6},
}

@article{ismail_comparative_2012,
	title = {Comparative {Nucleotide} {Diversity} {Across} {North} {American} and {European} {Populus} {Species}},
	volume = {74},
	issn = {0022-2844, 1432-1432},
	url = {http://link.springer.com/10.1007/s00239-012-9504-5},
	doi = {10/f23j7s},
	language = {en},
	number = {5-6},
	urldate = {2021-06-08},
	journal = {Journal of Molecular Evolution},
	author = {Ismail, Mohamed and Soolanayakanahally, Raju Y. and Ingvarsson, Pär K. and Guy, Robert D. and Jansson, Stefan and Silim, Salim N. and El-Kassaby, Yousry A.},
	month = jun,
	year = {2012},
	pages = {257--272},
}

@article{robinson_genetic_2012,
	title = {Genetic {Variation} in {Functional} {Traits} {Influences} {Arthropod} {Community} {Composition} in {Aspen} ({Populus} tremula {L}.)},
	volume = {7},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0037679},
	doi = {10/f24ksj},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Robinson, Kathryn M. and Ingvarsson, Pär K. and Jansson, Stefan and Albrectsen, Benedicte R.},
	editor = {Kliebenstein, Daniel J.},
	month = may,
	year = {2012},
	pages = {e37679},
}

@incollection{dunwell_how_2012,
	address = {Totowa, NJ},
	title = {How to {Grow} {Transgenic} {Arabidopsis} in the {Field}},
	volume = {847},
	isbn = {978-1-61779-557-2 978-1-61779-558-9},
	url = {http://link.springer.com/10.1007/978-1-61779-558-9_37},
	urldate = {2021-06-08},
	booktitle = {Transgenic {Plants}},
	publisher = {Humana Press},
	author = {Jänkänpää, Hanna Johansson and Jansson, Stefan},
	editor = {Dunwell, Jim M. and Wetten, Andy C.},
	year = {2012},
	doi = {10.1007/978-1-61779-558-9_37},
	note = {Series Title: Methods in Molecular Biology},
	pages = {483--494},
}

@article{jankanpaa_metabolic_2012,
	title = {Metabolic profiling reveals metabolic shifts in {Arabidopsis} plants grown under different light conditions: {Metabolic} profiling under different light regime},
	volume = {35},
	issn = {01407791},
	shorttitle = {Metabolic profiling reveals metabolic shifts in {Arabidopsis} plants grown under different light conditions},
	url = {http://doi.wiley.com/10.1111/j.1365-3040.2012.02519.x},
	doi = {10/f2z77r},
	language = {en},
	number = {10},
	urldate = {2021-06-08},
	journal = {Plant, Cell \& Environment},
	author = {Jänkänpää, Hanna Johansson and Mishra, Yogesh and Schröder, Wolfgang P. and Jansson, Stefan},
	month = oct,
	year = {2012},
	pages = {1824--1836},
}

@article{suorsa_proton_2012,
	title = {{PROTON} {GRADIENT} {REGULATION5} {Is} {Essential} for {Proper} {Acclimation} of {Arabidopsis} {Photosystem} {I} to {Naturally} and {Artificially} {Fluctuating} {Light} {Conditions}},
	volume = {24},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/24/7/2934-2948/6100862},
	doi = {10/f242kc},
	language = {en},
	number = {7},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Suorsa, Marjaana and Järvi, Sari and Grieco, Michele and Nurmi, Markus and Pietrzykowska, Malgorzata and Rantala, Marjaana and Kangasjärvi, Saijaliisa and Paakkarinen, Virpi and Tikkanen, Mikko and Jansson, Stefan and Aro, Eva-Mari},
	month = jul,
	year = {2012},
	pages = {2934--2948},
}

@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{mishra_expression_2011,
	title = {Expression, purification, crystallization and preliminary {X}-ray crystallographic studies of alkyl hydroperoxide reductase ({AhpC}) from the cyanobacterium \textit{{Anabaena}} sp. {PCC} 7120},
	volume = {67},
	issn = {1744-3091},
	url = {http://scripts.iucr.org/cgi-bin/paper?S1744309111025747},
	doi = {10/djxscc},
	number = {10},
	urldate = {2021-06-08},
	journal = {Acta Crystallographica Section F Structural Biology and Crystallization Communications},
	author = {Mishra, Yogesh and Hall, Michael and Chaurasia, Neha and Rai, Lal Chand and Jansson, Stefan and Schröder, Wolfgang P. and Sauer, Uwe H.},
	month = oct,
	year = {2011},
	pages = {1203--1206},
}

@article{wagner_fitness_2011,
	title = {Fitness analyses of \textit{{Arabidopsis} thaliana} mutants depleted of {FtsH} metalloproteases and characterization of three {FtsH6} deletion mutants exposed to high light stress, senescence and chilling},
	volume = {191},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2011.03684.x},
	doi = {10/d4frq4},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Wagner, Raik and Aigner, Harald and Pružinská, Adriana and Jänkänpää, Hanna Johansson and Jansson, Stefan and Funk, Christiane},
	month = jul,
	year = {2011},
	pages = {449--458},
}

@article{albrectsen_endophytic_2010,
	title = {Endophytic fungi in {European} aspen ({Populus} tremula) leaves—diversity, detection, and a suggested correlation with herbivory resistance},
	volume = {41},
	issn = {1560-2745, 1878-9129},
	url = {http://link.springer.com/10.1007/s13225-009-0011-y},
	doi = {10/cg5zgd},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Fungal Diversity},
	author = {Albrectsen, Benedicte R. and Björkén, Lars and Varad, Akkamahadevi and Hagner, Åsa and Wedin, Mats and Karlsson, Jan and Jansson, Stefan},
	month = mar,
	year = {2010},
	pages = {17--28},
}

@article{ma_genetic_2010,
	title = {Genetic {Differentiation}, {Clinal} {Variation} and {Phenotypic} {Associations} {With} {Growth} {Cessation} {Across} the \textit{{Populus} tremula} {Photoperiodic} {Pathway}},
	volume = {186},
	issn = {1943-2631},
	url = {https://academic.oup.com/genetics/article/186/3/1033/6063664},
	doi = {10/c7k7hc},
	abstract = {Abstract
            Perennial plants monitor seasonal changes through changes in environmental conditions such as the quantity and quality of light. To ensure a correct initiation of critical developmental processes, such as the initiation and cessation of growth, plants have adapted to a spatially variable light regime and genes in the photoperiodic pathway have been implicated as likely sources for these adaptations. Here we examine genetic variation in genes from the photoperiodic pathway in Populus tremula (Salicaceae) for signatures diversifying selection in response to varying light regimes across a latitudinal gradient. We fail to identify any loci with unusually high levels of genetic differentiation among populations despite identifying four SNPs that show significant allele frequency clines with latitude. We do, however, observe large covariance in allelic effects across populations for growth cessation, a highly adaptive trait in P. tremula. High covariance in allelic effects is a signature compatible with diversifying selection along an environmental gradient. We also observe significantly higher heterogeneity in genetic differentiation among SNPs from the photoperiod genes than among SNPs from randomly chosen genes. This suggests that spatially variable selection could be affecting genes from the photoperiod pathway even if selection is not strong enough to cause individual loci to be identified as outliers. SNPs from three genes in the photoperiod pathway (PHYB2, LHY1, and LHY2) show significant associations with natural variation in growth cessation. Collectively these SNPs explain 10–15\% of the phenotypic variation in growth cessation. Covariances in allelic effects across populations help explain an additional 5–7\% of the phenotypic variation in growth cessation.},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Genetics},
	author = {Ma, Xiao-Fei and Hall, David and Onge, Katherine R St and Jansson, Stefan and Ingvarsson, Pär K},
	month = nov,
	year = {2010},
	pages = {1033--1044},
}

Abstract Perennial plants monitor seasonal changes through changes in environmental conditions such as the quantity and quality of light. To ensure a correct initiation of critical developmental processes, such as the initiation and cessation of growth, plants have adapted to a spatially variable light regime and genes in the photoperiodic pathway have been implicated as likely sources for these adaptations. Here we examine genetic variation in genes from the photoperiodic pathway in Populus tremula (Salicaceae) for signatures diversifying selection in response to varying light regimes across a latitudinal gradient. We fail to identify any loci with unusually high levels of genetic differentiation among populations despite identifying four SNPs that show significant allele frequency clines with latitude. We do, however, observe large covariance in allelic effects across populations for growth cessation, a highly adaptive trait in P. tremula. High covariance in allelic effects is a signature compatible with diversifying selection along an environmental gradient. We also observe significantly higher heterogeneity in genetic differentiation among SNPs from the photoperiod genes than among SNPs from randomly chosen genes. This suggests that spatially variable selection could be affecting genes from the photoperiod pathway even if selection is not strong enough to cause individual loci to be identified as outliers. SNPs from three genes in the photoperiod pathway (PHYB2, LHY1, and LHY2) show significant associations with natural variation in growth cessation. Collectively these SNPs explain 10–15% of the phenotypic variation in growth cessation. Covariances in allelic effects across populations help explain an additional 5–7% of the phenotypic variation in growth cessation.

@article{courtois-moreau_unique_2009,
	title = {A unique program for cell death in xylem fibers of \textit{{Populus}} stem},
	volume = {58},
	issn = {09607412, 1365313X},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2008.03777.x},
	doi = {10/bqdrgm},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Courtois-Moreau, Charleen L. and Pesquet, Edouard and Sjödin, Andreas and Muñiz, Luis and Bollhöner, Benjamin and Kaneda, Minako and Samuels, Lacey and Jansson, Stefan and Tuominen, Hannele},
	month = apr,
	year = {2009},
	pages = {260--274},
}

@article{garcia-cerdan_antisense_2009,
	title = {Antisense {Inhibition} of the {PsbX} {Protein} {Affects} {PSII} {Integrity} in the {Higher} {Plant} {Arabidopsis} thaliana},
	volume = {50},
	issn = {1471-9053, 0032-0781},
	url = {https://academic.oup.com/pcp/article-lookup/doi/10.1093/pcp/pcn188},
	doi = {10/fbkmdx},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Plant and Cell Physiology},
	author = {García-Cerdán, José G. and Sveshnikov, Dmitry and Dewez, David and Jansson, Stefan and Funk, Christiane and Schröder, Wolfgang P.},
	month = feb,
	year = {2009},
	pages = {191--202},
}

@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{frenkel_improper_2009,
	title = {Improper excess light energy dissipation in {Arabidopsis} results in a metabolic reprogramming},
	volume = {9},
	issn = {1471-2229},
	url = {https://doi.org/10.1186/1471-2229-9-12},
	doi = {10/ffdbr8},
	abstract = {Plant performance is affected by the level of expression of PsbS, a key photoprotective protein involved in the process of feedback de-excitation (FDE), or the qE component of non-photochemical quenching, NPQ.},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Plant Biology},
	author = {Frenkel, Martin and Külheim, Carsten and Jänkänpää, Hanna Johansson and Skogström, Oskar and Dall'Osto, Luca and Ågren, Jon and Bassi, Roberto and Moritz, Thomas and Moen, Jon and Jansson, Stefan},
	month = jan,
	year = {2009},
	keywords = {Herbivore Preference, Partial Little Square Discriminant Analysis, Partial Little Square Discriminant Analysis Model, Photooxidative Stress, Photosynthetic Light Reaction},
	pages = {12},
}

Plant performance is affected by the level of expression of PsbS, a key photoprotective protein involved in the process of feedback de-excitation (FDE), or the qE component of non-photochemical quenching, NPQ.

@article{bylesjo_integrated_2009,
	title = {Integrated {Analysis} of {Transcript}, {Protein} and {Metabolite} {Data} {To} {Study} {Lignin} {Biosynthesis} in {Hybrid} {Aspen}},
	volume = {8},
	issn = {1535-3893, 1535-3907},
	url = {https://pubs.acs.org/doi/10.1021/pr800298s},
	doi = {10/ddqkpn},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Journal of Proteome Research},
	author = {Bylesjö, Max and Nilsson, Robert and Srivastava, Vaibhav and Grönlund, Andreas and Johansson, Annika I. and Jansson, Stefan and Karlsson, Jan and Moritz, Thomas and Wingsle, Gunnar and Trygg, Johan},
	month = jan,
	year = {2009},
	pages = {199--210},
}

@article{albrectsen_large_2009,
	title = {Large scale geographic clines of parasite damage to \textit{{Populus} tremula} {L}},
	issn = {09067590, 16000587},
	url = {http://doi.wiley.com/10.1111/j.1600-0587.2009.05982.x},
	doi = {10/c38874},
	language = {en},
	urldate = {2021-06-08},
	journal = {Ecography},
	author = {Albrectsen, Benedicte R. and Witzell, Johanna and Robinson, Kathryn M. and Wulff, Sören and Luquez, Virginia M. C. and Ågren, Rickard and Jansson, Stefan},
	month = oct,
	year = {2009},
}

@article{babst_local_2009,
	title = {Local and systemic transcriptome responses to herbivory and jasmonic acid in {Populus}},
	volume = {5},
	issn = {1614-2942, 1614-2950},
	url = {http://link.springer.com/10.1007/s11295-009-0200-6},
	doi = {10/fmhhv9},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Tree Genetics \& Genomes},
	author = {Babst, Benjamin A. and Sjödin, Andreas and Jansson, Stefan and Orians, Colin M.},
	month = jul,
	year = {2009},
	pages = {459--474},
}

@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{fracheboud_control_2009,
	title = {The {Control} of {Autumn} {Senescence} in {European} {Aspen}},
	volume = {149},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/149/4/1982/6107938},
	doi = {10/b8n86h},
	abstract = {Abstract
            The initiation, progression, and natural variation of autumn senescence in European aspen (Populus tremula) was investigated by monitoring chlorophyll degradation in (1) trees growing in natural stands and (2) cloned trees growing in a greenhouse under various light regimes. The main trigger for the initiation of autumn senescence in aspen is the shortening photoperiod, but there was a large degree of variation in the onset of senescence, both within local populations and among trees originating from different populations, where it correlated with the latitude of their respective origins. The variation for onset of senescence with a population was much larger than the variation of bud set. Once started, autumn senescence was accelerated by low temperature and longer nights, and clones that started to senescence late had a faster senescence. Bud set and autumn senescence appeared to be under the control of two independent critical photoperiods, but senescence could not be initiated until a certain time after bud set, suggesting that bud set and growth arrest are important for the trees to acquire competence to respond to the photoperiodic trigger to undergo autumn senescence. A timetable of events related to bud set and autumn senescence is presented.},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Fracheboud, Yvan and Luquez, Virginia and Björkén, Lars and Sjödin, Andreas and Tuominen, Hannele and Jansson, Stefan},
	month = apr,
	year = {2009},
	pages = {1982--1991},
}

Abstract The initiation, progression, and natural variation of autumn senescence in European aspen (Populus tremula) was investigated by monitoring chlorophyll degradation in (1) trees growing in natural stands and (2) cloned trees growing in a greenhouse under various light regimes. The main trigger for the initiation of autumn senescence in aspen is the shortening photoperiod, but there was a large degree of variation in the onset of senescence, both within local populations and among trees originating from different populations, where it correlated with the latitude of their respective origins. The variation for onset of senescence with a population was much larger than the variation of bud set. Once started, autumn senescence was accelerated by low temperature and longer nights, and clones that started to senescence late had a faster senescence. Bud set and autumn senescence appeared to be under the control of two independent critical photoperiods, but senescence could not be initiated until a certain time after bud set, suggesting that bud set and growth arrest are important for the trees to acquire competence to respond to the photoperiodic trigger to undergo autumn senescence. A timetable of events related to bud set and autumn senescence is presented.

@article{damkjaer_photosystem_2009,
	title = {The {Photosystem} {II} {Light}-{Harvesting} {Protein} {Lhcb3} {Affects} the {Macrostructure} of {Photosystem} {II} and the {Rate} of {State} {Transitions} in \textit{{Arabidopsis}}},
	volume = {21},
	issn = {1532-298X, 1040-4651},
	url = {https://academic.oup.com/plcell/article/21/10/3245/6096237},
	doi = {10/fb96fz},
	abstract = {Abstract
            The main trimeric light-harvesting complex of higher plants (LHCII) consists of three different Lhcb proteins (Lhcb1-3). We show that Arabidopsis thaliana T-DNA knockout plants lacking Lhcb3 (koLhcb3) compensate for the lack of Lhcb3 by producing increased amounts of Lhcb1 and Lhcb2. As in wild-type plants, LHCII-photosystem II (PSII) supercomplexes were present in Lhcb3 knockout plants (koLhcb3), and preservation of the LHCII trimers (M trimers) indicates that the Lhcb3 in M trimers has been replaced by Lhcb1 and/or Lhcb2. However, the rotational position of the M LHCII trimer was altered, suggesting that the Lhcb3 subunit affects the macrostructural arrangement of the LHCII antenna. The absence of Lhcb3 did not result in any significant alteration in PSII efficiency or qE type of nonphotochemical quenching, but the rate of transition from State 1 to State 2 was increased in koLhcb3, although the final extent of state transition was unchanged. The level of phosphorylation of LHCII was increased in the koLhcb3 plants compared with wild-type plants in both State 1 and State 2. The relative increase in phosphorylation upon transition from State 1 to State 2 was also significantly higher in koLhcb3. It is suggested that the main function of Lhcb3 is to modulate the rate of state transitions.},
	language = {en},
	number = {10},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Damkjær, Jakob T. and Kereïche, Sami and Johnson, Matthew P. and Kovacs, Laszlo and Kiss, Anett Z. and Boekema, Egbert J. and Ruban, Alexander V. and Horton, Peter and Jansson, Stefan},
	month = dec,
	year = {2009},
	pages = {3245--3256},
}

Abstract The main trimeric light-harvesting complex of higher plants (LHCII) consists of three different Lhcb proteins (Lhcb1-3). We show that Arabidopsis thaliana T-DNA knockout plants lacking Lhcb3 (koLhcb3) compensate for the lack of Lhcb3 by producing increased amounts of Lhcb1 and Lhcb2. As in wild-type plants, LHCII-photosystem II (PSII) supercomplexes were present in Lhcb3 knockout plants (koLhcb3), and preservation of the LHCII trimers (M trimers) indicates that the Lhcb3 in M trimers has been replaced by Lhcb1 and/or Lhcb2. However, the rotational position of the M LHCII trimer was altered, suggesting that the Lhcb3 subunit affects the macrostructural arrangement of the LHCII antenna. The absence of Lhcb3 did not result in any significant alteration in PSII efficiency or qE type of nonphotochemical quenching, but the rate of transition from State 1 to State 2 was increased in koLhcb3, although the final extent of state transition was unchanged. The level of phosphorylation of LHCII was increased in the koLhcb3 plants compared with wild-type plants in both State 1 and State 2. The relative increase in phosphorylation upon transition from State 1 to State 2 was also significantly higher in koLhcb3. It is suggested that the main function of Lhcb3 is to modulate the rate of state transitions.

@article{wientjes_role_2009,
	title = {The {Role} of {Lhca} {Complexes} in the {Supramolecular} {Organization} of {Higher} {Plant} {Photosystem} {I}},
	volume = {284},
	issn = {00219258},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0021925820324923},
	doi = {10/bpvfwk},
	language = {en},
	number = {12},
	urldate = {2021-06-08},
	journal = {Journal of Biological Chemistry},
	author = {Wientjes, Emilie and Oostergetel, Gert T. and Jansson, Stefan and Boekema, Egbert J. and Croce, Roberta},
	month = mar,
	year = {2009},
	pages = {7803--7810},
}

@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{frenkel_illustrated_2008,
	title = {An illustrated gardener's guide to transgenic \textit{{Arabidopsis}} field experiments},
	volume = {180},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2008.02591.x},
	doi = {10/ds43gk},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {New Phytologist},
	author = {Frenkel, Martin and Johansson Jänkänpää, Hanna and Moen, Jon and Jansson, Stefan},
	month = oct,
	year = {2008},
	pages = {545--555},
}

@article{sjodin_global_2008,
	title = {Global expression profiling in leaves of free-growing aspen},
	volume = {8},
	issn = {1471-2229},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-8-61},
	doi = {10/dsf6k8},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {BMC Plant Biology},
	author = {Sjodin, Andreas and Wissel, Kirsten and Bylesjo, Max and Trygg, Johan and Jansson, Stefan},
	year = {2008},
	pages = {61},
}

@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{luquez_natural_2008,
	title = {Natural phenological variation in aspen ({Populus} tremula): the {SwAsp} collection},
	volume = {4},
	issn = {1614-2942, 1614-2950},
	shorttitle = {Natural phenological variation in aspen ({Populus} tremula)},
	url = {http://link.springer.com/10.1007/s11295-007-0108-y},
	doi = {10/bwk27s},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {Tree Genetics \& Genomes},
	author = {Luquez, Virginia and Hall, David and Albrectsen, Benedicte R. and Karlsson, Jan and Ingvarsson, Pär and Jansson, Stefan},
	month = apr,
	year = {2008},
	pages = {279--292},
}

@article{ingvarsson_nucleotide_2008,
	title = {Nucleotide {Polymorphism} and {Phenotypic} {Associations} {Within} and {Around} the \textit{phytochrome {B2}} {Locus} in {European} {Aspen} ( \textit{{Populus} tremula} , {Salicaceae})},
	volume = {178},
	issn = {1943-2631},
	url = {https://academic.oup.com/genetics/article/178/4/2217/6073872},
	doi = {10/bd8hh3},
	abstract = {Abstract
            We investigated the utility of association mapping to dissect the genetic basis of naturally occurring variation in bud phenology in European aspen (Populus tremula). With this aim, we surveyed nucleotide polymorphism in 13 fragments spanning an 80-kb region surrounding the phytochrome B2 (phyB2) locus. Although polymorphism varies substantially across the phyB2 region, we detected no signs for deviations from neutral expectations. We also identified a total of 41 single nucleotide polymorphisms (SNPs) that were subsequently scored in a mapping population consisting of 120 trees. We identified two nonsynonymous SNPs in the phytochrome B2 gene that were independently associated with variation in the timing of bud set and that explained between 1.5 and 5\% of the observed phenotypic variation in bud set. Earlier studies have shown that the frequencies of both these SNPs vary clinally with latitude. Linkage disequilibrium across the region was low, suggesting that the SNPs we identified are strong candidates for being causally linked to variation in bud set in our mapping populations. One of the SNPs (T608N) is located in the “hinge region,” close to the chromophore binding site of the phyB2 protein. The other SNP (L1078P) is located in a region supposed to mediate downstream signaling from the phyB2 locus. The lack of population structure, combined with low levels of linkage disequilibrium, suggests that association mapping is a fruitful method for dissecting naturally occurring variation in Populus tremula.},
	language = {en},
	number = {4},
	urldate = {2021-06-10},
	journal = {Genetics},
	author = {Ingvarsson, Pär K and Garcia, M Victoria and Luquez, Virginia and Hall, David and Jansson, Stefan},
	month = apr,
	year = {2008},
	pages = {2217--2226},
}

Abstract We investigated the utility of association mapping to dissect the genetic basis of naturally occurring variation in bud phenology in European aspen (Populus tremula). With this aim, we surveyed nucleotide polymorphism in 13 fragments spanning an 80-kb region surrounding the phytochrome B2 (phyB2) locus. Although polymorphism varies substantially across the phyB2 region, we detected no signs for deviations from neutral expectations. We also identified a total of 41 single nucleotide polymorphisms (SNPs) that were subsequently scored in a mapping population consisting of 120 trees. We identified two nonsynonymous SNPs in the phytochrome B2 gene that were independently associated with variation in the timing of bud set and that explained between 1.5 and 5% of the observed phenotypic variation in bud set. Earlier studies have shown that the frequencies of both these SNPs vary clinally with latitude. Linkage disequilibrium across the region was low, suggesting that the SNPs we identified are strong candidates for being causally linked to variation in bud set in our mapping populations. One of the SNPs (T608N) is located in the “hinge region,” close to the chromophore binding site of the phyB2 protein. The other SNP (L1078P) is located in a region supposed to mediate downstream signaling from the phyB2 locus. The lack of population structure, combined with low levels of linkage disequilibrium, suggests that association mapping is a fruitful method for dissecting naturally occurring variation in Populus tremula.

@article{jansson_senescence_2008,
	title = {Senescence: developmental program or timetable?},
	volume = {179},
	issn = {0028-646X, 1469-8137},
	shorttitle = {Senescence},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2008.02471.x},
	doi = {10/drc9xn},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {New Phytologist},
	author = {Jansson, Stefan and Thomas, Howard},
	month = aug,
	year = {2008},
	pages = {575--579},
}

@article{hall_adaptive_2007,
	title = {Adaptive {Population} {Differentiation} in {Phenology} across a {Latitudinal} {Gradient} in {European} {Aspen} ({Populus} tremula, {L}.): {A} {Comparison} of {Neutral} {Markers}, {Candidate} {Genes} and {Phenotypic} {Traits}},
	volume = {61},
	issn = {0014-3820, 1558-5646},
	shorttitle = {Adaptive {Population} {Differentiation} in {Phenology} across a {Latitudinal} {Gradient} in {European} {Aspen} ({Populus} tremula, {L}.)},
	url = {http://doi.wiley.com/10.1111/j.1558-5646.2007.00230.x},
	doi = {10/bv9gz6},
	language = {en},
	number = {12},
	urldate = {2021-06-10},
	journal = {Evolution},
	author = {Hall, David and Luquez, Virginia and Garcia, Victoria M. and St Onge, Kate R. and Jansson, Stefan and Ingvarsson, Pär K.},
	month = dec,
	year = {2007},
	pages = {2849--2860},
}

@article{segerman_characterization_2007,
	title = {Characterization of genes with tissue-specific differential expression patterns in {Populus}},
	volume = {3},
	issn = {1614-2942, 1614-2950},
	url = {http://link.springer.com/10.1007/s11295-006-0077-6},
	doi = {10/ct8snb},
	language = {en},
	number = {4},
	urldate = {2021-06-10},
	journal = {Tree Genetics \& Genomes},
	author = {Segerman, Bo and Jansson, Stefan and Karlsson, Jan},
	month = aug,
	year = {2007},
	pages = {351--362},
}

@article{lee_growth-phase-dependent_2007,
	title = {Growth-phase-dependent gene expression profiling of poplar ({Populus} alba × {Populus} tremula var. glandulosa) suspension cells},
	volume = {131},
	issn = {0031-9317, 1399-3054},
	url = {http://doi.wiley.com/10.1111/j.1399-3054.2007.00987.x},
	doi = {10/b8dzcg},
	language = {en},
	number = {4},
	urldate = {2021-06-10},
	journal = {Physiologia Plantarum},
	author = {Lee, Hyoshin and Bae, Eun-Kyung and Park, So-Young and Sjödin, Andreas and Lee, Jae-Soon and Noh, Eun-Woon and Jansson, Stefan},
	month = dec,
	year = {2007},
	pages = {599--613},
}

@article{frenkel_hierarchy_2007,
	title = {Hierarchy amongst photosynthetic acclimation responses for plant fitness},
	volume = {129},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1399-3054.2006.00831.x},
	doi = {10.1111/j.1399-3054.2006.00831.x},
	abstract = {We have compared the seed production of Arabidopsis wild-type and mutant plants impaired in the regulation of the photosynthetic light reactions grown under natural conditions in the field. Mutant plants (npq4) lacking feedback de-excitation were, as previously demonstrated, severely affected in seed production. Seed sets of plants deficient in state transitions (stn7) were 19\% smaller than those of wild-type plants, whereas plants missing the STN8 kinase required for the phosphorylation of the core photosystem II reaction centre polypeptides (stn8) had a normal seed production. Plants lacking both STN7 and STN8 kinases were strongly affected, indicating that these mutations act synergistically. In contrast, npq4×stn7 double mutants had the same seed set as npq4 mutants.},
	language = {en},
	number = {2},
	urldate = {2024-06-28},
	journal = {Physiologia Plantarum},
	author = {Frenkel, Martin and Bellafiore, Stephane and Rochaix, Jean-David and Jansson, Stefan},
	year = {2007},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1399-3054.2006.00831.x},
	pages = {455--459},
}

We have compared the seed production of Arabidopsis wild-type and mutant plants impaired in the regulation of the photosynthetic light reactions grown under natural conditions in the field. Mutant plants (npq4) lacking feedback de-excitation were, as previously demonstrated, severely affected in seed production. Seed sets of plants deficient in state transitions (stn7) were 19% smaller than those of wild-type plants, whereas plants missing the STN8 kinase required for the phosphorylation of the core photosystem II reaction centre polypeptides (stn8) had a normal seed production. Plants lacking both STN7 and STN8 kinases were strongly affected, indicating that these mutations act synergistically. In contrast, npq4×stn7 double mutants had the same seed set as npq4 mutants.

@article{bylesjo_orthogonal_2007,
	title = {Orthogonal projections to latent structures as a strategy for microarray data normalization},
	volume = {8},
	issn = {1471-2105},
	url = {https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-207},
	doi = {10/dfs78z},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {BMC Bioinformatics},
	author = {Bylesjö, Max and Eriksson, Daniel and Sjödin, Andreas and Jansson, Stefan and Moritz, Thomas and Trygg, Johan},
	month = dec,
	year = {2007},
	pages = {207},
}

@article{jansson_populus_2007,
	title = {Populus: {A} {Model} {System} for {Plant} {Biology}},
	volume = {58},
	issn = {1543-5008},
	shorttitle = {Populus},
	url = {https://www.annualreviews.org/doi/10.1146/annurev.arplant.58.032806.103956},
	doi = {10/d42zfw},
	abstract = {With the completion of the Populus trichocarpa genome sequence and the development of various genetic, genomic, and biochemical tools, Populus now offers many possibilities to study questions that cannot be as easily addressed in Arabidopsis and rice, the two prime model systems of plant biology and genomics. Tree-specific traits such as wood formation, long-term perennial growth, and seasonality are obvious areas of research, but research in other areas such as control of flowering, biotic interactions, and evolution of adaptive traits is enriched by adding a tree to the suite of model systems. Furthermore, the reproductive biology of Populus (a dioeceous wind-pollinated long-lived tree) offers both new possibilities and challenges in the study and analysis of natural genetic and phenotypic variation. The relatively close phylogenetic relationship of Populus to Arabidopsis in the Eurosid clade of Eudicotyledonous plants aids in comparative functional studies and comparative genomics, and has the potential to greatly facilitate studies on genome and gene family evolution in eudicots.},
	number = {1},
	urldate = {2021-06-21},
	journal = {Annual Review of Plant Biology},
	author = {Jansson, Stefan and Douglas, Carl J.},
	month = jun,
	year = {2007},
	note = {Publisher: Annual Reviews},
	pages = {435--458},
}

With the completion of the Populus trichocarpa genome sequence and the development of various genetic, genomic, and biochemical tools, Populus now offers many possibilities to study questions that cannot be as easily addressed in Arabidopsis and rice, the two prime model systems of plant biology and genomics. Tree-specific traits such as wood formation, long-term perennial growth, and seasonality are obvious areas of research, but research in other areas such as control of flowering, biotic interactions, and evolution of adaptive traits is enriched by adding a tree to the suite of model systems. Furthermore, the reproductive biology of Populus (a dioeceous wind-pollinated long-lived tree) offers both new possibilities and challenges in the study and analysis of natural genetic and phenotypic variation. The relatively close phylogenetic relationship of Populus to Arabidopsis in the Eurosid clade of Eudicotyledonous plants aids in comparative functional studies and comparative genomics, and has the potential to greatly facilitate studies on genome and gene family evolution in eudicots.

@article{jensen_structure_2007,
	title = {Structure, function and regulation of plant photosystem {I}},
	volume = {1767},
	issn = {00052728},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0005272807000722},
	doi = {10/fdc7p3},
	language = {en},
	number = {5},
	urldate = {2021-06-10},
	journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
	author = {Jensen, Poul Erik and Bassi, Roberto and Boekema, Egbert J. and Dekker, Jan P. and Jansson, Stefan and Leister, Dario and Robinson, Colin and Scheller, Henrik Vibe},
	month = may,
	year = {2007},
	pages = {335--352},
}

@article{klimmek_abundantly_2006,
	title = {Abundantly and rarely expressed {Lhc} protein genes exhibit distinct regulation patterns in plants},
	volume = {140},
	issn = {0032-0889},
	doi = {10/fbrp2z},
	abstract = {We have analyzed gene regulation of the Lhc supergene family in poplar ( Populus spp.) and Arabidopsis ( Arabidopsis thaliana) using digital expression profiling. Multivariate analysis of the tissue-specific, environmental, and developmental Lhc expression patterns in Arabidopsis and poplar was employed to characterize four rarely expressed Lhc genes, Lhca5, Lhca6, Lhcb7, and Lhcb4.3. Those genes have high expression levels under different conditions and in different tissues than the abundantly expressed Lhca1 to 4 and Lhcb1 to 6 genes that code for the 10 major types of higher plant light-harvesting proteins. However, in some of the datasets analyzed, the Lhcb4 and Lhcb6 genes as well as an Arabidopsis gene not present in poplar ( Lhcb2.3) exhibited minor differences to the main cooperative Lhc gene expression pattern. The pattern of the rarely expressed Lhc genes was always found to be more similar to that of PsbS and the various light-harvesting- like genes, which might indicate distinct physiological functions for the rarely and abundantly expressed Lhc proteins. The previously undetected Lhcb7 gene encodes a novel plant Lhcb-type protein that possibly contains an additional, fourth, transmembrane N-terminal helix with a highly conserved motif. As the Lhcb4.3 gene seems to be present only in Eurosid species and as its regulation pattern varies significantly from that of Lhcb4.1 and Lhcb4.2, we conclude it to encode a distinct Lhc protein type, Lhcb8.},
	language = {English},
	number = {3},
	journal = {Plant Physiology},
	author = {Klimmek, F. and Sjodin, A. and Noutsos, C. and Leister, D. and Jansson, S.},
	month = mar,
	year = {2006},
	note = {Place: Rockville
Publisher: Amer Soc Plant Biologists
WOS:000235868900001},
	keywords = {a/b-binding proteins, arabidopsis, chloroplast transit   peptides, draft sequence, energy-dissipation, light-harvesting-complex, membrane-proteins, photosystem-ii, pigment-binding, posttranscriptional   mechanisms},
	pages = {793--804},
}

We have analyzed gene regulation of the Lhc supergene family in poplar ( Populus spp.) and Arabidopsis ( Arabidopsis thaliana) using digital expression profiling. Multivariate analysis of the tissue-specific, environmental, and developmental Lhc expression patterns in Arabidopsis and poplar was employed to characterize four rarely expressed Lhc genes, Lhca5, Lhca6, Lhcb7, and Lhcb4.3. Those genes have high expression levels under different conditions and in different tissues than the abundantly expressed Lhca1 to 4 and Lhcb1 to 6 genes that code for the 10 major types of higher plant light-harvesting proteins. However, in some of the datasets analyzed, the Lhcb4 and Lhcb6 genes as well as an Arabidopsis gene not present in poplar ( Lhcb2.3) exhibited minor differences to the main cooperative Lhc gene expression pattern. The pattern of the rarely expressed Lhc genes was always found to be more similar to that of PsbS and the various light-harvesting- like genes, which might indicate distinct physiological functions for the rarely and abundantly expressed Lhc proteins. The previously undetected Lhcb7 gene encodes a novel plant Lhcb-type protein that possibly contains an additional, fourth, transmembrane N-terminal helix with a highly conserved motif. As the Lhcb4.3 gene seems to be present only in Eurosid species and as its regulation pattern varies significantly from that of Lhcb4.1 and Lhcb4.2, we conclude it to encode a distinct Lhc protein type, Lhcb8.

@article{bohlenius_coft_2006,
	title = {{CO}/{FT} regulatory module controls timing of flowering and seasonal growth cessation in trees},
	volume = {312},
	issn = {0036-8075},
	doi = {10/csznqf},
	abstract = {Forest trees display a perennial growth behavior characterized by a multiple-year delay in flowering and, in temperate regions, an annual cycling between growth and dormancy. We show here that the CO/FT regulatory module, which controls flowering time in response to variations in daylength in annual plants, controls flowering in aspen trees. Unexpectedly, however, it also controls the short-day-induced growth cessation and bud set occurring in the fall. This regulatory mechanism can explain the ecogenetic variation in a highly adaptive trait: the critical daylength for growth cessation displayed by aspen trees sampled across a latitudinal gradient spanning northern Europe.},
	language = {English},
	number = {5776},
	journal = {Science},
	author = {Bohlenius, H. and Huang, T. and Charbonnel-Campaa, L. and Brunner, A. M. and Jansson, S. and Strauss, S. H. and Nilsson, O.},
	month = may,
	year = {2006},
	note = {Place: Washington
Publisher: Amer Assoc Advancement Science
WOS:000237628800042},
	keywords = {arabidopsis, aspen populus-tremula, black cottonwood, bud set, candidate gene, ft, induction, phytochrome, protein, shoot   apex},
	pages = {1040--1043},
}

Forest trees display a perennial growth behavior characterized by a multiple-year delay in flowering and, in temperate regions, an annual cycling between growth and dormancy. We show here that the CO/FT regulatory module, which controls flowering time in response to variations in daylength in annual plants, controls flowering in aspen trees. Unexpectedly, however, it also controls the short-day-induced growth cessation and bud set occurring in the fall. This regulatory mechanism can explain the ecogenetic variation in a highly adaptive trait: the critical daylength for growth cessation displayed by aspen trees sampled across a latitudinal gradient spanning northern Europe.

@article{ingvarsson_clinal_2006,
	title = {Clinal variation in {phyB2}, a candidate gene for day-length-induced growth cessation and bud set, across a latitudinal gradient in {European} aspen ({Populus} tremula)},
	volume = {172},
	issn = {0016-6731},
	doi = {10.1534/genetics.105.047522},
	abstract = {The initiation of growth cessation and dormancy represents a Critical ecological and evolutionary tradeoff between survival and growth in most. forest trees. The Most important environmental cue regulating the initiation of dormancy is a shortening of the photoperiod and phytochrome genes have been implicated in short-day-induced bud set and growth cessation in Populus. We characterized patterns of DNA sequence variation at the putative candidate gene phyB2 in 4 populations of European aspen (Populus tremula) and scored single-nucleotide polymorphisms in an additional 12 populations collected along a latitudinal gradient in Sweden. We also measured bud set from a subset Of these trees in a growth chamber experiment. Buds set. showed significant clinal variation With latitude, explaining similar to 90\% Of the population variation in bud Set. A sliding-window scan of phyB2 identified six putative regions with enhanced population differentiation and four SNPs showed significant clinal variation. The clinal variation at individual SNPs is suggestive of all adaptive response in phyB2 to local photoperiodic conditions. Three of four SNPs showing clinal variation were located in regions With excessive genetic differentiation, demonstrating that searching for regions of high genetic differentiation call be useful for identifying sites putatively involved in local adaptation.},
	language = {English},
	number = {3},
	journal = {Genetics},
	author = {Ingvarsson, P. K. and Garcia, M. V. and Hall, D. and Luquez, V. and Jansson, S.},
	month = mar,
	year = {2006},
	note = {Place: Bethesda
Publisher: Genetics Society America
WOS:000236668100040},
	keywords = {adaptation, arabidopsis, coalescent, linkage disequilibrium, nucleotide diversity, phenology, polymorphism, populations, quantitative trait loci, selection},
	pages = {1845--1853},
}

The initiation of growth cessation and dormancy represents a Critical ecological and evolutionary tradeoff between survival and growth in most. forest trees. The Most important environmental cue regulating the initiation of dormancy is a shortening of the photoperiod and phytochrome genes have been implicated in short-day-induced bud set and growth cessation in Populus. We characterized patterns of DNA sequence variation at the putative candidate gene phyB2 in 4 populations of European aspen (Populus tremula) and scored single-nucleotide polymorphisms in an additional 12 populations collected along a latitudinal gradient in Sweden. We also measured bud set from a subset Of these trees in a growth chamber experiment. Buds set. showed significant clinal variation With latitude, explaining similar to 90% Of the population variation in bud Set. A sliding-window scan of phyB2 identified six putative regions with enhanced population differentiation and four SNPs showed significant clinal variation. The clinal variation at individual SNPs is suggestive of all adaptive response in phyB2 to local photoperiodic conditions. Three of four SNPs showing clinal variation were located in regions With excessive genetic differentiation, demonstrating that searching for regions of high genetic differentiation call be useful for identifying sites putatively involved in local adaptation.

@article{svalastog_comparative_2006,
	title = {Comparative analysis of the risk-handling procedures for gene technology applications in medical and plant science},
	volume = {12},
	issn = {1353-3452},
	doi = {10/b58tj9},
	abstract = {In this paper we analyse how the risks associated with research on transgenic plants are regulated in Sweden. The paper outlines the way in which pilot projects in the plant sciences are overseen in Sweden, and discusses the international and national background to the current regulatory system. The historical, and hitherto unexplored, reasons for the evolution of current administrative and legislative procedures in plant science are of particular interest. Specifically, we discuss similarities and differences in the regulation of medicine and plant science, and we examine the tendency towards dichotomizing risk-focusing on social/ethical risks in medicine and biological risks in plant science. The context of this article is the Synpraxia research project, an inter-disciplinary program combining expertise in sciences and the humanities.},
	language = {English},
	number = {3},
	journal = {Science and Engineering Ethics},
	author = {Svalastog, Anna Lydia and Gustafsson, Petter and Jansson, Stefan},
	month = jul,
	year = {2006},
	note = {Place: Guildford
Publisher: Opragen Publications
WOS:000239947700006},
	keywords = {World War II, gene technology, medical ethics, plant science, public   opinion},
	pages = {465--479},
}

In this paper we analyse how the risks associated with research on transgenic plants are regulated in Sweden. The paper outlines the way in which pilot projects in the plant sciences are overseen in Sweden, and discusses the international and national background to the current regulatory system. The historical, and hitherto unexplored, reasons for the evolution of current administrative and legislative procedures in plant science are of particular interest. Specifically, we discuss similarities and differences in the regulation of medicine and plant science, and we examine the tendency towards dichotomizing risk-focusing on social/ethical risks in medicine and biological risks in plant science. The context of this article is the Synpraxia research project, an inter-disciplinary program combining expertise in sciences and the humanities.

@article{albrectsen_micro_2006,
	title = {From micro towards the macro scale},
	volume = {172},
	issn = {0028-646X},
	doi = {10.1111/j.1469-8137.2006.01869.x},
	language = {English},
	number = {1},
	journal = {New Phytologist},
	author = {Albrectsen, Benedicte R. and Jansson, Stefan},
	year = {2006},
	note = {Place: Hoboken
Publisher: Wiley
WOS:000239988100003},
	keywords = {arabidopsis, biofuel, coevolution, developmental biology, diversity, genes, plant defence   strategy, plants, scientific outreach, small RNA},
	pages = {7--10},
}

@article{kovacs_lack_2006,
	title = {Lack of the {Light}-{Harvesting} {Complex} {CP24} {Affects} the {Structure} and {Function} of the {Grana} {Membranes} of {Higher} {Plant} {Chloroplasts}},
	volume = {18},
	issn = {1040-4651},
	url = {https://doi.org/10.1105/tpc.106.045641},
	doi = {10.1105/tpc.106.045641},
	abstract = {The photosystem II (PSII) light-harvesting antenna in higher plants contains a number of highly conserved gene products whose function is unknown. Arabidopsis thaliana plants depleted of one of these, the CP24 light-harvesting complex, have been analyzed. CP24-deficient plants showed a decrease in light-limited photosynthetic rate and growth, but the pigment and protein content of the thylakoid membranes were otherwise almost unchanged. However, there was a major change in the macroorganization of PSII within these membranes; electron microscopy and image analysis revealed the complete absence of the C2S2M2 light-harvesting complex II (LHCII)/PSII supercomplex predominant in wild-type plants. Instead, only C2S2 supercomplexes, which are deficient in the LHCIIb M-trimers, were found. Spectroscopic analysis confirmed the disruption of the wild-type macroorganization of PSII. It was found that the functions of the PSII antenna were disturbed: connectivity between PSII centers was reduced, and maximum photochemical yield was lowered; rapidly reversible nonphotochemical quenching was inhibited; and the state transitions were altered kinetically. CP24 is therefore an important factor in determining the structure and function of the PSII light-harvesting antenna, providing the linker for association of the M-trimer into the PSII complex, allowing a specific macroorganization that is necessary both for maximum quantum efficiency and for photoprotective dissipation of excess excitation energy.},
	number = {11},
	urldate = {2021-06-11},
	journal = {The Plant Cell},
	author = {Kovács, László and Damkjær, Jakob and Kereïche, Sami and Ilioaia, Cristian and Ruban, Alexander V. and Boekema, Egbert J. and Jansson, Stefan and Horton, Peter},
	month = nov,
	year = {2006},
	pages = {3106--3120},
}

The photosystem II (PSII) light-harvesting antenna in higher plants contains a number of highly conserved gene products whose function is unknown. Arabidopsis thaliana plants depleted of one of these, the CP24 light-harvesting complex, have been analyzed. CP24-deficient plants showed a decrease in light-limited photosynthetic rate and growth, but the pigment and protein content of the thylakoid membranes were otherwise almost unchanged. However, there was a major change in the macroorganization of PSII within these membranes; electron microscopy and image analysis revealed the complete absence of the C2S2M2 light-harvesting complex II (LHCII)/PSII supercomplex predominant in wild-type plants. Instead, only C2S2 supercomplexes, which are deficient in the LHCIIb M-trimers, were found. Spectroscopic analysis confirmed the disruption of the wild-type macroorganization of PSII. It was found that the functions of the PSII antenna were disturbed: connectivity between PSII centers was reduced, and maximum photochemical yield was lowered; rapidly reversible nonphotochemical quenching was inhibited; and the state transitions were altered kinetically. CP24 is therefore an important factor in determining the structure and function of the PSII light-harvesting antenna, providing the linker for association of the M-trimer into the PSII complex, allowing a specific macroorganization that is necessary both for maximum quantum efficiency and for photoprotective dissipation of excess excitation energy.

@article{lucinski_lhca5_2006,
	title = {Lhca5 interaction with plant photosystem {I}},
	volume = {580},
	copyright = {FEBS Letters 580 (2006) 1873-3468 © 2015 Federation of European Biochemical Societies},
	issn = {1873-3468},
	url = {https://febs.onlinelibrary.wiley.com/doi/abs/10.1016/j.febslet.2006.10.063},
	doi = {10.1016/j.febslet.2006.10.063},
	abstract = {In the outer antenna (LHCI) of higher plant photosystem I (PSI) four abundantly expressed light-harvesting protein of photosystem I (Lhca)-type proteins are organized in two heterodimeric domains (Lhca1/Lhca4 and Lhca2/Lhca3). Our cross-linking studies on PSI-LHCI preparations from wildtype Arabidopsis and pea plants indicate an exclusive interaction of the rarely expressed Lhca5 light-harvesting protein with LHCI in the Lhca2/Lhca3-site. In PSI particles with an altered LHCI composition Lhca5 assembles in the Lhca1/Lhca4 site, partly as a homodimer. This flexibility indicates a binding-competitive model for the LHCI assembly in plants regulated by molecular interactions of the Lhca proteins with the PSI core.},
	language = {en},
	number = {27},
	urldate = {2021-06-11},
	journal = {FEBS Letters},
	author = {Lucinski, Robert and Schmid, Volkmar H. R. and Jansson, Stefan and Klimmek, Frank},
	year = {2006},
	note = {\_eprint: https://febs.onlinelibrary.wiley.com/doi/pdf/10.1016/j.febslet.2006.10.063},
	keywords = {Cross-linking, LHCI, Lhca, Lhca5, Light-harvesting complex I, PSI, Photosystem I, chl, chlorophyll, depleted in Lhca protein, light-harvesting complex I, light-harvesting protein of photosystem I, photosystem I, wildtype, wt, ΔLhca},
	pages = {6485--6488},
}

In the outer antenna (LHCI) of higher plant photosystem I (PSI) four abundantly expressed light-harvesting protein of photosystem I (Lhca)-type proteins are organized in two heterodimeric domains (Lhca1/Lhca4 and Lhca2/Lhca3). Our cross-linking studies on PSI-LHCI preparations from wildtype Arabidopsis and pea plants indicate an exclusive interaction of the rarely expressed Lhca5 light-harvesting protein with LHCI in the Lhca2/Lhca3-site. In PSI particles with an altered LHCI composition Lhca5 assembles in the Lhca1/Lhca4 site, partly as a homodimer. This flexibility indicates a binding-competitive model for the LHCI assembly in plants regulated by molecular interactions of the Lhca proteins with the PSI core.

@article{bylesjo_masqot-gui_2006,
	title = {{MASQOT}-{GUI}: spot quality assessment for the two-channel microarray platform},
	volume = {22},
	issn = {1367-4803},
	shorttitle = {{MASQOT}-{GUI}},
	url = {https://doi.org/10.1093/bioinformatics/btl434},
	doi = {10.1093/bioinformatics/btl434},
	abstract = {Summary: MASQOT-GUI provides an open-source, platform-independent software pipeline for two-channel microarray spot quality control. This includes gridding, segmentation, quantification, quality assessment and data visualization. It hosts a set of independent applications, with interactions between the tools as well as import and export support for external software. The implementation of automated multivariate quality control assessment, which is a unique feature of MASQOT-GUI, is based on the previously documented and evaluated MASQOT methodology. Further abilities of the application are outlined and illustrated.Availability: MASQOT-GUI is Java-based and licensed under the GNU LGPL. Source code and installation files are available for download at Contact: This email address is being protected from spambots. You need JavaScript enabled to view it. information: Supplementary data are available at Bioinformatics online},
	number = {20},
	urldate = {2021-06-11},
	journal = {Bioinformatics},
	author = {Bylesjö, Max and Sjödin, Andreas and Eriksson, Daniel and Antti, Henrik and Moritz, Thomas and Jansson, Stefan and Trygg, Johan},
	month = oct,
	year = {2006},
	pages = {2554--2555},
}

Summary: MASQOT-GUI provides an open-source, platform-independent software pipeline for two-channel microarray spot quality control. This includes gridding, segmentation, quantification, quality assessment and data visualization. It hosts a set of independent applications, with interactions between the tools as well as import and export support for external software. The implementation of automated multivariate quality control assessment, which is a unique feature of MASQOT-GUI, is based on the previously documented and evaluated MASQOT methodology. Further abilities of the application are outlined and illustrated.Availability: MASQOT-GUI is Java-based and licensed under the GNU LGPL. Source code and installation files are available for download at Contact: This email address is being protected from spambots. You need JavaScript enabled to view it. information: Supplementary data are available at Bioinformatics online

@article{demmig-adams_modulation_2006,
	title = {Modulation of {PsbS} and flexible vs sustained energy dissipation by light environment in different species},
	volume = {127},
	issn = {0031-9317},
	doi = {10.1111/j.1399-3054.2006.00698.x},
	abstract = {Contrasting acclimation strategies of photosynthesis and photoprotection were identified for annual mesophytes (spinach, pumpkin, and Arabidopsis) vs the tropical evergreen Monstera deliciosa. The annual species utilized full sunlight for photosynthesis to a much greater extent than the evergreen species. Conversely, the evergreen species exhibited a greater capacity for photoprotective thermal energy dissipation as well as a greater expression of the PsbS protein in full sun than the annual species. In all species, the majority of thermal energy dissipation [assessed as non-photochemical fluorescence quenching (NPQ)] was the flexible, Delta pH-dependent form of NPQ over the entire range of growth light environments. However, in response to a transfer of shade-grown plants to high light, the evergreen species exhibited a high level of sustained thermal dissipation (ql), but the annual species did not. This sustained energy dissipation in the evergreen species was not Delta pH-dependent nor did the low level of PsbS in shade leaves increase upon transfer to high light for several days. Sustained Delta pH-independent NPQ was correlated (a) initially, with sustained DI protein phosphorylation and xanthophyll cycle arrest and U subsequently, with an accumulation over several days of PsbS-related one-helix proteins and newly synthesized zeaxanthin and lutein.},
	language = {English},
	number = {4},
	journal = {Physiologia Plantarum},
	author = {Demmig-Adams, Barbara and Ebbert, Volker and Mellman, David L. and Mueh, Kristine E. and Schaffer, Lisa and Funk, Christiane and Zarter, C. Ryan and Adamska, Iwona and Jansson, Stefan and Adams III, William W.},
	month = aug,
	year = {2006},
	note = {Place: Hoboken
Publisher: Wiley-Blackwell
WOS:000239561900014},
	keywords = {arabidopsis-thaliana, chlorophyll   fluorescence, excess excitation, inducible polypeptides, overwintering evergreens, photosystem-ii, protein, shade leaves, synechocystis pcc6803, xanthophyll cycle},
	pages = {670--680},
}

Contrasting acclimation strategies of photosynthesis and photoprotection were identified for annual mesophytes (spinach, pumpkin, and Arabidopsis) vs the tropical evergreen Monstera deliciosa. The annual species utilized full sunlight for photosynthesis to a much greater extent than the evergreen species. Conversely, the evergreen species exhibited a greater capacity for photoprotective thermal energy dissipation as well as a greater expression of the PsbS protein in full sun than the annual species. In all species, the majority of thermal energy dissipation [assessed as non-photochemical fluorescence quenching (NPQ)] was the flexible, Delta pH-dependent form of NPQ over the entire range of growth light environments. However, in response to a transfer of shade-grown plants to high light, the evergreen species exhibited a high level of sustained thermal dissipation (ql), but the annual species did not. This sustained energy dissipation in the evergreen species was not Delta pH-dependent nor did the low level of PsbS in shade leaves increase upon transfer to high light for several days. Sustained Delta pH-independent NPQ was correlated (a) initially, with sustained DI protein phosphorylation and xanthophyll cycle arrest and U subsequently, with an accumulation over several days of PsbS-related one-helix proteins and newly synthesized zeaxanthin and lutein.

@article{ruban_plasticity_2006,
	title = {Plasticity in the composition of the light harvesting antenna of higher plants preserves structural integrity and biological function},
	volume = {281},
	issn = {0021-9258},
	doi = {10.1074/jbc.M511415200},
	abstract = {Arabidopsis plants in which the major trimeric light harvesting complex ( LHCIIb) is eliminated by antisense expression still exhibit the typical macrostructure of photosystem II in the granal membranes. Here the detailed analysis of the composition and the functional state of the light harvesting antennae of both photosystem I and II of these plants is presented. Two new populations of trimers were found, both functional in energy transfer to the PSII reaction center, a homotrimer of CP26 and a heterotrimer of CP26 and Lhcb3. These trimers possess characteristic features thought to be specific for the native LHCIIb trimers they are replacing: the long wavelength form of lutein and at least one extra chlorophyll b, but they were less stable. A new population of loosely bound LHCI was also found, contributing to an increased antenna size for photosystem I, which may in part compensate for the loss of the phosphorylated LHCIIb that can associate with this photosystem. Thus, the loss of LHCIIb has triggered concerted compensatory responses in the composition of antennae of both photosystems. These responses clearly show the importance of LHCIIb in the structure and assembly of the photosynthetic membrane and illustrate the extreme plasticity at the level of the composition of the light harvesting system.},
	language = {English},
	number = {21},
	journal = {Journal of Biological Chemistry},
	author = {Ruban, Alexander V. and Solovieva, Svetlana and Lee, Pamela J. and Ilioaia, Cristian and Wentworth, Mark and Ganeteg, Ulrika and Klimmek, Frank and Chow, Wah Soon and Anderson, Jan M. and Jansson, Stefan and Horton, Peter},
	month = may,
	year = {2006},
	note = {Place: Rockville
Publisher: Amer Soc Biochemistry Molecular Biology Inc
WOS:000237671300051},
	keywords = {a/b-binding-proteins, acclimation, arabidopsis, complex-ii, crystal-structure, energy, photosystem-ii, spectroscopic analysis, supramolecular organization, xanthophylls},
	pages = {14981--14990},
}

Arabidopsis plants in which the major trimeric light harvesting complex ( LHCIIb) is eliminated by antisense expression still exhibit the typical macrostructure of photosystem II in the granal membranes. Here the detailed analysis of the composition and the functional state of the light harvesting antennae of both photosystem I and II of these plants is presented. Two new populations of trimers were found, both functional in energy transfer to the PSII reaction center, a homotrimer of CP26 and a heterotrimer of CP26 and Lhcb3. These trimers possess characteristic features thought to be specific for the native LHCIIb trimers they are replacing: the long wavelength form of lutein and at least one extra chlorophyll b, but they were less stable. A new population of loosely bound LHCI was also found, contributing to an increased antenna size for photosystem I, which may in part compensate for the loss of the phosphorylated LHCIIb that can associate with this photosystem. Thus, the loss of LHCIIb has triggered concerted compensatory responses in the composition of antennae of both photosystems. These responses clearly show the importance of LHCIIb in the structure and assembly of the photosynthetic membrane and illustrate the extreme plasticity at the level of the composition of the light harvesting system.

@article{garcia-lorenzo_protease_2006,
	title = {Protease gene families in {Populus} and {Arabidopsis}},
	volume = {6},
	issn = {1471-2229},
	url = {https://doi.org/10.1186/1471-2229-6-30},
	doi = {10.1186/1471-2229-6-30},
	abstract = {Proteases play key roles in plants, maintaining strict protein quality control and degrading specific sets of proteins in response to diverse environmental and developmental stimuli. Similarities and differences between the proteases expressed in different species may give valuable insights into their physiological roles and evolution.},
	number = {1},
	urldate = {2021-06-11},
	journal = {BMC Plant Biology},
	author = {García-Lorenzo, Maribel and Sjödin, Andreas and Jansson, Stefan and Funk, Christiane},
	month = dec,
	year = {2006},
	keywords = {Leaf Senescence, Protease Family, Protease Gene, Putative Protease, Tension Wood},
	pages = {30},
}

Proteases play key roles in plants, maintaining strict protein quality control and degrading specific sets of proteins in response to diverse environmental and developmental stimuli. Similarities and differences between the proteases expressed in different species may give valuable insights into their physiological roles and evolution.

@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{tuskan_genome_2006,
	title = {The genome of black cottonwood, {Populus} trichocarpa ({Torr}. \& {Gray})},
	volume = {313},
	issn = {0036-8075},
	doi = {10/c7hs34},
	abstract = {We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.},
	language = {English},
	number = {5793},
	journal = {Science},
	author = {Tuskan, G. A. and DiFazio, S. and Jansson, S. and Bohlmann, J. and Grigoriev, I. and Hellsten, U. and Putnam, N. and Ralph, S. and Rombauts, S. and Salamov, A. and Schein, J. and Sterck, L. and Aerts, A. and Bhalerao, Rishikesh P. and Bhalerao, R. P. and Blaudez, D. and Boerjan, W. and Brun, A. and Brunner, A. and Busov, V. and Campbell, M. and Carlson, J. and Chalot, M. and Chapman, J. and Chen, G.-L. and Cooper, D. and Coutinho, P. M. and Couturier, J. and Covert, S. and Cronk, Q. and Cunningham, R. and Davis, J. and Degroeve, S. and Dejardin, A. and dePamphilis, C. and Detter, J. and Dirks, B. and Dubchak, I. and Duplessis, S. and Ehlting, J. and Ellis, B. and Gendler, K. and Goodstein, D. and Gribskov, M. and Grimwood, J. and Groover, A. and Gunter, L. and Hamberger, B. and Heinze, B. and Helariutta, Y. and Henrissat, B. and Holligan, D. and Holt, R. and Huang, W. and Islam-Faridi, N. and Jones, S. and Jones-Rhoades, M. and Jorgensen, R. and Joshi, C. and Kangasjarvi, J. and Karlsson, J. and Kelleher, C. and Kirkpatrick, R. and Kirst, M. and Kohler, A. and Kalluri, U. and Larimer, F. and Leebens-Mack, J. and Leple, J.-C. and Locascio, P. and Lou, Y. and Lucas, S. and Martin, F. and Montanini, B. and Napoli, C. and Nelson, D. R. and Nelson, C. and Nieminen, K. and Nilsson, O. and Pereda, V. and Peter, G. and Philippe, R. and Pilate, G. and Poliakov, A. and Razumovskaya, J. and Richardson, P. and Rinaldi, C. and Ritland, K. and Rouze, P. and Ryaboy, D. and Schmutz, J. and Schrader, J. and Segerman, B. and Shin, H. and Siddiqui, A. and Sterky, F. and Terry, A. and Tsai, C.-J. and Uberbacher, E. and Unneberg, P. and Vahala, J. and Wall, K. and Wessler, S. and Yang, G. and Yin, T. and Douglas, C. and Marra, M. and Sandberg, G. and Van de Peer, Y. and Rokhsar, D.},
	month = sep,
	year = {2006},
	note = {Place: Washington
Publisher: Amer Assoc Advancement Science
WOS:000240498900035},
	keywords = {arabidopsis-thaliana, cinnamyl alcohol-dehydrogenase, gene-expression, gravitational induction, hybrid poplar, lignin biosynthesis, phenylpropanoid metabolism, quaking   aspen, resistance genes, transcriptional regulators},
	pages = {1596--1604},
}

We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.

@article{sjodin_upsc-base_2006,
	title = {{UPSC}-{BASE} - {Populus} transcriptomics online},
	volume = {48},
	issn = {0960-7412},
	doi = {10/cxqkhm},
	abstract = {The increasing accessibility and use of microarrays in transcriptomics has accentuated the need for purpose-designed storage and analysis tools. Here we present UPSC-BASE, a database for analysis and storage of Populus DNA microarray data. A microarray analysis pipeline has also been established to allow consistent and efficient analysis (from small to large scale) of samples in various experimental designs. A range of optimized experimental protocols is provided for each step in generating the data. Within UPSC-BASE, researchers can perform standard and advanced microarray analysis procedures in a user-friendly environment. Background corrections, normalizations, quality-control tools, visualizations, hypothesis tests and export tools are provided without requirements for expert-level knowledge. Although the database has been developed primarily for handling Populus DNA microarrays, most of the tools are generic and can be used for other types of microarray. UPSC-BASE is also a repository of Populus microarray information, providing data from 21 experiments on a total of 407 microarray hybridizations in the public domain of the database. There are also an additional 10 experiments containing 347 hybridizations, where the automatically analysed data are searchable.},
	language = {English},
	number = {5},
	journal = {Plant Journal},
	author = {Sjodin, Andreas and Bylesjo, Max and Skogstrom, Oskar and Eriksson, Daniel and Nilsson, Peter and Ryden, Patrik and Jansson, Stefan and Karlsson, Jan},
	month = dec,
	year = {2006},
	note = {Place: Hoboken
Publisher: Wiley
WOS:000242042900013},
	keywords = {bioconductor, cdna microarray data, database, design, expression profiling, functional genomics, gene-expression patterns, genomics, microarray, normalization, poplar, resource, sequence tags, tool, transcriptome},
	pages = {806--817},
}

The increasing accessibility and use of microarrays in transcriptomics has accentuated the need for purpose-designed storage and analysis tools. Here we present UPSC-BASE, a database for analysis and storage of Populus DNA microarray data. A microarray analysis pipeline has also been established to allow consistent and efficient analysis (from small to large scale) of samples in various experimental designs. A range of optimized experimental protocols is provided for each step in generating the data. Within UPSC-BASE, researchers can perform standard and advanced microarray analysis procedures in a user-friendly environment. Background corrections, normalizations, quality-control tools, visualizations, hypothesis tests and export tools are provided without requirements for expert-level knowledge. Although the database has been developed primarily for handling Populus DNA microarrays, most of the tools are generic and can be used for other types of microarray. UPSC-BASE is also a repository of Populus microarray information, providing data from 21 experiments on a total of 407 microarray hybridizations in the public domain of the database. There are also an additional 10 experiments containing 347 hybridizations, where the automatically analysed data are searchable.

@article{zarter_winter_2006,
	title = {Winter acclimation of {PsbS} and related proteins in the evergreen {Arctostaphylos} uva-ursi as influenced by altitude and light environment},
	volume = {29},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-3040.2005.01466.x},
	doi = {10/dffrdg},
	abstract = {The evergreen groundcover bearberry (Arctostaphylos uva-ursi[L.] Sprengel) was characterized over two successive years (2002–2004) from both sun-exposed and shaded sites at a montane ponderosa pine and subalpine forest community of 1900- and 2800-m-high altitudes, respectively. During summer, photosynthetic capacities and pre-dawn photosystem II (PSII) efficiency were similarly high in all four populations, and in winter, only the sun-exposed and shaded populations at 2800 m exhibited complete down-regulation of photosynthetic oxygen evolution capacity and consistent sustained down-regulation of PSII efficiency. This photosynthetic down-regulation at high altitude involved a substantial decrease in PSII components [pheophytin, D1 protein, oxygen evolving complex ([OEC)], a strong up-regulation of several anti-early-light-inducible protein (Elip)- and anti-high-light-inducible protein (Hlip)-reactive bands and a warm-sustained retention of zeaxanthin and antheraxanthin (Z + A). PsbS, the protein modulating the rapid engagement and disengagement of Z + A in energy dissipation, exhibited its most pronounced winter increases in the shade at 1900 m, and thus apparently assumes a greater role in providing rapidly reversible zeaxanthin-dependent photoprotection during winter when light becomes excessive in the shaded population, which remains photosynthetically active. It is attractive to hypothesize that PsbS relatives (Elips/Hlips) may be involved in sustained zeaxanthin-dependent photoprotection under the more extreme winter conditions at 2800 m.},
	language = {en},
	number = {5},
	urldate = {2021-06-11},
	journal = {Plant, Cell \& Environment},
	author = {Zarter, C. Ryan and Adams, William W. and Ebbert, Volker and Adamska, Iwona and Jansson, Stefan and Demmig-Adams, Barbara},
	year = {2006},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-3040.2005.01466.x},
	keywords = {D1 protein, Elip, Hlip, OEC, PsbS, energy dissipation, photoinhibition, photosynthesis, winter stress, zeaxanthin},
	pages = {869--878},
}

The evergreen groundcover bearberry (Arctostaphylos uva-ursi[L.] Sprengel) was characterized over two successive years (2002–2004) from both sun-exposed and shaded sites at a montane ponderosa pine and subalpine forest community of 1900- and 2800-m-high altitudes, respectively. During summer, photosynthetic capacities and pre-dawn photosystem II (PSII) efficiency were similarly high in all four populations, and in winter, only the sun-exposed and shaded populations at 2800 m exhibited complete down-regulation of photosynthetic oxygen evolution capacity and consistent sustained down-regulation of PSII efficiency. This photosynthetic down-regulation at high altitude involved a substantial decrease in PSII components [pheophytin, D1 protein, oxygen evolving complex ([OEC)], a strong up-regulation of several anti-early-light-inducible protein (Elip)- and anti-high-light-inducible protein (Hlip)-reactive bands and a warm-sustained retention of zeaxanthin and antheraxanthin (Z + A). PsbS, the protein modulating the rapid engagement and disengagement of Z + A in energy dissipation, exhibited its most pronounced winter increases in the shade at 1900 m, and thus apparently assumes a greater role in providing rapidly reversible zeaxanthin-dependent photoprotection during winter when light becomes excessive in the shaded population, which remains photosynthetically active. It is attractive to hypothesize that PsbS relatives (Elips/Hlips) may be involved in sustained zeaxanthin-dependent photoprotection under the more extreme winter conditions at 2800 m.

@article{keskitalo_cellular_2005,
	title = {A {Cellular} {Timetable} of {Autumn} {Senescence}},
	volume = {139},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.105.066845},
	doi = {10/cdw8rv},
	abstract = {We have studied autumn leaf senescence in a free-growing aspen (Populus tremula) by following changes in pigment, metabolite and nutrient content, photosynthesis, and cell and organelle integrity. The senescence process started on September 11, 2003, apparently initiated solely by the photoperiod, and progressed steadily without any obvious influence of other environmental signals. For example, after this date, senescing leaves accumulated anthocyanins in response to conditions inducing photooxidative stress, but at the beginning of September the leaves did not. Degradation of leaf constituents took place over an 18-d period, and, although the cells in each leaf did not all senesce in parallel, senescence in the tree as a whole was synchronous. Lutein and β-carotene were degraded in parallel with chlorophyll, whereas neoxanthin and the xanthophyll cycle pigments were retained longer. Chloroplasts in each cell were rapidly converted to gerontoplasts and many, although not all, cells died. From September 19, when chlorophyll levels had dropped by 50\%, mitochondrial respiration provided the energy for nutrient remobilization. Remobilization seemed to stop on September 29, probably due to the cessation of phloem transport, but, up to abscission of the last leaves (over 1 week later), some cells were metabolically active and had chlorophyll-containing gerontoplasts. About 80\% of the nitrogen and phosphorus was remobilized, and on September 29 a sudden change occurred in the δ15n of the cellular content, indicating that volatile compounds may have been released.},
	number = {4},
	urldate = {2021-06-11},
	journal = {Plant Physiology},
	author = {Keskitalo, Johanna and Bergquist, Gustaf and Gardeström, Per and Jansson, Stefan},
	month = dec,
	year = {2005},
	pages = {1635--1648},
}

We have studied autumn leaf senescence in a free-growing aspen (Populus tremula) by following changes in pigment, metabolite and nutrient content, photosynthesis, and cell and organelle integrity. The senescence process started on September 11, 2003, apparently initiated solely by the photoperiod, and progressed steadily without any obvious influence of other environmental signals. For example, after this date, senescing leaves accumulated anthocyanins in response to conditions inducing photooxidative stress, but at the beginning of September the leaves did not. Degradation of leaf constituents took place over an 18-d period, and, although the cells in each leaf did not all senesce in parallel, senescence in the tree as a whole was synchronous. Lutein and β-carotene were degraded in parallel with chlorophyll, whereas neoxanthin and the xanthophyll cycle pigments were retained longer. Chloroplasts in each cell were rapidly converted to gerontoplasts and many, although not all, cells died. From September 19, when chlorophyll levels had dropped by 50%, mitochondrial respiration provided the energy for nutrient remobilization. Remobilization seemed to stop on September 29, probably due to the cessation of phloem transport, but, up to abscission of the last leaves (over 1 week later), some cells were metabolically active and had chlorophyll-containing gerontoplasts. About 80% of the nitrogen and phosphorus was remobilized, and on September 29 a sudden change occurred in the δ15n of the cellular content, indicating that volatile compounds may have been released.

@article{moreau_genomic_2005,
	title = {A genomic approach to investigate developmental cell death in woody tissues of {Populus} trees},
	volume = {6},
	issn = {1474-760X},
	doi = {10.1186/gb-2005-6-4-r34},
	abstract = {Background: Poplar ( Populus sp.) has emerged as the main model system for molecular and genetic studies of forest trees. A Populus expressed sequence tag ( EST) database (POPULUSDB) was previously created from 19 cDNA libraries each originating from different Populus tree tissues, and opened to the public in September 2004. We used this dataset for in silico transcript profiling of a particular process in the woody tissues of the Populus stem: the programmed death of xylem fibers. Results: One EST library in POPULUSDB originates from woody tissues of the Populus stem where xylem fibers undergo cell death. Analysis of EST abundances and library distribution within the POPULUSDB revealed a large number of previously uncharacterized transcripts that were unique in this library and possibly related to the death of xylem fibers. The in silico analysis was complemented by a microarray analysis utilizing a novel Populus cDNA array with a unigene set of 25,000 sequences. Conclusions: In silico analysis, combined with the microarray analysis, revealed the usefulness of non-normalized EST libraries in elucidating transcriptional regulation of previously uncharacterized physiological processes. The data suggested the involvement of two novel extracellular serine proteases, nodulin-like proteins and an Arabidopsis thaliana OPEN STOMATA 1 (AtOST1) homolog in signaling fiber-cell death, as well as mechanisms responsible for hormonal control, nutrient remobilization, regulation of vacuolar integrity and autolysis of the dying fibers.},
	language = {English},
	number = {4},
	journal = {Genome Biology},
	author = {Moreau, C. and Aksenov, N. and Lorenzo, M. G. and Segerman, B. and Funk, C. and Nilsson, P. and Jansson, S. and Tuominen, H.},
	year = {2005},
	note = {Place: London
Publisher: Bmc
WOS:000228436000011},
	keywords = {arabidopsis, arabinogalactan proteins, expression, poplar, secondary   growth, senescence, serine proteases, tracheary element differentiation, transcriptome, xylogenesis},
	pages = {R34},
}

Background: Poplar ( Populus sp.) has emerged as the main model system for molecular and genetic studies of forest trees. A Populus expressed sequence tag ( EST) database (POPULUSDB) was previously created from 19 cDNA libraries each originating from different Populus tree tissues, and opened to the public in September 2004. We used this dataset for in silico transcript profiling of a particular process in the woody tissues of the Populus stem: the programmed death of xylem fibers. Results: One EST library in POPULUSDB originates from woody tissues of the Populus stem where xylem fibers undergo cell death. Analysis of EST abundances and library distribution within the POPULUSDB revealed a large number of previously uncharacterized transcripts that were unique in this library and possibly related to the death of xylem fibers. The in silico analysis was complemented by a microarray analysis utilizing a novel Populus cDNA array with a unigene set of 25,000 sequences. Conclusions: In silico analysis, combined with the microarray analysis, revealed the usefulness of non-normalized EST libraries in elucidating transcriptional regulation of previously uncharacterized physiological processes. The data suggested the involvement of two novel extracellular serine proteases, nodulin-like proteins and an Arabidopsis thaliana OPEN STOMATA 1 (AtOST1) homolog in signaling fiber-cell death, as well as mechanisms responsible for hormonal control, nutrient remobilization, regulation of vacuolar integrity and autolysis of the dying fibers.

@article{unneberg_analysis_2005,
	title = {Analysis of 70,000 {EST} sequences to study divergence between two closely related {Populus} species},
	volume = {1},
	issn = {1614-2950},
	url = {https://doi.org/10.1007/s11295-005-0014-0},
	doi = {10.1007/s11295-005-0014-0},
	abstract = {The Populus genus has evolved as the model organism for forest tree genomics, which has been further emphasised with the sequencing of the Populus trichocarpa genome. Populus species are widely spread over the Northern Hemisphere and provide a great source of genetic diversity, which can be used for mapping of quantitative trait loci, positional cloning, association mapping and studies in environmental adaptation. Collections of expressed sequence tags (ESTs) are rich sources in studies of genetic diversity. Here, we report on an in-depth analysis of 70,000 ESTs from two Populus species, Populus tremula and Populus trichocarpa. We present data on the level of conservation in transcript sequences and supply a collection of potential single nucleotide polymorphisms.},
	language = {en},
	number = {3},
	urldate = {2021-06-11},
	journal = {Tree Genetics \& Genomes},
	author = {Unneberg, Per and Strömberg, Michael and Lundeberg, Joakim and Jansson, Stefan and Sterky, Fredrik},
	month = nov,
	year = {2005},
	pages = {109--115},
}

The Populus genus has evolved as the model organism for forest tree genomics, which has been further emphasised with the sequencing of the Populus trichocarpa genome. Populus species are widely spread over the Northern Hemisphere and provide a great source of genetic diversity, which can be used for mapping of quantitative trait loci, positional cloning, association mapping and studies in environmental adaptation. Collections of expressed sequence tags (ESTs) are rich sources in studies of genetic diversity. Here, we report on an in-depth analysis of 70,000 ESTs from two Populus species, Populus tremula and Populus trichocarpa. We present data on the level of conservation in transcript sequences and supply a collection of potential single nucleotide polymorphisms.

@article{zelisko_atftsh6_2005,
	title = {{AtFtsH6} is involved in the degradation of the light-harvesting complex {II} during high-light acclimation and senescence},
	volume = {102},
	copyright = {Copyright © 2005, The National Academy of Sciences},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/102/38/13699},
	doi = {10.1073/pnas.0503472102},
	abstract = {Degradation of the most abundant membrane protein on earth, the light-harvesting complex of Photosystem II (LHC II), is highly regulated under various environmental conditions, e.g., light stress, to prevent photochemical damage to the reaction center. We identified the LHC II degrading protease in Arabidopsis thaliana as a Zn2+-dependent metalloprotease, activated by the removal of unknown extrinsic factors, similar to the proteolytic activity directed against Lhcb3 in barley. By using a reversed genetic approach, the chloroplast-targeted protease FtsH6 was identified as being responsible for the degradation. T-DNA KO A. thaliana mutants, lacking ftsH6, were unable to degrade either Lhcb3 during dark-induced senescence or Lhcb1 and Lhcb3 during highlight acclimation. The A. thaliana ftsH6 gene has a clear orthologue in the genome of Populus trichocarpa. It is likely that FtsH6 is a general LHC II protease and that FtsH6-dependent LHC II proteolysis is a feature of all higher plants.},
	language = {en},
	number = {38},
	urldate = {2021-06-11},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Żelisko, Agnieszka and García-Lorenzo, Maribel and Jackowski, Grzegorz and Jansson, Stefan and Funk, Christiane},
	month = sep,
	year = {2005},
	pmid = {16157880},
	note = {Publisher: National Academy of Sciences
Section: Biological Sciences},
	keywords = {membrane protein, photosynthesis, protease},
	pages = {13699--13704},
}

Degradation of the most abundant membrane protein on earth, the light-harvesting complex of Photosystem II (LHC II), is highly regulated under various environmental conditions, e.g., light stress, to prevent photochemical damage to the reaction center. We identified the LHC II degrading protease in Arabidopsis thaliana as a Zn2+-dependent metalloprotease, activated by the removal of unknown extrinsic factors, similar to the proteolytic activity directed against Lhcb3 in barley. By using a reversed genetic approach, the chloroplast-targeted protease FtsH6 was identified as being responsible for the degradation. T-DNA KO A. thaliana mutants, lacking ftsH6, were unable to degrade either Lhcb3 during dark-induced senescence or Lhcb1 and Lhcb3 during highlight acclimation. The A. thaliana ftsH6 gene has a clear orthologue in the genome of Populus trichocarpa. It is likely that FtsH6 is a general LHC II protease and that FtsH6-dependent LHC II proteolysis is a feature of all higher plants.

@article{sterck_est_2005,
	title = {{EST} data suggest that poplar is an ancient polyploid},
	volume = {167},
	issn = {1469-8137},
	url = {https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/j.1469-8137.2005.01378.x},
	doi = {10/c6wh5d},
	abstract = {• We analysed the publicly available expressed sequence tag (EST) collections for the genus Populus to examine whether evidence can be found for large-scale gene-duplication events in the evolutionary past of this genus. • The ESTs were clustered into unigenes for each poplar species examined. Gene families were constructed for all proteins deduced from these unigenes, and KS dating was performed on all paralogs within a gene family. The fraction of paralogs was then plotted against the KS values, which resulted in a distribution reflecting the age of duplicated genes in poplar. • Sufficient EST data were available for seven different poplar species spanning four of the six sections of the genus Populus. For all these species, there was evidence that a large-scale gene-duplication event had occurred. • From our analysis it is clear that all poplar species have shared the same large-scale gene-duplication event, suggesting that this event must have occurred in the ancestor of poplar, or at least very early in the evolution of the Populus genus.},
	language = {en},
	number = {1},
	urldate = {2021-06-11},
	journal = {New Phytologist},
	author = {Sterck, Lieven and Rombauts, Stephane and Jansson, Stefan and Sterky, Fredrik and Rouzé, Pierre and Peer, Yves Van de},
	year = {2005},
	note = {\_eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-8137.2005.01378.x},
	keywords = {EST (expressed sequence tag) data, KS dating, Populus (poplar), evolution, fossil record, genome duplication, polyploidy},
	pages = {165--170},
}

• We analysed the publicly available expressed sequence tag (EST) collections for the genus Populus to examine whether evidence can be found for large-scale gene-duplication events in the evolutionary past of this genus. • The ESTs were clustered into unigenes for each poplar species examined. Gene families were constructed for all proteins deduced from these unigenes, and KS dating was performed on all paralogs within a gene family. The fraction of paralogs was then plotted against the KS values, which resulted in a distribution reflecting the age of duplicated genes in poplar. • Sufficient EST data were available for seven different poplar species spanning four of the six sections of the genus Populus. For all these species, there was evidence that a large-scale gene-duplication event had occurred. • From our analysis it is clear that all poplar species have shared the same large-scale gene-duplication event, suggesting that this event must have occurred in the ancestor of poplar, or at least very early in the evolution of the Populus genus.

@article{villarejo_evidence_2005,
	title = {Evidence for a protein transported through the secretory pathway en route to the higher plant chloroplast},
	volume = {7},
	copyright = {2005 Nature Publishing Group},
	issn = {1476-4679},
	url = {https://www.nature.com/articles/ncb1330},
	doi = {10/fmrqwn},
	abstract = {In contrast to animal and fungal cells, green plant cells contain one or multiple chloroplasts, the organelle(s) in which photosynthetic reactions take place. Chloroplasts are believed to have originated from an endosymbiotic event and contain DNA that codes for some of their proteins. Most chloroplast proteins are encoded by the nuclear genome and imported with the help of sorting signals that are intrinsic parts of the polypeptides. Here, we show that a chloroplast-located protein in higher plants takes an alternative route through the secretory pathway, and becomes N-glycosylated before entering the chloroplast.},
	language = {en},
	number = {12},
	urldate = {2021-06-11},
	journal = {Nature Cell Biology},
	author = {Villarejo, Arsenio and Burén, Stefan and Larsson, Susanne and Déjardin, Annabelle and Monné, Magnus and Rudhe, Charlotta and Karlsson, Jan and Jansson, Stefan and Lerouge, Patrice and Rolland, Norbert and von Heijne, Gunnar and Grebe, Markus and Bakó, Laszlo and Samuelsson, Göran},
	month = dec,
	year = {2005},
	note = {Number: 12
Publisher: Nature Publishing Group},
	pages = {1224--1231},
}

In contrast to animal and fungal cells, green plant cells contain one or multiple chloroplasts, the organelle(s) in which photosynthetic reactions take place. Chloroplasts are believed to have originated from an endosymbiotic event and contain DNA that codes for some of their proteins. Most chloroplast proteins are encoded by the nuclear genome and imported with the help of sorting signals that are intrinsic parts of the polypeptides. Here, we show that a chloroplast-located protein in higher plants takes an alternative route through the secretory pathway, and becomes N-glycosylated before entering the chloroplast.

@article{ihalainen_excitation_2005,
	title = {Excitation energy trapping in photosystem {I} complexes depleted in {Lhca1} and {Lhca4}},
	volume = {579},
	copyright = {FEBS Letters 579 (2005) 1873-3468 © 2015 Federation of European Biochemical Societies},
	issn = {1873-3468},
	url = {https://febs.onlinelibrary.wiley.com/doi/abs/10.1016/j.febslet.2005.06.091},
	doi = {10.1016/j.febslet.2005.06.091},
	abstract = {We report a time-resolved fluorescence spectroscopy characterization of photosystem I (PSI) particles prepared from Arabidopsis lines with knock-out mutations against the peripheral antenna proteins of Lhca1 or Lhca4. The first mutant retains Lhca2 and Lhca3 while the second retains one other light-harvesting protein of photosystem I (Lhca) protein, probably Lhca5. The results indicate that Lhca2/3 and Lhca1/4 each provides about equally effective energy transfer routes to the PSI core complex, and that Lhca5 provides a less effective energy transfer route. We suggest that the specific location of each Lhca protein within the PSI–LHCI supercomplex is more important than the presence of so-called red chlorophylls in the Lhca proteins.},
	language = {en},
	number = {21},
	urldate = {2021-06-11},
	journal = {FEBS Letters},
	author = {Ihalainen, Janne A. and Klimmek, Frank and Ganeteg, Ulrika and Stokkum, Ivo H. M. van and Grondelle, Rienk van and Jansson, Stefan and Dekker, Jan P.},
	year = {2005},
	note = {\_eprint: https://febs.onlinelibrary.wiley.com/doi/pdf/10.1016/j.febslet.2005.06.091},
	keywords = {DAS, Excitation energy trapping, LHCI, Lhca, Light-harvesting, PSI, Photosynthesis, WT, decay-associated spectra, light-harvesting complex I, light-harvesting protein of photosystem I, photosystem I, wild type},
	pages = {4787--4791},
}

We report a time-resolved fluorescence spectroscopy characterization of photosystem I (PSI) particles prepared from Arabidopsis lines with knock-out mutations against the peripheral antenna proteins of Lhca1 or Lhca4. The first mutant retains Lhca2 and Lhca3 while the second retains one other light-harvesting protein of photosystem I (Lhca) protein, probably Lhca5. The results indicate that Lhca2/3 and Lhca1/4 each provides about equally effective energy transfer routes to the PSI core complex, and that Lhca5 provides a less effective energy transfer route. We suggest that the specific location of each Lhca protein within the PSI–LHCI supercomplex is more important than the presence of so-called red chlorophylls in the Lhca proteins.

@article{bylesjo_masqot_2005,
	title = {{MASQOT}: a method for {cDNA} microarray spot quality control},
	volume = {6},
	issn = {1471-2105},
	shorttitle = {{MASQOT}},
	url = {https://doi.org/10.1186/1471-2105-6-250},
	doi = {10.1186/1471-2105-6-250},
	abstract = {cDNA microarray technology has emerged as a major player in the parallel detection of biomolecules, but still suffers from fundamental technical problems. Identifying and removing unreliable data is crucial to prevent the risk of receiving illusive analysis results. Visual assessment of spot quality is still a common procedure, despite the time-consuming work of manually inspecting spots in the range of hundreds of thousands or more.},
	number = {1},
	urldate = {2021-06-11},
	journal = {BMC Bioinformatics},
	author = {Bylesjö, Max and Eriksson, Daniel and Sjödin, Andreas and Sjöström, Michael and Jansson, Stefan and Antti, Henrik and Trygg, Johan},
	month = oct,
	year = {2005},
	keywords = {Classification Training, Foreground Region, Microarray Slide, Partial Little Square, Spot Quality},
	pages = {250},
}

cDNA microarray technology has emerged as a major player in the parallel detection of biomolecules, but still suffers from fundamental technical problems. Identifying and removing unreliable data is crucial to prevent the risk of receiving illusive analysis results. Visual assessment of spot quality is still a common procedure, despite the time-consuming work of manually inspecting spots in the range of hundreds of thousands or more.

@article{storf_pigment_2005,
	title = {Pigment {Binding}, {Fluorescence} {Properties}, and {Oligomerization} {Behavior} of {Lhca5}, a {Novel} {Light}-harvesting {Protein}*},
	volume = {280},
	issn = {0021-9258},
	url = {https://www.sciencedirect.com/science/article/pii/S0021925819630103},
	doi = {10.1074/jbc.M411248200},
	abstract = {A new potential light-harvesting protein, named Lhca5, was recently detected in higher plants. Because of the low amount of Lhca5 in thylakoid membranes, the isolation of a native Lhca5 pigment-protein complex has not been achieved to date. Therefore, we used in vitro reconstitution to analyze whether Lhca5 binds pigments and is actually an additional light-harvesting protein. By this approach we could demonstrate that Lhca5 binds pigments in a unique stoichiometry. Analyses of pigment requirements for light-harvesting complex formation by Lhca5 revealed that chlorophyll b is the only indispensable pigment. Fluorescence measurements showed that ligated chlorophylls and carotenoids are arranged in a way that allows directed energy transfer within the light-harvesting complex. Reconstitutions of Lhca5 together with other Lhca proteins resulted in the formation of heterodimers with Lhca1. This result demonstrates that Lhca5 is indeed a protein belonging to the light-harvesting antenna of photosystem I. The properties of Lhca5 are compared with those of previously characterized Lhca proteins, and the consequences of an additional Lhca protein for the composition of the light-harvesting antenna of photosystem I are discussed in view of the recently published photosystem I structure of the pea.},
	language = {en},
	number = {7},
	urldate = {2021-06-11},
	journal = {Journal of Biological Chemistry},
	author = {Storf, Stefanie and Jansson, Stefan and Schmid, Volkmar H. R.},
	month = feb,
	year = {2005},
	pages = {5163--5168},
}

A new potential light-harvesting protein, named Lhca5, was recently detected in higher plants. Because of the low amount of Lhca5 in thylakoid membranes, the isolation of a native Lhca5 pigment-protein complex has not been achieved to date. Therefore, we used in vitro reconstitution to analyze whether Lhca5 binds pigments and is actually an additional light-harvesting protein. By this approach we could demonstrate that Lhca5 binds pigments in a unique stoichiometry. Analyses of pigment requirements for light-harvesting complex formation by Lhca5 revealed that chlorophyll b is the only indispensable pigment. Fluorescence measurements showed that ligated chlorophylls and carotenoids are arranged in a way that allows directed energy transfer within the light-harvesting complex. Reconstitutions of Lhca5 together with other Lhca proteins resulted in the formation of heterodimers with Lhca1. This result demonstrates that Lhca5 is indeed a protein belonging to the light-harvesting antenna of photosystem I. The properties of Lhca5 are compared with those of previously characterized Lhca proteins, and the consequences of an additional Lhca protein for the composition of the light-harvesting antenna of photosystem I are discussed in view of the recently published photosystem I structure of the pea.

@article{klimmek_structure_2005,
	title = {Structure of the {Higher} {Plant} {Light} {Harvesting} {Complex} {I}:  {In} {Vivo} {Characterization} and {Structural} {Interdependence} of the {Lhca} {Proteins}},
	volume = {44},
	issn = {0006-2960},
	shorttitle = {Structure of the {Higher} {Plant} {Light} {Harvesting} {Complex} {I}},
	url = {https://doi.org/10.1021/bi047873g},
	doi = {10/dfnxgm},
	abstract = {We have investigated the structure of the higher plant light harvesting complex of photosystem I (LHCI) by analyzing PSI−LHCI particles isolated from a set of Arabidopsis plant lines, each lacking a specific Lhca (Lhca1−4) polypeptide. Functional antenna size measurements support the recent finding that there are four Lhca proteins per PSI in the crystal structure [Ben-Shem, A., Frolow, F., and Nelson, N. (2003) Nature 426, 630−635]. According to HPLC analyses the number of pigment molecules bound within the LHCI is higher than expected from reconstitution studies or analyses of isolated native LHCI. Comparison of the spectra of the particles from the different lines reveals chlorophyll absorption bands peaking at 696, 688, 665, and 655 nm that are not present in isolated PSI or LHCI. These bands presumably originate from “gap” or “linker” pigments that are cooperatively coordinated by the Lhca and/or PSI proteins, which we have tentatively localized in the PSI−LHCI complex.},
	number = {8},
	urldate = {2021-06-11},
	journal = {Biochemistry},
	author = {Klimmek, Frank and Ganeteg, Ulrika and Ihalainen, Janne A. and van Roon, Henny and Jensen, Poul E. and Scheller, Henrik V. and Dekker, Jan P. and Jansson, Stefan},
	month = mar,
	year = {2005},
	note = {Publisher: American Chemical Society},
	pages = {3065--3073},
}

We have investigated the structure of the higher plant light harvesting complex of photosystem I (LHCI) by analyzing PSI−LHCI particles isolated from a set of Arabidopsis plant lines, each lacking a specific Lhca (Lhca1−4) polypeptide. Functional antenna size measurements support the recent finding that there are four Lhca proteins per PSI in the crystal structure [Ben-Shem, A., Frolow, F., and Nelson, N. (2003) Nature 426, 630−635]. According to HPLC analyses the number of pigment molecules bound within the LHCI is higher than expected from reconstitution studies or analyses of isolated native LHCI. Comparison of the spectra of the particles from the different lines reveals chlorophyll absorption bands peaking at 696, 688, 665, and 655 nm that are not present in isolated PSI or LHCI. These bands presumably originate from “gap” or “linker” pigments that are cooperatively coordinated by the Lhca and/or PSI proteins, which we have tentatively localized in the PSI−LHCI complex.

@article{morosinotto_association_2005,
	title = {The {Association} of the {Antenna} {System} to {Photosystem} {I} in {Higher} {Plants}: {COOPERATIVE} {INTERACTIONS} {STABILIZE} {THE} {SUPRAMOLECULAR} {COMPLEX} {AND} {ENHANCE} {RED}-{SHIFTED} {SPECTRAL} {FORMS}*},
	volume = {280},
	issn = {0021-9258},
	shorttitle = {The {Association} of the {Antenna} {System} to {Photosystem} {I} in {Higher} {Plants}},
	url = {https://www.sciencedirect.com/science/article/pii/S0021925820793798},
	doi = {10.1074/jbc.M502935200},
	abstract = {We report on the association of the antenna system to the reaction center in Photosystem I. Biochemical analysis of mutants depleted in antenna polypeptides showed that the binding of the antenna moiety is strongly cooperative. The minimal building block for the antenna system was shown to be a dimer. Specific protein-protein interactions play an important role in antenna association, and the gap pigments, bound at the interface between core and antenna, are proposed to mediate these interactions Gap pigments have been characterized by comparing the spectra of the Photosystem I to those of the isolated antenna and core components. CD spectroscopy showed that they are involved in pigment-pigment interactions, supporting their relevance in energy transfer from antenna to the reaction center. Moreover, gap pigments contribute to the red-shifted emission forms of Photosystem I antenna. When compared with Photosystem II, the association of peripheral antenna complexes in PSI appears to be more stable, but far less flexible and functional implications are discussed.},
	language = {en},
	number = {35},
	urldate = {2021-06-11},
	journal = {Journal of Biological Chemistry},
	author = {Morosinotto, Tomas and Ballottari, Matteo and Klimmek, Frank and Jansson, Stefan and Bassi, Roberto},
	month = sep,
	year = {2005},
	pages = {31050--31058},
}

We report on the association of the antenna system to the reaction center in Photosystem I. Biochemical analysis of mutants depleted in antenna polypeptides showed that the binding of the antenna moiety is strongly cooperative. The minimal building block for the antenna system was shown to be a dimer. Specific protein-protein interactions play an important role in antenna association, and the gap pigments, bound at the interface between core and antenna, are proposed to mediate these interactions Gap pigments have been characterized by comparing the spectra of the Photosystem I to those of the isolated antenna and core components. CD spectroscopy showed that they are involved in pigment-pigment interactions, supporting their relevance in energy transfer from antenna to the reaction center. Moreover, gap pigments contribute to the red-shifted emission forms of Photosystem I antenna. When compared with Photosystem II, the association of peripheral antenna complexes in PSI appears to be more stable, but far less flexible and functional implications are discussed.

@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{kulheim_what_2005,
	title = {What leads to reduced fitness in non-photochemical quenching mutants?},
	volume = {125},
	issn = {0031-9317},
	doi = {10/djtwsp},
	abstract = {Feedback de-excitation (FDE) is a process that protects photosystem II from damage during short periods of overexcitation. Arabidopsis thaliana mutants lacking this mechanism have reduced fitness in environments with variable light intensities. We have assayed the physiological consequences of mutations resulting in the lack of FDE and analysed the differences between field-grown plants and plants grown under fluctuating light in the laboratory. We show that FDE is an important mechanism in short-term responses to fluctuating light. Anthocyanin and carbohydrate levels indicated that the mutant plants were stressed to a higher degree than wild-type (WT) plants. Field-grown mutants were photo-inactivated to a greater degree than WT, whereas mutant plants in the fluctuating light environment in the laboratory seemed to downregulate the photosynthetic quantum yield, thereby avoiding photo-damage but resulting in impaired growth in the case of one mutant. Finally, we provide evidence that FDE is most important under conditions when photosynthesis limits plant growth, for example during flower and seed development.},
	language = {English},
	number = {2},
	journal = {Physiologia Plantarum},
	author = {Kulheim, C. and Jansson, S.},
	month = oct,
	year = {2005},
	note = {Place: Oxford
Publisher: Blackwell Publishing
WOS:000231677000006},
	keywords = {arabidopsis-thaliana, chlorophyll fluorescence, cold-acclimation, energy-dissipation, light-harvesting complex, low-temperature, photoinhibition, photosynthesis, plants, xanthophyll cycle},
	pages = {202--211},
}

Feedback de-excitation (FDE) is a process that protects photosystem II from damage during short periods of overexcitation. Arabidopsis thaliana mutants lacking this mechanism have reduced fitness in environments with variable light intensities. We have assayed the physiological consequences of mutations resulting in the lack of FDE and analysed the differences between field-grown plants and plants grown under fluctuating light in the laboratory. We show that FDE is an important mechanism in short-term responses to fluctuating light. Anthocyanin and carbohydrate levels indicated that the mutant plants were stressed to a higher degree than wild-type (WT) plants. Field-grown mutants were photo-inactivated to a greater degree than WT, whereas mutant plants in the fluctuating light environment in the laboratory seemed to downregulate the photosynthetic quantum yield, thereby avoiding photo-damage but resulting in impaired growth in the case of one mutant. Finally, we provide evidence that FDE is most important under conditions when photosynthesis limits plant growth, for example during flower and seed development.

@article{sterky_populus_2004,
	title = {A {Populus} {EST} resource for plant functional genomics},
	volume = {101},
	copyright = {Copyright © 2004, The National Academy of Sciences},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/101/38/13951},
	doi = {10/brt6bx},
	abstract = {Trees present a life form of paramount importance for terrestrial ecosystems and human societies because of their ecological structure and physiological function and provision of energy and industrial materials. The genus Populus is the internationally accepted model for molecular tree biology. We have analyzed 102,019 Populus ESTs that clustered into 11,885 clusters and 12,759 singletons. We also provide {\textgreater}4,000 assembled full clone sequences to serve as a basis for the upcoming annotation of the Populus genome sequence. A public web-based EST database (populusdb) provides digital expression profiles for 18 tissues that comprise the majority of differentiated organs. The coding content of Populus and Arabidopsis genomes shows very high similarity, indicating that differences between these annual and perennial angiosperm life forms result primarily from differences in gene regulation. The high similarity between Populus and Arabidopsis will allow studies of Populus to directly benefit from the detailed functional genomic information generated for Arabidopsis, enabling detailed insights into tree development and adaptation. These data will also valuable for functional genomic efforts in Arabidopsis.},
	language = {en},
	number = {38},
	urldate = {2021-06-15},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Sterky, Fredrik and Bhalerao, Rupali R. and Unneberg, Per and Segerman, Bo and Nilsson, Peter and Brunner, Amy M. and Charbonnel-Campaa, Laurence and Lindvall, Jenny Jonsson and Tandre, Karolina and Strauss, Steven H. and Sundberg, Björn and Gustafsson, Petter and Uhlén, Mathias and Bhalerao, Rishikesh P. and Nilsson, Ove and Sandberg, Göran and Karlsson, Jan and Lundeberg, Joakim and Jansson, Stefan},
	month = sep,
	year = {2004},
	pmid = {15353603},
	note = {Publisher: National Academy of Sciences
Section: Biological Sciences},
	pages = {13951--13956},
}

Trees present a life form of paramount importance for terrestrial ecosystems and human societies because of their ecological structure and physiological function and provision of energy and industrial materials. The genus Populus is the internationally accepted model for molecular tree biology. We have analyzed 102,019 Populus ESTs that clustered into 11,885 clusters and 12,759 singletons. We also provide \textgreater4,000 assembled full clone sequences to serve as a basis for the upcoming annotation of the Populus genome sequence. A public web-based EST database (populusdb) provides digital expression profiles for 18 tissues that comprise the majority of differentiated organs. The coding content of Populus and Arabidopsis genomes shows very high similarity, indicating that differences between these annual and perennial angiosperm life forms result primarily from differences in gene regulation. The high similarity between Populus and Arabidopsis will allow studies of Populus to directly benefit from the detailed functional genomic information generated for Arabidopsis, enabling detailed insights into tree development and adaptation. These data will also valuable for functional genomic efforts in Arabidopsis.

@article{andersson_transcriptional_2004,
	title = {A transcriptional timetable of autumn senescence},
	volume = {5},
	issn = {1474-760X},
	doi = {10/dw5fcc},
	abstract = {Background: We have developed genomic tools to allow the genus Populus ( aspens and cottonwoods) to be exploited as a full-featured model for investigating fundamental aspects of tree biology. We have undertaken large-scale expressed sequence tag ( EST) sequencing programs and created Populus microarrays with significant gene coverage. One of the important aspects of plant biology that cannot be studied in annual plants is the gene activity involved in the induction of autumn leaf senescence. Results: On the basis of 36,354 Populus ESTs, obtained from seven cDNA libraries, we have created a DNA microarray consisting of 13,490 clones, spotted in duplicate. Of these clones, 12,376 (92\%) were confirmed by resequencing and all sequences were annotated and functionally classified. Here we have used the microarray to study transcript abundance in leaves of a free-growing aspen tree ( Populus tremula) in northern Sweden during natural autumn senescence. Of the 13,490 spotted clones, 3,792 represented genes with significant expression in all leaf samples from the seven studied dates. Conclusions: We observed a major shift in gene expression, coinciding with massive chlorophyll degradation, that reflected a shift from photosynthetic competence to energy generation by mitochondrial respiration, oxidation of fatty acids and nutrient mobilization. Autumn senescence had much in common with senescence in annual plants; for example many proteases were induced. We also found evidence for increased transcriptional activity before the appearance of visible signs of senescence, presumably preparing the leaf for degradation of its components.},
	language = {English},
	number = {4},
	journal = {Genome Biology},
	author = {Andersson, A. and Keskitalo, J. and Sjodin, A. and Bhalerao, Rishikesh P. and Sterky, F. and Wissel, K. and Tandre, K. and Aspeborg, H. and Moyle, R. and Ohmiya, Y. and Bhalerao, R. and Brunner, A. and Gustafsson, P. and Karlsson, J. and Lundeberg, J. and Nilsson, O. and Sandberg, G. and Strauss, S. and Sundberg, B. and Uhlen, M. and Jansson, S. and Nilsson, P.},
	year = {2004},
	note = {Place: London
Publisher: Bmc
WOS:000220584700010},
	keywords = {aspen, biology, cytosolic glutamine-synthetase, gene-expression, genomics, leaf senescence, leaves, plants, programmed cell-death, proteins},
	pages = {R24},
}

Background: We have developed genomic tools to allow the genus Populus ( aspens and cottonwoods) to be exploited as a full-featured model for investigating fundamental aspects of tree biology. We have undertaken large-scale expressed sequence tag ( EST) sequencing programs and created Populus microarrays with significant gene coverage. One of the important aspects of plant biology that cannot be studied in annual plants is the gene activity involved in the induction of autumn leaf senescence. Results: On the basis of 36,354 Populus ESTs, obtained from seven cDNA libraries, we have created a DNA microarray consisting of 13,490 clones, spotted in duplicate. Of these clones, 12,376 (92%) were confirmed by resequencing and all sequences were annotated and functionally classified. Here we have used the microarray to study transcript abundance in leaves of a free-growing aspen tree ( Populus tremula) in northern Sweden during natural autumn senescence. Of the 13,490 spotted clones, 3,792 represented genes with significant expression in all leaf samples from the seven studied dates. Conclusions: We observed a major shift in gene expression, coinciding with massive chlorophyll degradation, that reflected a shift from photosynthetic competence to energy generation by mitochondrial respiration, oxidation of fatty acids and nutrient mobilization. Autumn senescence had much in common with senescence in annual plants; for example many proteases were induced. We also found evidence for increased transcriptional activity before the appearance of visible signs of senescence, presumably preparing the leaf for degradation of its components.

@article{lescot_annotation_2004,
	title = {Annotation of a 95-kb {Populus} deltoides genomic sequence reveals a disease resistance gene cluster and novel class {I} and class {II} transposable elements},
	volume = {109},
	issn = {1432-2242},
	url = {https://doi.org/10.1007/s00122-004-1621-0},
	doi = {10/d4g3m9},
	abstract = {Poplar has become a model system for functional genomics in woody plants. Here, we report the sequencing and annotation of the first large contiguous stretch of genomic sequence (95 kb) of poplar, corresponding to a bacterial artificial chromosome clone mapped 0.6 centiMorgan from the Melampsora larici-populina resistance locus. The annotation revealed 15 putative genetic objects, of which five were classified as hypothetical genes that were similar only with expressed sequence tags from poplar. Ten putative objects showed similarity with known genes, of which one was similar to a kinase. Three other objects corresponded to the toll/interleukin-1 receptor/nucleotide-binding site/leucine-rich repeat class of plant disease resistance genes, of which two were predicted to encode an amino terminal nuclear localization signal. Four objects were homologous to the Ty1/copia family of class I transposable elements, one of which was designated Retropop and interrupted one of the disease resistance genes. Two other objects constituted a novel Spm-like class II transposable element, which we designated Magali.},
	language = {en},
	number = {1},
	urldate = {2021-06-30},
	journal = {Theoretical and Applied Genetics},
	author = {Lescot, M. and Rombauts, S. and Zhang, J. and Aubourg, S. and Mathé, C. and Jansson, S. and Rouzé, P. and Boerjan, W.},
	month = jun,
	year = {2004},
	pages = {10--22},
}

Poplar has become a model system for functional genomics in woody plants. Here, we report the sequencing and annotation of the first large contiguous stretch of genomic sequence (95 kb) of poplar, corresponding to a bacterial artificial chromosome clone mapped 0.6 centiMorgan from the Melampsora larici-populina resistance locus. The annotation revealed 15 putative genetic objects, of which five were classified as hypothetical genes that were similar only with expressed sequence tags from poplar. Ten putative objects showed similarity with known genes, of which one was similar to a kinase. Three other objects corresponded to the toll/interleukin-1 receptor/nucleotide-binding site/leucine-rich repeat class of plant disease resistance genes, of which two were predicted to encode an amino terminal nuclear localization signal. Four objects were homologous to the Ty1/copia family of class I transposable elements, one of which was designated Retropop and interrupted one of the disease resistance genes. Two other objects constituted a novel Spm-like class II transposable element, which we designated Magali.

@article{ensminger_intermittent_2004,
	title = {Intermittent low temperatures constrain spring recovery of photosynthesis in boreal {Scots} pine forests},
	volume = {10},
	issn = {1354-1013},
	doi = {10/bg8q75},
	abstract = {During winter and early spring, evergreen boreal conifers are severely stressed because light energy cannot be used when photosynthesis is pre-empted by low ambient temperatures. To study photosynthetic performance dynamics in a severe boreal climate, seasonal changes in photosynthetic pigments, chloroplast proteins and photochemical efficiency were studied in a Scots pine forest near Zotino, Central Siberia. In winter, downregulation of photosynthesis involved loss of chlorophylls, a twofold increase in xanthophyll cycle pigments and sustained high levels of the light stress-induced zeaxanthin pigment. The highest levels of xanthophylls and zeaxanthin did not occur during the coldest winter period, but rather in April when light was increasing, indicating an increased capacity for thermal dissipation of excitation energy at that time. Concomitantly, in early spring the D1 protein of the photosystem II (PSII) reaction centre and the light-harvesting complex of PSII dropped to their lowest annual levels. In April and May, recovery of PSII activity, chloroplast protein synthesis and rearrangements of pigments were observed as air temperatures increased above 0degreesC. Nevertheless, severe intermittent low-temperature episodes during this period not only halted but actually reversed the physiological recovery. During these spring low-temperature episodes, protective processes involved a complementary function of the PsbS and early light-induced protein thylakoid proteins. Full recovery of photosynthesis did not occur until the end of May. Our results show that even after winter cold hardening, photosynthetic activity in evergreens responds opportunistically to environmental change throughout the cold season. Therefore, climate change effects potentially improve the sink capacity of boreal forests for atmospheric carbon. However, earlier photosynthesis in spring in response to warmer temperatures is strongly constrained by environmental variation, counteracting the positive effects of an early recovery process.},
	language = {English},
	number = {6},
	journal = {Global Change Biology},
	author = {Ensminger, I. and Sveshnikov, D. and Campbell, D. A. and Funk, C. and Jansson, S. and Lloyd, J. and Shibistova, O. and Oquist, G.},
	month = jun,
	year = {2004},
	note = {Place: Hoboken
Publisher: Wiley
WOS:000221741800006},
	keywords = {Pinus sylvestris, carbon balance, chlorophyll   fluorescence, cold stress, light-use efficiency, northern forests, photoinhibition, photosystem-ii, pigment composition, psbs protein, seasonal variations, seasonal-changes, snow cover, stress, xanthophyll cycle},
	pages = {995--1008},
}

During winter and early spring, evergreen boreal conifers are severely stressed because light energy cannot be used when photosynthesis is pre-empted by low ambient temperatures. To study photosynthetic performance dynamics in a severe boreal climate, seasonal changes in photosynthetic pigments, chloroplast proteins and photochemical efficiency were studied in a Scots pine forest near Zotino, Central Siberia. In winter, downregulation of photosynthesis involved loss of chlorophylls, a twofold increase in xanthophyll cycle pigments and sustained high levels of the light stress-induced zeaxanthin pigment. The highest levels of xanthophylls and zeaxanthin did not occur during the coldest winter period, but rather in April when light was increasing, indicating an increased capacity for thermal dissipation of excitation energy at that time. Concomitantly, in early spring the D1 protein of the photosystem II (PSII) reaction centre and the light-harvesting complex of PSII dropped to their lowest annual levels. In April and May, recovery of PSII activity, chloroplast protein synthesis and rearrangements of pigments were observed as air temperatures increased above 0degreesC. Nevertheless, severe intermittent low-temperature episodes during this period not only halted but actually reversed the physiological recovery. During these spring low-temperature episodes, protective processes involved a complementary function of the PsbS and early light-induced protein thylakoid proteins. Full recovery of photosynthesis did not occur until the end of May. Our results show that even after winter cold hardening, photosynthetic activity in evergreens responds opportunistically to environmental change throughout the cold season. Therefore, climate change effects potentially improve the sink capacity of boreal forests for atmospheric carbon. However, earlier photosynthesis in spring in response to warmer temperatures is strongly constrained by environmental variation, counteracting the positive effects of an early recovery process.

@article{ganeteg_is_2004,
	title = {Is {Each} {Light}-{Harvesting} {Complex} {Protein} {Important} for {Plant} {Fitness}?},
	volume = {134},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.103.033324},
	doi = {10/bmspz3},
	abstract = {Many of the photosynthetic genes are conserved among all higher plants, indicating that there is strong selective pressure to maintain the genes of each protein. However, mutants of these genes often lack visible growth phenotypes, suggesting that they are important only under certain conditions or have overlapping functions. To assess the importance of specific genes encoding the light-harvesting complex (LHC) proteins for the survival of the plant in the natural environment, we have combined two different scientific traditions by using an ecological fitness assay on a set of genetically modified Arabidopsis plants with differing LHC protein contents. The fitness of all of the LHC-deficient plants was reduced in some of the growth environments, supporting the hypothesis that each of the genes has been conserved because they provide ecological flexibility, which is of great adaptive value given the highly variable conditions encountered in nature.},
	number = {1},
	urldate = {2021-06-15},
	journal = {Plant Physiology},
	author = {Ganeteg, Ulrika and Külheim, Carsten and Andersson, Jenny and Jansson, Stefan},
	month = jan,
	year = {2004},
	pages = {502--509},
}

Many of the photosynthetic genes are conserved among all higher plants, indicating that there is strong selective pressure to maintain the genes of each protein. However, mutants of these genes often lack visible growth phenotypes, suggesting that they are important only under certain conditions or have overlapping functions. To assess the importance of specific genes encoding the light-harvesting complex (LHC) proteins for the survival of the plant in the natural environment, we have combined two different scientific traditions by using an ecological fitness assay on a set of genetically modified Arabidopsis plants with differing LHC protein contents. The fitness of all of the LHC-deficient plants was reduced in some of the growth environments, supporting the hypothesis that each of the genes has been conserved because they provide ecological flexibility, which is of great adaptive value given the highly variable conditions encountered in nature.

@article{ganeteg_lhca5_2004,
	title = {Lhca5 – an {LHC}-{Type} {Protein} {Associated} with {Photosystem} {I}},
	volume = {54},
	issn = {1573-5028},
	url = {https://doi.org/10.1023/B:PLAN.0000040813.05224.94},
	doi = {10/bkhvhq},
	abstract = {The light-harvesting antenna of higher plant photosystem (PS) I is known to be composed of four different types of light-harvesting complex (LHC) proteins (Lhca1–4). However, the genomic sequence of Arabidopsis thaliana contains open reading frames coding for two additional LHC type proteins (Lhca5–6) that are presumably associated with PSI. While Lhca6 might not be expressed at all, ESTs have been detected for the Lhca5 gene in Arabidopsis and a number of other plant species. Here we demonstrate the presence of the Lhca5 gene product in the thylakoid membrane of Arabidopsis as an additional type of Lhca-protein associated with PSI. Lhca5 seems to be regulated differently from the other LHC proteins since Lhca5 mRNA levels increase under high light conditions. Analyses reported here of Lhca5 in plants lacking individual Lhca1–4 proteins show that it is more abundant in plants lacking Lhca1/4, and suggest that it interacts in a direct physical fashion with Lhca2 or Lhca3. We propose that Lhca5 binds chlorophylls in a similar fashion to the other Lhca proteins and is associated with PSI only in sub-stoichiometric amounts.},
	language = {en},
	number = {5},
	urldate = {2021-06-15},
	journal = {Plant Molecular Biology},
	author = {Ganeteg, Ulrika and Klimmek, Frank and Jansson, Stefan},
	month = mar,
	year = {2004},
	pages = {641--651},
}

The light-harvesting antenna of higher plant photosystem (PS) I is known to be composed of four different types of light-harvesting complex (LHC) proteins (Lhca1–4). However, the genomic sequence of Arabidopsis thaliana contains open reading frames coding for two additional LHC type proteins (Lhca5–6) that are presumably associated with PSI. While Lhca6 might not be expressed at all, ESTs have been detected for the Lhca5 gene in Arabidopsis and a number of other plant species. Here we demonstrate the presence of the Lhca5 gene product in the thylakoid membrane of Arabidopsis as an additional type of Lhca-protein associated with PSI. Lhca5 seems to be regulated differently from the other LHC proteins since Lhca5 mRNA levels increase under high light conditions. Analyses reported here of Lhca5 in plants lacking individual Lhca1–4 proteins show that it is more abundant in plants lacking Lhca1/4, and suggest that it interacts in a direct physical fashion with Lhca2 or Lhca3. We propose that Lhca5 binds chlorophylls in a similar fashion to the other Lhca proteins and is associated with PSI only in sub-stoichiometric amounts.

@article{andersson_absence_2003,
	title = {Absence of the {Lhcb1} and {Lhcb2} proteins of the light-harvesting complex of photosystem {II} – effects on photosynthesis, grana stacking and fitness},
	volume = {35},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-313X.2003.01811.x},
	doi = {10.1046/j.1365-313X.2003.01811.x},
	abstract = {We have constructed Arabidopsis thaliana plants that are virtually devoid of the major light-harvesting complex, LHC II. This was accomplished by introducing the Lhcb2.1 coding region in the antisense orientation into the genome by Agrobacterium-mediated transformation. Lhcb1 and Lhcb2 were absent, while Lhcb3, a protein present in LHC II associated with photosystem (PS) II, was retained. Plants had a pale green appearance and showed reduced chlorophyll content and an elevated chlorophyll a/b ratio. The content of PS II reaction centres was unchanged on a leaf area basis, but there was evidence for increases in the relative levels of other light harvesting proteins, notably CP26, associated with PS II, and Lhca4, associated with PS I. Electron microscopy showed the presence of grana. Photosynthetic rates at saturating irradiance were the same in wild-type and antisense plants, but there was a 10–15\% reduction in quantum yield that reflected the decrease in light absorption by the leaf. The antisense plants were not able to perform state transitions, and their capacity for non-photochemical quenching was reduced. There was no difference in growth between wild-type and antisense plants under controlled climate conditions, but the antisense plants performed worse compared to the wild type in the field, with decreases in seed production of up to 70\%.},
	language = {en},
	number = {3},
	urldate = {2024-06-28},
	journal = {The Plant Journal},
	author = {Andersson, Jenny and Wentworth, Mark and Walters, Robin G. and Howard, Caroline A. and Ruban, Alexander V. and Horton, Peter and Jansson, Stefan},
	year = {2003},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-313X.2003.01811.x},
	keywords = {Arabidopsis, LHC II, antisense, fitness, photosynthesis, state transitions},
	pages = {350--361},
}

We have constructed Arabidopsis thaliana plants that are virtually devoid of the major light-harvesting complex, LHC II. This was accomplished by introducing the Lhcb2.1 coding region in the antisense orientation into the genome by Agrobacterium-mediated transformation. Lhcb1 and Lhcb2 were absent, while Lhcb3, a protein present in LHC II associated with photosystem (PS) II, was retained. Plants had a pale green appearance and showed reduced chlorophyll content and an elevated chlorophyll a/b ratio. The content of PS II reaction centres was unchanged on a leaf area basis, but there was evidence for increases in the relative levels of other light harvesting proteins, notably CP26, associated with PS II, and Lhca4, associated with PS I. Electron microscopy showed the presence of grana. Photosynthetic rates at saturating irradiance were the same in wild-type and antisense plants, but there was a 10–15% reduction in quantum yield that reflected the decrease in light absorption by the leaf. The antisense plants were not able to perform state transitions, and their capacity for non-photochemical quenching was reduced. There was no difference in growth between wild-type and antisense plants under controlled climate conditions, but the antisense plants performed worse compared to the wild type in the field, with decreases in seed production of up to 70%.

@article{bhalerao_gene_2003,
	title = {Gene {Expression} in {Autumn} {Leaves}},
	volume = {131},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.012732},
	doi = {10.1104/pp.012732},
	abstract = {Two cDNA libraries were prepared, one from leaves of a field-grown aspen (Populus tremula) tree, harvested just before any visible sign of leaf senescence in the autumn, and one from young but fully expanded leaves of greenhouse-grown aspen (Populus tremula × tremuloides). Expressed sequence tags (ESTs; 5,128 and 4,841, respectively) were obtained from the two libraries. A semiautomatic method of annotation and functional classification of the ESTs, according to a modified Munich Institute of Protein Sequences classification scheme, was developed, utilizing information from three different databases. The patterns of gene expression in the two libraries were strikingly different. In the autumn leaf library, ESTs encoding metallothionein, early light-inducible proteins, and cysteine proteases were most abundant. Clones encoding other proteases and proteins involved in respiration and breakdown of lipids and pigments, as well as stress-related genes, were also well represented. We identified homologs to many known senescence-associated genes, as well as seven different genes encoding cysteine proteases, two encoding aspartic proteases, five encoding metallothioneins, and 35 additional genes that were up-regulated in autumn leaves. We also indirectly estimated the rate of plastid protein synthesis in the autumn leaves to be less that 10\% of that in young leaves.},
	number = {2},
	urldate = {2024-06-28},
	journal = {Plant Physiology},
	author = {Bhalerao, Rupali and Keskitalo, Johanna and Sterky, Fredrik and Erlandsson, Rikard and Björkbacka, Harry and Birve, Simon Jonsson and Karlsson, Jan and Gardeström, Per and Gustafsson, Petter and Lundeberg, Joakim and Jansson, Stefan},
	month = feb,
	year = {2003},
	pages = {430--442},
}

Two cDNA libraries were prepared, one from leaves of a field-grown aspen (Populus tremula) tree, harvested just before any visible sign of leaf senescence in the autumn, and one from young but fully expanded leaves of greenhouse-grown aspen (Populus tremula × tremuloides). Expressed sequence tags (ESTs; 5,128 and 4,841, respectively) were obtained from the two libraries. A semiautomatic method of annotation and functional classification of the ESTs, according to a modified Munich Institute of Protein Sequences classification scheme, was developed, utilizing information from three different databases. The patterns of gene expression in the two libraries were strikingly different. In the autumn leaf library, ESTs encoding metallothionein, early light-inducible proteins, and cysteine proteases were most abundant. Clones encoding other proteases and proteins involved in respiration and breakdown of lipids and pigments, as well as stress-related genes, were also well represented. We identified homologs to many known senescence-associated genes, as well as seven different genes encoding cysteine proteases, two encoding aspartic proteases, five encoding metallothioneins, and 35 additional genes that were up-regulated in autumn leaves. We also indirectly estimated the rate of plastid protein synthesis in the autumn leaves to be less that 10% of that in young leaves.

@article{ruban_plants_2003,
	title = {Plants lacking the main light-harvesting complex retain photosystem {II} macro-organization},
	volume = {421},
	copyright = {2003 Macmillan Magazines Ltd.},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/nature01344},
	doi = {10.1038/nature01344},
	abstract = {Photosystem II (PSII) is a key component of photosynthesis, the process of converting sunlight into the chemical energy of life. In plant cells, it forms a unique oligomeric macrostructure in membranes of the chloroplasts1. Several light-harvesting antenna complexes are organized precisely in the PSII macrostructure—the major trimeric complexes (LHCII)2 that bind 70\% of PSII chlorophyll and three minor monomeric complexes3—which together form PSII supercomplexes4,5,6. The antenna complexes are essential for collecting sunlight and regulating photosynthesis7,8,9, but the relationship between these functions and their molecular architecture is unresolved. Here we report that antisense Arabidopsis plants lacking the proteins that form LHCII trimers10 have PSII supercomplexes with almost identical abundance and structure to those found in wild-type plants. The place of LHCII is taken by a normally minor and monomeric complex, CP26, which is synthesized in large amounts and organized into trimers. Trimerization is clearly not a specific attribute of LHCII. Our results highlight the importance of the PSII macrostructure: in the absence of one of its main components, another protein is recruited to allow it to assemble and function.},
	language = {en},
	number = {6923},
	urldate = {2024-06-28},
	journal = {Nature},
	author = {Ruban, A. V. and Wentworth, M. and Yakushevska, A. E. and Andersson, J. and Lee, P. J. and Keegstra, W. and Dekker, J. P. and Boekema, E. J. and Jansson, S. and Horton, P.},
	month = feb,
	year = {2003},
	note = {Publisher: Nature Publishing Group},
	keywords = {Humanities and Social Sciences, Science, multidisciplinary},
	pages = {648--652},
}

Photosystem II (PSII) is a key component of photosynthesis, the process of converting sunlight into the chemical energy of life. In plant cells, it forms a unique oligomeric macrostructure in membranes of the chloroplasts1. Several light-harvesting antenna complexes are organized precisely in the PSII macrostructure—the major trimeric complexes (LHCII)2 that bind 70% of PSII chlorophyll and three minor monomeric complexes3—which together form PSII supercomplexes4,5,6. The antenna complexes are essential for collecting sunlight and regulating photosynthesis7,8,9, but the relationship between these functions and their molecular architecture is unresolved. Here we report that antisense Arabidopsis plants lacking the proteins that form LHCII trimers10 have PSII supercomplexes with almost identical abundance and structure to those found in wild-type plants. The place of LHCII is taken by a normally minor and monomeric complex, CP26, which is synthesized in large amounts and organized into trimers. Trimerization is clearly not a specific attribute of LHCII. Our results highlight the importance of the PSII macrostructure: in the absence of one of its main components, another protein is recruited to allow it to assemble and function.

@article{yakushevska_structure_2003,
	title = {The {Structure} of {Photosystem} {II} in {Arabidopsis}: {Localization} of the {CP26} and {CP29} {Antenna} {Complexes}},
	volume = {42},
	issn = {0006-2960},
	shorttitle = {The {Structure} of {Photosystem} {II} in {Arabidopsis}},
	url = {https://doi.org/10.1021/bi027109z},
	doi = {10/c63zsj},
	abstract = {A genetic approach has been adopted to investigate the organization of the light-harvesting proteins in the photosystem II (PSII) complex in plants. PSII membrane fragments were prepared from wild-type Arabidopis thaliana and plants expressing antisense constructs to Lhcb4 and Lhcb5 genes, lacking CP29 and CP26, respectively (Andersson et al. (2001) Plant Cell 13, 1193−1204). Ordered PS II arrays and PS II supercomplexes were isolated from the membranes of plants lacking CP26 but could not be prepared from those lacking CP29. Membranes and supercomplexes lacking CP26 were less stable than those prepared from the wild type. Transmission electron microscopy aided by single-particle image analysis was applied to the ordered arrays and the isolated PSII complexes. The difference between the images obtained from wild type and antisense plants showed the location of CP26 to be near CP43 and one of the light-harvesting complex trimers. Therefore, the location of the CP26 within PSII was directly established for the first time, and the location of the CP29 complex was determined by elimination. Alterations in the packing of the PSII complexes in the thylakoid membrane also resulted from the absence of CP26. The minor light-harvesting complexes each have a unique location and important roles in the stabilization of the oligomeric PSII structure.},
	number = {3},
	urldate = {2021-07-05},
	journal = {Biochemistry},
	author = {Yakushevska, Alevtyna E. and Keegstra, Wilko and Boekema, Egbert J. and Dekker, Jan P. and Andersson, Jenny and Jansson, Stefan and Ruban, Alexander V. and Horton, Peter},
	month = jan,
	year = {2003},
	note = {Publisher: American Chemical Society},
	pages = {608--613},
}

A genetic approach has been adopted to investigate the organization of the light-harvesting proteins in the photosystem II (PSII) complex in plants. PSII membrane fragments were prepared from wild-type Arabidopis thaliana and plants expressing antisense constructs to Lhcb4 and Lhcb5 genes, lacking CP29 and CP26, respectively (Andersson et al. (2001) Plant Cell 13, 1193−1204). Ordered PS II arrays and PS II supercomplexes were isolated from the membranes of plants lacking CP26 but could not be prepared from those lacking CP29. Membranes and supercomplexes lacking CP26 were less stable than those prepared from the wild type. Transmission electron microscopy aided by single-particle image analysis was applied to the ordered arrays and the isolated PSII complexes. The difference between the images obtained from wild type and antisense plants showed the location of CP26 to be near CP43 and one of the light-harvesting complex trimers. Therefore, the location of the CP26 within PSII was directly established for the first time, and the location of the CP29 complex was determined by elimination. Alterations in the packing of the PSII complexes in the thylakoid membrane also resulted from the absence of CP26. The minor light-harvesting complexes each have a unique location and important roles in the stabilization of the oligomeric PSII structure.

@article{wissel_what_2003,
	title = {What {Affects} {mRNA} {Levels} in {Leaves} of {Field}-{Grown} {Aspen}? {A} {Study} of {Developmental} and {Environmental} {Influences}},
	volume = {133},
	issn = {0032-0889},
	shorttitle = {What {Affects} {mRNA} {Levels} in {Leaves} of {Field}-{Grown} {Aspen}?},
	url = {https://doi.org/10.1104/pp.103.028191},
	doi = {10.1104/pp.103.028191},
	abstract = {We have analyzed the abundance of mRNAs expressed from 11 nuclear genes in leaves of a free-growing aspen (Populus tremula) tree throughout the growing season. We used multivariate statistics to determine the influence of environmental factors (i.e. the weather before sampling) and developmental responses to seasonal changes at the mRNA level for each of these genes. The gene encoding a germin-like protein was only expressed early in the season, whereas the other tested genes were expressed throughout the season and showed mRNA variations on a day-to-day basis. For six of the genes, reliable models were found that described the mRNA level as a function of weather, but the leaf age was also important for all genes except one encoding an early light-inducible protein (which appeared to be regulated purely by environmental factors under these conditions). The results confirmed the importance of several environmental factors previously shown to regulate the genes, but we also detected a number of less obvious factors (such as the variation in weather parameters and the weather of the previous day) that correlated with the mRNA levels of individual genes. The study shows the power of multivariate statistical methods in analyzing gene regulation under field conditions.},
	number = {3},
	urldate = {2024-06-28},
	journal = {Plant Physiology},
	author = {Wissel, Kirsten and Pettersson, Fredrik and Berglund, Anders and Jansson, Stefan},
	month = nov,
	year = {2003},
	pages = {1190--1197},
}

We have analyzed the abundance of mRNAs expressed from 11 nuclear genes in leaves of a free-growing aspen (Populus tremula) tree throughout the growing season. We used multivariate statistics to determine the influence of environmental factors (i.e. the weather before sampling) and developmental responses to seasonal changes at the mRNA level for each of these genes. The gene encoding a germin-like protein was only expressed early in the season, whereas the other tested genes were expressed throughout the season and showed mRNA variations on a day-to-day basis. For six of the genes, reliable models were found that described the mRNA level as a function of weather, but the leaf age was also important for all genes except one encoding an early light-inducible protein (which appeared to be regulated purely by environmental factors under these conditions). The results confirmed the importance of several environmental factors previously shown to regulate the genes, but we also detected a number of less obvious factors (such as the variation in weather parameters and the weather of the previous day) that correlated with the mRNA levels of individual genes. The study shows the power of multivariate statistical methods in analyzing gene regulation under field conditions.

@article{wullschleger_genomics_2002,
	title = {Genomics and {Forest} {Biology}: {Populus} {Emerges} as the {Perennial} {Favorite}},
	volume = {14},
	issn = {1040-4651},
	shorttitle = {Genomics and {Forest} {Biology}},
	url = {https://doi.org/10.1105/tpc.141120},
	doi = {10/bwdnsd},
	abstract = {Forest biologists have developed strong justifications for why trees should be viewed as model systems in plant biology, including the obvious challenges in extrapolating findings from annual, herbaceous plants to organisms that are distinguished by perennial growth, large size, complex crown architecture, extensive secondary xylem, dormancy, and juvenile–mature phase changes (Bradshaw et al., 2000; Taylor, 2002). Similar justification has been used to argue why the genome of a tree should be sequenced. The U.S. Department of Energy (DOE), Office of Science, announced earlier this year plans to sequence the first tree genome, that of the black cottonwood (Populus trichocarpa) (Figure 1) Figure 1.Populus: A Model System for Tree Genomics.At left, 7-year-old hybrid poplars being harvested in western Oregon. Top right, expression of a poplar DEFICIENS homolog in female floral meristems of black cottonwood (Sheppard et al., 2000); bottom right, germinating pollen grains being tested for viability using a fluorescent stain. .},
	number = {11},
	urldate = {2021-10-19},
	journal = {The Plant Cell},
	author = {Wullschleger, Stan D. and Jansson, Stefan and Taylor, Gail},
	month = nov,
	year = {2002},
	pages = {2651--2655},
}

Forest biologists have developed strong justifications for why trees should be viewed as model systems in plant biology, including the obvious challenges in extrapolating findings from annual, herbaceous plants to organisms that are distinguished by perennial growth, large size, complex crown architecture, extensive secondary xylem, dormancy, and juvenile–mature phase changes (Bradshaw et al., 2000; Taylor, 2002). Similar justification has been used to argue why the genome of a tree should be sequenced. The U.S. Department of Energy (DOE), Office of Science, announced earlier this year plans to sequence the first tree genome, that of the black cottonwood (Populus trichocarpa) (Figure 1) Figure 1.Populus: A Model System for Tree Genomics.At left, 7-year-old hybrid poplars being harvested in western Oregon. Top right, expression of a poplar DEFICIENS homolog in female floral meristems of black cottonwood (Sheppard et al., 2000); bottom right, germinating pollen grains being tested for viability using a fluorescent stain. .

@article{kulheim_rapid_2002,
	title = {Rapid {Regulation} of {Light} {Harvesting} and {Plant} {Fitness} in the {Field}},
	volume = {297},
	url = {https://www.science.org/lookup/doi/10.1126/science.1072359},
	doi = {10.1126/science.1072359},
	number = {5578},
	urldate = {2021-10-19},
	journal = {Science},
	author = {Külheim, Carsten and Ågren, Jon and Jansson, Stefan},
	month = jul,
	year = {2002},
	note = {Publisher: American Association for the Advancement of Science},
	pages = {91--93},
}

@article{savitch_two_2002,
	title = {Two different strategies for light utilization in photosynthesis in relation to growth and cold acclimation},
	volume = {25},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-3040.2002.00861.x},
	doi = {10/fdjtd5},
	abstract = {Seedlings of Lodgepole pine (Pinus contorta L.) and winter wheat (Triticum aestivum L. cv. Monopol) were cold acclimated under controlled conditions to induce frost hardiness. Lodgepole pine responded to cold acclimation by partial inhibition of photosynthesis with an associated partial loss of photosystem II reaction centres, and a reduction in needle chlorophyll content. This was accompanied by a low daily carbon gain, and the development of a high and sustained capacity for non-photochemical quenching of absorbed light. This sustained dissipation of absorbed light as heat correlated with an increased de-epoxidation of the xanthophyll cycle pigments forming the quenching forms antheraxanthin and zeaxanthin. In addition, the PsbS protein known to bind chlorophyll and the xanthophyll cycle pigments increased strongly during cold acclimation of pine. In contrast, winter wheat maintained high photosynthetic rates, showed no loss of chlorophyll content per leaf area, and exhibited a high daily carbon gain and a minimal non-photochemical quenching after cold acclimation. In accordance, cold acclimation of wheat neither increased the de-epoxidation of the xanthophylls nor the content of the PsbS protein. These different responses of photosynthesis to cold acclimation are correlated with pine, reducing its need for assimilates when entering dormancy associated with termination of primary growth, whereas winter wheat maintains a high need for assimilates as it continues to grow and develop throughout the cold-acclimation period. It appears that without evolving a sustained ability for controlled dissipation of absorbed light as heat throughout the winter, winter green conifers would not have managed to adapt and establish themselves so successfully in the cold climatic zones of the northern hemisphere.},
	language = {en},
	number = {6},
	urldate = {2021-10-19},
	journal = {Plant, Cell \& Environment},
	author = {Savitch, L. V. and Leonardos, E. D. and Krol, M. and Jansson, S. and Grodzinski, B. and Huner, N. P. A. and Öquist, G.},
	year = {2002},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-3040.2002.00861.x},
	keywords = {Pinus contorta, PsbS protein, Triticum aestivum, cold acclimation, dormancy, evergreen, frost hardening, photo-inhibition, photosynthesis, xanthophyll cycle},
	pages = {761--771},
}

Seedlings of Lodgepole pine (Pinus contorta L.) and winter wheat (Triticum aestivum L. cv. Monopol) were cold acclimated under controlled conditions to induce frost hardiness. Lodgepole pine responded to cold acclimation by partial inhibition of photosynthesis with an associated partial loss of photosystem II reaction centres, and a reduction in needle chlorophyll content. This was accompanied by a low daily carbon gain, and the development of a high and sustained capacity for non-photochemical quenching of absorbed light. This sustained dissipation of absorbed light as heat correlated with an increased de-epoxidation of the xanthophyll cycle pigments forming the quenching forms antheraxanthin and zeaxanthin. In addition, the PsbS protein known to bind chlorophyll and the xanthophyll cycle pigments increased strongly during cold acclimation of pine. In contrast, winter wheat maintained high photosynthetic rates, showed no loss of chlorophyll content per leaf area, and exhibited a high daily carbon gain and a minimal non-photochemical quenching after cold acclimation. In accordance, cold acclimation of wheat neither increased the de-epoxidation of the xanthophylls nor the content of the PsbS protein. These different responses of photosynthesis to cold acclimation are correlated with pine, reducing its need for assimilates when entering dormancy associated with termination of primary growth, whereas winter wheat maintains a high need for assimilates as it continues to grow and develop throughout the cold-acclimation period. It appears that without evolving a sustained ability for controlled dissipation of absorbed light as heat throughout the winter, winter green conifers would not have managed to adapt and establish themselves so successfully in the cold climatic zones of the northern hemisphere.

@article{bailey_acclimation_2001,
	title = {Acclimation of {Arabidopsis} thaliana to the light environment: the existence of separate low light and high light responses},
	volume = {213},
	issn = {1432-2048},
	shorttitle = {Acclimation of {Arabidopsis} thaliana to the light environment},
	url = {https://doi.org/10.1007/s004250100556},
	doi = {10/c3n6p7},
	abstract = {The capacity for photosynthetic acclimation in Arabidopsis thaliana (L.) Heynh. cv. Landsberg erecta was assessed during growth over a broad range of irradiance. Discontinuities in the response to growth irradiance were revealed for the light- and CO2-saturated rate of photosynthesis (Pmax) and the ratio of chlorophyll a to chlorophyll b (Chl a/b). Three separate phases in the response of Pmax and Chl a/b to growth light were evident, with increases at low and high irradiance ranges and a plateau at intermediate irradiance. By measuring all chlorophyll-containing components of the thylakoid membrane that contribute to Chl a/b we reveal that distinct strategies for growth at low and high irradiance underlie the discontinuous response. These strategies include, in addition to changes in the major light-harvesting complexes of photosystem II (LHCII), large shifts in the amounts of both reaction centres as well as significant changes in the levels of minor LHCII and LHCI components.},
	language = {en},
	number = {5},
	urldate = {2021-11-02},
	journal = {Planta},
	author = {Bailey, Shaun and Walters, Robin G. and Jansson, Stefan and Horton, Peter},
	month = sep,
	year = {2001},
	pages = {794--801},
}

The capacity for photosynthetic acclimation in Arabidopsis thaliana (L.) Heynh. cv. Landsberg erecta was assessed during growth over a broad range of irradiance. Discontinuities in the response to growth irradiance were revealed for the light- and CO2-saturated rate of photosynthesis (Pmax) and the ratio of chlorophyll a to chlorophyll b (Chl a/b). Three separate phases in the response of Pmax and Chl a/b to growth light were evident, with increases at low and high irradiance ranges and a plateau at intermediate irradiance. By measuring all chlorophyll-containing components of the thylakoid membrane that contribute to Chl a/b we reveal that distinct strategies for growth at low and high irradiance underlie the discontinuous response. These strategies include, in addition to changes in the major light-harvesting complexes of photosystem II (LHCII), large shifts in the amounts of both reaction centres as well as significant changes in the levels of minor LHCII and LHCI components.

@article{andersson_antisense_2001,
	title = {Antisense {Inhibition} of the {Photosynthetic} {Antenna} {Proteins} {CP29} and {CP26}: {Implications} for the {Mechanism} of {Protective} {Energy} {Dissipation}},
	volume = {13},
	issn = {1040-4651},
	shorttitle = {Antisense {Inhibition} of the {Photosynthetic} {Antenna} {Proteins} {CP29} and {CP26}},
	url = {https://doi.org/10.1105/tpc.13.5.1193},
	doi = {10.1105/tpc.13.5.1193},
	abstract = {The specific roles of the chlorophyll a/b binding proteins CP29 and CP26 in light harvesting and energy dissipation within the photosynthetic apparatus have been investigated. Arabidopsis was transformed with antisense constructs against the genes encoding the CP29 or CP26 apoprotein, which gave rise to several transgenic lines with remarkably low amounts of the antisense target proteins. The decrease in the level of CP24 protein in the CP29 antisense lines indicates a physical interaction between these complexes. Analysis of chlorophyll fluorescence showed that removal of the proteins affected photosystem II function, probably as a result of changes in the organization of the light-harvesting antenna. However, whole plant measurements showed that overall photosynthetic rates were similar to those in the wild type. Both antisense lines were capable of the qE type of nonphotochemical fluorescence quenching, although there were minor changes in the capacity for quenching and in its induction kinetics. High-light-induced violaxanthin deepoxidation to zeaxanthin was not affected, although the pool size of these pigments was decreased slightly. We conclude that CP29 and CP26 are unlikely to be sites for nonphotochemical quenching.},
	number = {5},
	urldate = {2021-11-02},
	journal = {The Plant Cell},
	author = {Andersson, Jenny and Walters, Robin G. and Horton, Peter and Jansson, Stefan},
	month = may,
	year = {2001},
	pages = {1193--1204},
}

The specific roles of the chlorophyll a/b binding proteins CP29 and CP26 in light harvesting and energy dissipation within the photosynthetic apparatus have been investigated. Arabidopsis was transformed with antisense constructs against the genes encoding the CP29 or CP26 apoprotein, which gave rise to several transgenic lines with remarkably low amounts of the antisense target proteins. The decrease in the level of CP24 protein in the CP29 antisense lines indicates a physical interaction between these complexes. Analysis of chlorophyll fluorescence showed that removal of the proteins affected photosystem II function, probably as a result of changes in the organization of the light-harvesting antenna. However, whole plant measurements showed that overall photosynthetic rates were similar to those in the wild type. Both antisense lines were capable of the qE type of nonphotochemical fluorescence quenching, although there were minor changes in the capacity for quenching and in its induction kinetics. High-light-induced violaxanthin deepoxidation to zeaxanthin was not affected, although the pool size of these pigments was decreased slightly. We conclude that CP29 and CP26 are unlikely to be sites for nonphotochemical quenching.

@article{jackowski_identification_2001,
	title = {Identification of {Lhcb1}/{Lhcb2}/{Lhcb3} heterotrimers of the main light-harvesting chlorophyll a/b–protein complex of {Photosystem} {II} ({LHC} {II})},
	volume = {1504},
	issn = {0005-2728},
	url = {https://www.sciencedirect.com/science/article/pii/S0005272800002620},
	doi = {10/dfzb58},
	abstract = {Using non-denaturing isoelectric focusing in polyacrylamide vertical slab gel, we have purified to homogeneity three trimeric subcomplexes of LHC II from Arabidopsis thylakoid membranes. The polypeptide composition of the subcomplexes were studied by immunoblotting. Our results indicate the existence in vivo of LHC II heterotrimers containing Lhcb1, Lhcb2 and Lhcb3 gene products.},
	language = {en},
	number = {2},
	urldate = {2021-11-02},
	journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
	author = {Jackowski, Grzegorz and Kacprzak, Karol and Jansson, Stefan},
	month = apr,
	year = {2001},
	keywords = {(), Light harvesting complex II, Subcomplex, Trimer},
	pages = {340--345},
}

Using non-denaturing isoelectric focusing in polyacrylamide vertical slab gel, we have purified to homogeneity three trimeric subcomplexes of LHC II from Arabidopsis thylakoid membranes. The polypeptide composition of the subcomplexes were studied by immunoblotting. Our results indicate the existence in vivo of LHC II heterotrimers containing Lhcb1, Lhcb2 and Lhcb3 gene products.

@article{ganeteg_properties_2001,
	title = {The {Properties} of the {Chlorophyll} a/b-{Binding}  {Proteins} {Lhca2} and {Lhca3} {Studied} in {Vivo} {Using} {Antisense}  {Inhibition}},
	volume = {127},
	issn = {0032-0889},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC117971/},
	abstract = {The specific functions of the light-harvesting proteins Lhca2 and
 Lhca3 were studied in Arabidopsis ecotype Colombia antisense plants in
 which the proteins were individually repressed. The antisense effect
 was specific in each plant, but levels of Lhca proteins other than the
 targeted products were also affected. The contents of Lhca1 and Lhca4
 were unaffected, but Lhca3 (in Lhca2-repressed plants) was almost
 completely depleted, and Lhca2 decreased to about 30\% of wild-type
 levels in Lhca3-repressed plants. This suggests that the Lhca2 and
 Lhca3 proteins are in physical contact with each other and that they
 require each other for stability. Photosystem I fluorescence at 730 nm
 is thought to emanate from pigments bound to Lhca1 and Lhca4. However,
 fluorescence emission and excitation spectra suggest that Lhca2 and
 Lhca3, which fluoresce in vitro at 680 nm, also could contribute to
 far-red fluorescence in vivo. Spectral forms with absorption maxima at
 695 and 715 nm, apparently with emission maxima at 702 and 735 nm,
 respectively, might be associated with Lhca2 and Lhca3.},
	number = {1},
	urldate = {2021-11-02},
	journal = {Plant Physiology},
	author = {Ganeteg, Ulrika and Strand, Åsa and Gustafsson, Petter and Jansson, Stefan},
	month = sep,
	year = {2001},
	pmid = {11553743},
	pmcid = {PMC117971},
	pages = {150--158},
}

The specific functions of the light-harvesting proteins Lhca2 and Lhca3 were studied in Arabidopsis ecotype Colombia antisense plants in which the proteins were individually repressed. The antisense effect was specific in each plant, but levels of Lhca proteins other than the targeted products were also affected. The contents of Lhca1 and Lhca4 were unaffected, but Lhca3 (in Lhca2-repressed plants) was almost completely depleted, and Lhca2 decreased to about 30% of wild-type levels in Lhca3-repressed plants. This suggests that the Lhca2 and Lhca3 proteins are in physical contact with each other and that they require each other for stability. Photosystem I fluorescence at 730 nm is thought to emanate from pigments bound to Lhca1 and Lhca4. However, fluorescence emission and excitation spectra suggest that Lhca2 and Lhca3, which fluoresce in vitro at 680 nm, also could contribute to far-red fluorescence in vivo. Spectral forms with absorption maxima at 695 and 715 nm, apparently with emission maxima at 702 and 735 nm, respectively, might be associated with Lhca2 and Lhca3.

@article{li_pigment-binding_2000,
	title = {A pigment-binding protein essential for regulation of photosynthetic light harvesting},
	volume = {403},
	copyright = {2000 Macmillan Magazines Ltd.},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/35000131},
	doi = {10.1038/35000131},
	abstract = {Photosynthetic light harvesting in plants is regulated in response to changes in incident light intensity. Absorption of light that exceeds a plant's capacity for fixation of CO2 results in thermal dissipation of excitation energy in the pigment antenna of photosystem II by a poorly understood mechanism. This regulatory process, termed nonphotochemical quenching, maintains the balance between dissipation and utilization of light energy to minimize generation of oxidizing molecules, thereby protecting the plant against photo-oxidative damage. To identify specific proteins that are involved in nonphotochemical quenching, we have isolated mutants of Arabidopsis thaliana that cannot dissipate excess absorbed light energy. Here we show that the gene encoding PsbS, an intrinsic chlorophyll-binding protein of photosystem II, is necessary for nonphotochemical quenching but not for efficient light harvesting and photosynthesis. These results indicate that PsbS may be the site for nonphotochemical quenching, a finding that has implications for the functional evolution of pigment-binding proteins.},
	language = {en},
	number = {6768},
	urldate = {2021-11-08},
	journal = {Nature},
	author = {Li, Xiao-Ping and Björkman, Olle and Shih, Connie and Grossman, Arthur R. and Rosenquist, Magnus and Jansson, Stefan and Niyogi, Krishna K.},
	month = jan,
	year = {2000},
	note = {Bandiera\_abtest: a
Cg\_type: Nature Research Journals
Number: 6768
Primary\_atype: Research
Publisher: Nature Publishing Group},
	keywords = {Humanities and Social Sciences, Science, multidisciplinary},
	pages = {391--395},
}

Photosynthetic light harvesting in plants is regulated in response to changes in incident light intensity. Absorption of light that exceeds a plant's capacity for fixation of CO2 results in thermal dissipation of excitation energy in the pigment antenna of photosystem II by a poorly understood mechanism. This regulatory process, termed nonphotochemical quenching, maintains the balance between dissipation and utilization of light energy to minimize generation of oxidizing molecules, thereby protecting the plant against photo-oxidative damage. To identify specific proteins that are involved in nonphotochemical quenching, we have isolated mutants of Arabidopsis thaliana that cannot dissipate excess absorbed light energy. Here we show that the gene encoding PsbS, an intrinsic chlorophyll-binding protein of photosystem II, is necessary for nonphotochemical quenching but not for efficient light harvesting and photosynthesis. These results indicate that PsbS may be the site for nonphotochemical quenching, a finding that has implications for the functional evolution of pigment-binding proteins.

@article{jansson_arabidopsis_2000,
	title = {An {Arabidopsis} thaliana protein homologous to cyanobacterial high-light-inducible proteins},
	volume = {42},
	issn = {1573-5028},
	url = {https://doi.org/10.1023/A:1006365213954},
	doi = {10/fkkqd2},
	abstract = {An Arabidopsis thaliana cDNA clone encoding a novel 110 amino acid thylakoid protein has been sequenced. The in vitro synthesized protein is taken up by intact chloroplasts, inserted into the thylakoid membrane and the transit peptide is cleaved off during this process. The mature protein is predicted to contain 69 amino acids, to form one membrane-spanning α-helix and to have its N-terminus at the stromal side of the thylakoid membrane. The protein showed similarity to the LHC, ELIP and PsbS proteins of higher plants, but more pronounced to the high-light-inducible proteins (HLIPs) of cyanobacteria and red algae, to which no homologue previously has been detected in higher plants. As for HLIP and ELIP, high light increases the mRNA levels of the corresponding gene. Sequence comparisons indicate that the protein may bind chlorophyll and form dimers in the thylakoid membrane. The level of expression of the protein seems to be far lower than that of normal PSI and PSII subunits.},
	language = {en},
	number = {2},
	urldate = {2021-11-08},
	journal = {Plant Molecular Biology},
	author = {Jansson, Stefan and Andersson, Jenny and Jung Kim, Soo and Jackowski, Grzegorz},
	month = jan,
	year = {2000},
	pages = {345--351},
}

An Arabidopsis thaliana cDNA clone encoding a novel 110 amino acid thylakoid protein has been sequenced. The in vitro synthesized protein is taken up by intact chloroplasts, inserted into the thylakoid membrane and the transit peptide is cleaved off during this process. The mature protein is predicted to contain 69 amino acids, to form one membrane-spanning α-helix and to have its N-terminus at the stromal side of the thylakoid membrane. The protein showed similarity to the LHC, ELIP and PsbS proteins of higher plants, but more pronounced to the high-light-inducible proteins (HLIPs) of cyanobacteria and red algae, to which no homologue previously has been detected in higher plants. As for HLIP and ELIP, high light increases the mRNA levels of the corresponding gene. Sequence comparisons indicate that the protein may bind chlorophyll and form dimers in the thylakoid membrane. The level of expression of the protein seems to be far lower than that of normal PSI and PSII subunits.

@article{jansson_proposal_1999,
	title = {A {Proposal} for {Extending} the {Nomenclature} of {Light}-{Harvesting} {Proteins} of the {Three} {Transmembrane} {Helix} {Type}},
	volume = {17},
	issn = {1572-9818},
	url = {https://doi.org/10.1023/A:1007620508007},
	doi = {10.1023/A:1007620508007},
	language = {en},
	number = {3},
	urldate = {2021-11-08},
	journal = {Plant Molecular Biology Reporter},
	author = {Jansson, Stefan and Green, Beverley and Grossman, Arthur R. and Hiller, Roger},
	month = sep,
	year = {1999},
	pages = {221--224},
}

@article{jansson_guide_1999,
	title = {A guide to the {Lhc} genes and their relatives in {Arabidopsis}},
	volume = {4},
	issn = {1360-1385},
	url = {https://www.sciencedirect.com/science/article/pii/S1360138599014193},
	doi = {10.1016/S1360-1385(99)01419-3},
	abstract = {The Lhc super-gene family encodes the light-harvesting chlorophyll a/b-binding (LHC) proteins that constitute the antenna system of the photosynthetic apparatus, and also includes some relatives whose functions are more or less unknown. The Lhc super-gene family of Arabidopsis contains {\textgreater}30 members and the databases contain {\textgreater}1000 EST clones originating from these genes. This article presents an overview of these genes and provides some tools for researchers who want to use them in their studies.},
	language = {en},
	number = {6},
	urldate = {2021-11-08},
	journal = {Trends in Plant Science},
	author = {Jansson, Stefan},
	month = jun,
	year = {1999},
	keywords = {Antenna, Lhca, Lhcb, Light-harvesting chlorophyll a/b-binding proteins},
	pages = {236--240},
}

The Lhc super-gene family encodes the light-harvesting chlorophyll a/b-binding (LHC) proteins that constitute the antenna system of the photosynthetic apparatus, and also includes some relatives whose functions are more or less unknown. The Lhc super-gene family of Arabidopsis contains \textgreater30 members and the databases contain \textgreater1000 EST clones originating from these genes. This article presents an overview of these genes and provides some tools for researchers who want to use them in their studies.

@article{kim_distinct_1999,
	title = {Distinct “{Assisted}” and “{Spontaneous}” {Mechanisms} for the {Insertion} of {Polytopic} {Chlorophyll}-binding {Proteins} into the {Thylakoid} {Membrane}*},
	volume = {274},
	issn = {0021-9258},
	url = {https://www.sciencedirect.com/science/article/pii/S0021925819877876},
	doi = {10.1074/jbc.274.8.4715},
	abstract = {The biogenesis of several bacterial polytopic membrane proteins has been shown to require signal recognition particle (SRP) and protein transport machinery, and one such protein, the major light-harvesting chlorophyll-binding protein (LHCP) exhibits these requirements in chloroplasts. In this report we have used in vitro insertion assays to analyze four additional members of the chlorophyll-a/b-binding protein family. We show that two members, Lhca1 and Lhcb5, display an absolute requirement for stroma, nucleoside triphosphates, and protein transport apparatus, indicating an “assisted” pathway that probably resembles that of LHCP. Two other members, however, namely an early light-inducible protein 2 (Elip2) and photosystem II subunit S (PsbS), can insert efficiently in the complete absence of SRP, SecA activity, nucleoside triphosphates, or a functional Sec system. The data suggest a possibly spontaneous insertion mechanism that, to date, has been characterized only for simple single-span proteins. Of the membrane proteins whose insertion into thylakoids has been analyzed, five have now been shown to insert by a SRP/Sec-independent mechanism, suggesting that this is a mainstream form of targeting pathway. We also show that PsbS and Elip2 molecules are capable of following either “unassisted” or assisted pathways, and we discuss the implications for the mechanism and role of SRP in chloroplasts.},
	language = {en},
	number = {8},
	urldate = {2021-11-08},
	journal = {Journal of Biological Chemistry},
	author = {Kim, Soo Jung and Jansson, Stefan and Hoffman, Neil E. and Robinson, Colin and Mant, Alexandra},
	month = feb,
	year = {1999},
	pages = {4715--4721},
}

The biogenesis of several bacterial polytopic membrane proteins has been shown to require signal recognition particle (SRP) and protein transport machinery, and one such protein, the major light-harvesting chlorophyll-binding protein (LHCP) exhibits these requirements in chloroplasts. In this report we have used in vitro insertion assays to analyze four additional members of the chlorophyll-a/b-binding protein family. We show that two members, Lhca1 and Lhcb5, display an absolute requirement for stroma, nucleoside triphosphates, and protein transport apparatus, indicating an “assisted” pathway that probably resembles that of LHCP. Two other members, however, namely an early light-inducible protein 2 (Elip2) and photosystem II subunit S (PsbS), can insert efficiently in the complete absence of SRP, SecA activity, nucleoside triphosphates, or a functional Sec system. The data suggest a possibly spontaneous insertion mechanism that, to date, has been characterized only for simple single-span proteins. Of the membrane proteins whose insertion into thylakoids has been analyzed, five have now been shown to insert by a SRP/Sec-independent mechanism, suggesting that this is a mainstream form of targeting pathway. We also show that PsbS and Elip2 molecules are capable of following either “unassisted” or assisted pathways, and we discuss the implications for the mechanism and role of SRP in chloroplasts.

@article{krol_greening_1999,
	title = {Greening under {High} {Light} or {Cold} {Temperature} {Affects} the {Level}  of {Xanthophyll}-{Cycle} {Pigments}, {Early} {Light}-{Inducible} {Proteins}, and  {Light}-{Harvesting} {Polypeptides} in {Wild}-{Type} {Barley} and the  {Chlorina} f2 {Mutant}},
	volume = {120},
	issn = {0032-0889},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59251/},
	abstract = {Etiolated seedlings of wild type and
 the chlorina f2 mutant of barley (Hordeum
 vulgare) were exposed to greening at either 5°C or 20°C and
 continuous illumination varying from 50 to 800 μmol m−2
 s−1. Exposure to either moderate temperature and high
 light or low temperature and moderate light inhibited chlorophyll
 a and b accumulation in the wild type and
 in the f2 mutant. Continuous illumination under these
 greening conditions resulted in transient accumulations of zeaxanthin,
 concomitant transient decreases in violaxanthin, and fluctuations in
 the epoxidation state of the xanthophyll pool. Photoinhibition-induced
 xanthophyll-cycle activity was detectable after only 3 h of
 greening at 20°C and 250 μmol m−2 s−1.
 Immunoblot analyses of the accumulation of the 14-kD early
 light-inducible protein but not the major (Lhcb2) or minor (Lhcb5)
 light-harvesting polypeptides demonstrated transient kinetics similar
 to those observed for zeaxanthin accumulation during greening at either
 5°C or 20°C for both the wild type and the f2
 mutant. Furthermore, greening of the f2 mutant at either
 5°C or 20°C indicated that Lhcb2 is not essential for the
 regulation of the xanthophyll cycle in barley. These results are
 consistent with the thesis that early light-inducible proteins may bind
 zeaxanthin as well as other xanthophylls and dissipate excess light
 energy to protect the developing photosynthetic apparatus from excess
 excitation. We discuss the role of energy balance and photosystem II
 excitation pressure in the regulation of the xanthophyll cycle during
 chloroplast biogenesis in wild-type barley and the f2
 mutant.},
	number = {1},
	urldate = {2021-11-08},
	journal = {Plant Physiology},
	author = {Król, Marianna and Ivanov, Alexander G. and Jansson, Stefan and Kloppstech, Klaus and Huner, Norman P.A.},
	month = may,
	year = {1999},
	pmid = {10318697},
	pmcid = {PMC59251},
	pages = {193--204},
}

Etiolated seedlings of wild type and the chlorina f2 mutant of barley (Hordeum vulgare) were exposed to greening at either 5°C or 20°C and continuous illumination varying from 50 to 800 μmol m−2 s−1. Exposure to either moderate temperature and high light or low temperature and moderate light inhibited chlorophyll a and b accumulation in the wild type and in the f2 mutant. Continuous illumination under these greening conditions resulted in transient accumulations of zeaxanthin, concomitant transient decreases in violaxanthin, and fluctuations in the epoxidation state of the xanthophyll pool. Photoinhibition-induced xanthophyll-cycle activity was detectable after only 3 h of greening at 20°C and 250 μmol m−2 s−1. Immunoblot analyses of the accumulation of the 14-kD early light-inducible protein but not the major (Lhcb2) or minor (Lhcb5) light-harvesting polypeptides demonstrated transient kinetics similar to those observed for zeaxanthin accumulation during greening at either 5°C or 20°C for both the wild type and the f2 mutant. Furthermore, greening of the f2 mutant at either 5°C or 20°C indicated that Lhcb2 is not essential for the regulation of the xanthophyll cycle in barley. These results are consistent with the thesis that early light-inducible proteins may bind zeaxanthin as well as other xanthophylls and dissipate excess light energy to protect the developing photosynthetic apparatus from excess excitation. We discuss the role of energy balance and photosystem II excitation pressure in the regulation of the xanthophyll cycle during chloroplast biogenesis in wild-type barley and the f2 mutant.