Profile
Associate Professor.
Linking genome variation to phenotype in forest trees.
Publications
Christie, Nanette; Mannapperuma, Chanaka; Ployet, Raphael; Merwe, Karen; Mähler, Niklas; Delhomme, Nicolas; Naidoo, Sanushka; Mizrachi, Eshchar; Street, Nathaniel R.; Myburg, Alexander A.
qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE) Journal Article
In: BMC Bioinformatics 2021 22:1, vol. 22, no. 1, pp. 1–21, 2021, ISSN: 1471-2105.
@article{Christie2021,
title = {qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE)},
author = {Nanette Christie and Chanaka Mannapperuma and Raphael Ployet and Karen Merwe and Niklas Mähler and Nicolas Delhomme and Sanushka Naidoo and Eshchar Mizrachi and Nathaniel R. Street and Alexander A. Myburg},
url = {https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04514-9},
doi = {10.1186/S12859-021-04514-9},
issn = {1471-2105},
year = {2021},
date = {2021-12-01},
journal = {BMC Bioinformatics 2021 22:1},
volume = {22},
number = {1},
pages = {1--21},
publisher = {BioMed Central},
abstract = {Affordable high-throughput DNA and RNA sequencing technologies are allowing genomic analysis of plant and animal populations and as a result empowering new systems genetics approaches to study complex traits. The availability of intuitive tools to browse and analyze the resulting large-scale genetic and genomic datasets remain a significant challenge. Furthermore, these integrative genomics approaches require innovative methods to dissect the flow and interconnectedness of biological information underlying complex trait variation. The Plant Genome Integrative Explorer (PlantGenIE.org) is a multi-species database and domain that houses online tools for model and woody plant species including Eucalyptus. Since the Eucalyptus Genome Integrative Explorer (EucGenIE) is integrated within PlantGenIE, it shares genome and expression analysis tools previously implemented within the various subdomains (ConGenIE, PopGenIE and AtGenIE). Despite the success in setting up integrative genomics databases, online tools for systems genetics modelling and high-resolution dissection of complex trait variation in plant populations have been lacking. We have developed qtlXplorer (
https://eucgenie.org/QTLXplorer
) for visualizing and exploring systems genetics data from genome-wide association studies including quantitative trait loci (QTLs) and expression-based QTL (eQTL) associations. This module allows users to, for example, find co-located QTLs and eQTLs using an interactive version of Circos, or explore underlying genes using JBrowse. It provides users with a means to build systems genetics models and generate hypotheses from large-scale population genomics data. We also substantially upgraded the EucGenIE resource and show how it enables users to combine genomics and systems genetics approaches to discover candidate genes involved in biotic stress responses and wood formation by focusing on two multigene families, laccases and peroxidases. qtlXplorer adds a new dimension, population genomics, to the EucGenIE and PlantGenIE environment. The resource will be of interest to researchers and molecular breeders working in Eucalyptus and other woody plant species. It provides an example of how systems genetics data can be integrated with functional genetics data to provide biological insight and formulate hypotheses. Importantly, integration within PlantGenIE enables novel comparative genomics analyses to be performed from population-scale data.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Affordable high-throughput DNA and RNA sequencing technologies are allowing genomic analysis of plant and animal populations and as a result empowering new systems genetics approaches to study complex traits. The availability of intuitive tools to browse and analyze the resulting large-scale genetic and genomic datasets remain a significant challenge. Furthermore, these integrative genomics approaches require innovative methods to dissect the flow and interconnectedness of biological information underlying complex trait variation. The Plant Genome Integrative Explorer (PlantGenIE.org) is a multi-species database and domain that houses online tools for model and woody plant species including Eucalyptus. Since the Eucalyptus Genome Integrative Explorer (EucGenIE) is integrated within PlantGenIE, it shares genome and expression analysis tools previously implemented within the various subdomains (ConGenIE, PopGenIE and AtGenIE). Despite the success in setting up integrative genomics databases, online tools for systems genetics modelling and high-resolution dissection of complex trait variation in plant populations have been lacking. We have developed qtlXplorer (
https://eucgenie.org/QTLXplorer
) for visualizing and exploring systems genetics data from genome-wide association studies including quantitative trait loci (QTLs) and expression-based QTL (eQTL) associations. This module allows users to, for example, find co-located QTLs and eQTLs using an interactive version of Circos, or explore underlying genes using JBrowse. It provides users with a means to build systems genetics models and generate hypotheses from large-scale population genomics data. We also substantially upgraded the EucGenIE resource and show how it enables users to combine genomics and systems genetics approaches to discover candidate genes involved in biotic stress responses and wood formation by focusing on two multigene families, laccases and peroxidases. qtlXplorer adds a new dimension, population genomics, to the EucGenIE and PlantGenIE environment. The resource will be of interest to researchers and molecular breeders working in Eucalyptus and other woody plant species. It provides an example of how systems genetics data can be integrated with functional genetics data to provide biological insight and formulate hypotheses. Importantly, integration within PlantGenIE enables novel comparative genomics analyses to be performed from population-scale data.
https://eucgenie.org/QTLXplorer
) for visualizing and exploring systems genetics data from genome-wide association studies including quantitative trait loci (QTLs) and expression-based QTL (eQTL) associations. This module allows users to, for example, find co-located QTLs and eQTLs using an interactive version of Circos, or explore underlying genes using JBrowse. It provides users with a means to build systems genetics models and generate hypotheses from large-scale population genomics data. We also substantially upgraded the EucGenIE resource and show how it enables users to combine genomics and systems genetics approaches to discover candidate genes involved in biotic stress responses and wood formation by focusing on two multigene families, laccases and peroxidases. qtlXplorer adds a new dimension, population genomics, to the EucGenIE and PlantGenIE environment. The resource will be of interest to researchers and molecular breeders working in Eucalyptus and other woody plant species. It provides an example of how systems genetics data can be integrated with functional genetics data to provide biological insight and formulate hypotheses. Importantly, integration within PlantGenIE enables novel comparative genomics analyses to be performed from population-scale data.
Vergara, Alexander; Haas, Julia Christa; Aro, Tuuli; Stachula, Paulina; Street, Nathaniel Robert; Hurry, Vaughan
Norway spruce deploys tissue-specific responses during acclimation to cold Journal Article
In: Plant Cell and Environment, 2021, ISSN: 13653040.
@article{Vergara2021,
title = {Norway spruce deploys tissue-specific responses during acclimation to cold},
author = {Alexander Vergara and Julia Christa Haas and Tuuli Aro and Paulina Stachula and Nathaniel Robert Street and Vaughan Hurry},
url = {https://onlinelibrary.wiley.com/doi/full/10.1111/pce.14241 https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.14241 https://onlinelibrary.wiley.com/doi/10.1111/pce.14241},
doi = {10.1111/pce.14241},
issn = {13653040},
year = {2021},
date = {2021-12-01},
journal = {Plant Cell and Environment},
publisher = {John Wiley & Sons, Ltd},
abstract = {Climate change in the conifer-dominated boreal forest is expected to lead to warmer but more dynamic winter air temperatures, reducing the depth and duration of snow cover and lowering winter soil temperatures. To gain insight into the mechanisms that have enabled conifers to dominate extreme cold environments, we performed genome-wide RNA-Seq analysis from needles and roots of non-dormant two-year Norway spruce (Picea abies (L.) H. Karst), and contrasted these response to herbaceous model Arabidopsis We show that the main transcriptional response of Norway spruce needles exposed to cold was delayed relative to Arabidopsis, and this delay was associated with slower development of freezing tolerance. Despite this difference in timing, Norway spruce principally utilizes early response transcription factors (TFs) belonging to the same gene families as Arabidopsis, indicating broad evolutionary conservation of cold response networks. In keeping with their different metabolic and developmental states, needles and root of Norway spruce showed contrasting results. Regulatory network analysis identified both conserved TFs with known roles in cold acclimation (e.g. homologs of ICE1, AKS3, and of the NAC and AP2/ERF superfamilies), but also a root-specific bHLH101 homolog, providing functional insights into cold stress response strategies in Norway spruce.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Climate change in the conifer-dominated boreal forest is expected to lead to warmer but more dynamic winter air temperatures, reducing the depth and duration of snow cover and lowering winter soil temperatures. To gain insight into the mechanisms that have enabled conifers to dominate extreme cold environments, we performed genome-wide RNA-Seq analysis from needles and roots of non-dormant two-year Norway spruce (Picea abies (L.) H. Karst), and contrasted these response to herbaceous model Arabidopsis We show that the main transcriptional response of Norway spruce needles exposed to cold was delayed relative to Arabidopsis, and this delay was associated with slower development of freezing tolerance. Despite this difference in timing, Norway spruce principally utilizes early response transcription factors (TFs) belonging to the same gene families as Arabidopsis, indicating broad evolutionary conservation of cold response networks. In keeping with their different metabolic and developmental states, needles and root of Norway spruce showed contrasting results. Regulatory network analysis identified both conserved TFs with known roles in cold acclimation (e.g. homologs of ICE1, AKS3, and of the NAC and AP2/ERF superfamilies), but also a root-specific bHLH101 homolog, providing functional insights into cold stress response strategies in Norway spruce.
Schneider, Andreas N.; Sundh, John; Sundström, Görel; Richau, Kerstin; Delhomme, Nicolas; Grabherr, Manfred; Hurry, Vaughan; Street, Nathaniel R.
Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce Journal Article
In: mSystems, vol. 6, no. 1, 2021, ISSN: 2379-5077.
@article{Schneider2021,
title = {Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce},
author = {Andreas N. Schneider and John Sundh and Görel Sundström and Kerstin Richau and Nicolas Delhomme and Manfred Grabherr and Vaughan Hurry and Nathaniel R. Street},
url = {https://journals.asm.org/doi/abs/10.1128/mSystems.00884-20},
doi = {10.1128/MSYSTEMS.00884-20/SUPPL_FILE/MSYSTEMS.00884-20-SF006.EPS},
issn = {2379-5077},
year = {2021},
date = {2021-02-01},
journal = {mSystems},
volume = {6},
number = {1},
publisher = {American Society for Microbiology},
abstract = {A deeper understanding of microbial communities associated with plants is revealing their importance for plant health and productivity. RNA extracted from plant field samples represents the host and other organisms present. The health, growth, and fitness of boreal forest trees are impacted and improved by their associated microbiomes. Microbial gene expression and functional activity can be assayed with RNA sequencing (RNA-Seq) data from host samples. In contrast, phylogenetic marker gene amplicon sequencing data are used to assess taxonomic composition and community structure of the microbiome. Few studies have considered how much of this structural and taxonomic information is included in transcriptomic data from matched samples. Here, we described fungal communities using both host-derived RNA-Seq and fungal ITS1 DNA amplicon sequencing to compare the outcomes between the methods. We used a panel of root and needle samples from the coniferous tree species Picea abies (Norway spruce) growing in untreated (nutrient-deficient) and nutrient-enriched plots at the Flakaliden forest research site in boreal northern Sweden. We show that the relationship between samples and alpha and beta diversity indicated by the fungal transcriptome is in agreement with that generated by the ITS data, while also identifying a lack of taxonomic overlap due to limitations imposed by current database coverage. Furthermore, we demonstrate how metatranscriptomics data additionally provide biologically informative functional insights. At the community level, there were changes in starch and sucrose metabolism, biosynthesis of amino acids, and pentose and glucuronate interconversions, while processing of organic macromolecules, including aromatic and heterocyclic compounds, was enriched in transcripts assigned to the genus Cortinarius . IMPORTANCE A deeper understanding of microbial communities associated with plants is revealing their importance for plant health and productivity. RNA extracted from plant field samples represents the host and other organisms present. Typically, gene expression studies focus on the plant component or, in a limited number of studies, expression in one or more associated organisms. However, metatranscriptomic data are rarely used for taxonomic profiling, which is currently performed using amplicon approaches. We created an assembly-based, reproducible, and hardware-agnostic workflow to taxonomically and functionally annotate fungal RNA-Seq data obtained from Norway spruce roots, which we compared to matching ITS amplicon sequencing data. While we identified some limitations and caveats, we show that functional, taxonomic, and compositional insights can all be obtained from RNA-Seq data. These findings highlight the potential of metatranscriptomics to advance our understanding of interaction, response, and effect between host plants and their associated microbial communities.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
A deeper understanding of microbial communities associated with plants is revealing their importance for plant health and productivity. RNA extracted from plant field samples represents the host and other organisms present. The health, growth, and fitness of boreal forest trees are impacted and improved by their associated microbiomes. Microbial gene expression and functional activity can be assayed with RNA sequencing (RNA-Seq) data from host samples. In contrast, phylogenetic marker gene amplicon sequencing data are used to assess taxonomic composition and community structure of the microbiome. Few studies have considered how much of this structural and taxonomic information is included in transcriptomic data from matched samples. Here, we described fungal communities using both host-derived RNA-Seq and fungal ITS1 DNA amplicon sequencing to compare the outcomes between the methods. We used a panel of root and needle samples from the coniferous tree species Picea abies (Norway spruce) growing in untreated (nutrient-deficient) and nutrient-enriched plots at the Flakaliden forest research site in boreal northern Sweden. We show that the relationship between samples and alpha and beta diversity indicated by the fungal transcriptome is in agreement with that generated by the ITS data, while also identifying a lack of taxonomic overlap due to limitations imposed by current database coverage. Furthermore, we demonstrate how metatranscriptomics data additionally provide biologically informative functional insights. At the community level, there were changes in starch and sucrose metabolism, biosynthesis of amino acids, and pentose and glucuronate interconversions, while processing of organic macromolecules, including aromatic and heterocyclic compounds, was enriched in transcripts assigned to the genus Cortinarius . IMPORTANCE A deeper understanding of microbial communities associated with plants is revealing their importance for plant health and productivity. RNA extracted from plant field samples represents the host and other organisms present. Typically, gene expression studies focus on the plant component or, in a limited number of studies, expression in one or more associated organisms. However, metatranscriptomic data are rarely used for taxonomic profiling, which is currently performed using amplicon approaches. We created an assembly-based, reproducible, and hardware-agnostic workflow to taxonomically and functionally annotate fungal RNA-Seq data obtained from Norway spruce roots, which we compared to matching ITS amplicon sequencing data. While we identified some limitations and caveats, we show that functional, taxonomic, and compositional insights can all be obtained from RNA-Seq data. These findings highlight the potential of metatranscriptomics to advance our understanding of interaction, response, and effect between host plants and their associated microbial communities.
Abreu, Ilka N.; Johansson, Annika I.; Sokołowska, Katarzyna; Niittylä, Totte; Sundberg, Björn; Hvidsten, Torgeir R.; Street, Nathaniel R.; Moritz, Thomas
A metabolite roadmap of the wood-forming tissue in Populus tremula Journal Article
In: New Phytologist, vol. 228, no. 5, pp. 1559–1572, 2020, ISSN: 14698137.
@article{Abreu2020,
title = {A metabolite roadmap of the wood-forming tissue in Populus tremula},
author = {Ilka N. Abreu and Annika I. Johansson and Katarzyna Sokołowska and Totte Niittylä and Björn Sundberg and Torgeir R. Hvidsten and Nathaniel R. Street and Thomas Moritz},
url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.16799},
doi = {10.1111/nph.16799},
issn = {14698137},
year = {2020},
date = {2020-12-01},
journal = {New Phytologist},
volume = {228},
number = {5},
pages = {1559--1572},
publisher = {Blackwell Publishing Ltd},
abstract = {Wood, or secondary xylem, is the product of xylogenesis, a developmental process that begins with the proliferation of cambial derivatives and ends with mature xylem fibers and vessels with lignified secondary cell walls. Fully mature xylem has undergone a series of cellular processes, including cell division, cell expansion, secondary wall formation, lignification and programmed cell death. A complex network of interactions between transcriptional regulators and signal transduction pathways controls wood formation. However, the role of metabolites during this developmental process has not been comprehensively characterized. To evaluate the role of metabolites during wood formation, we performed a high spatial resolution metabolomics study of the wood-forming zone of Populus tremula, including laser dissected aspen ray and fiber cells. We show that metabolites show specific patterns within the wood-forming zone, following the differentiation process from cell division to cell death. The data from profiled laser dissected aspen ray and fiber cells suggests that these two cell types host distinctly different metabolic processes. Furthermore, by integrating previously published transcriptomic and proteomic profiles generated from the same trees, we provide an integrative picture of molecular processes, for example, deamination of phenylalanine during lignification is of critical importance for nitrogen metabolism during wood formation.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Wood, or secondary xylem, is the product of xylogenesis, a developmental process that begins with the proliferation of cambial derivatives and ends with mature xylem fibers and vessels with lignified secondary cell walls. Fully mature xylem has undergone a series of cellular processes, including cell division, cell expansion, secondary wall formation, lignification and programmed cell death. A complex network of interactions between transcriptional regulators and signal transduction pathways controls wood formation. However, the role of metabolites during this developmental process has not been comprehensively characterized. To evaluate the role of metabolites during wood formation, we performed a high spatial resolution metabolomics study of the wood-forming zone of Populus tremula, including laser dissected aspen ray and fiber cells. We show that metabolites show specific patterns within the wood-forming zone, following the differentiation process from cell division to cell death. The data from profiled laser dissected aspen ray and fiber cells suggests that these two cell types host distinctly different metabolic processes. Furthermore, by integrating previously published transcriptomic and proteomic profiles generated from the same trees, we provide an integrative picture of molecular processes, for example, deamination of phenylalanine during lignification is of critical importance for nitrogen metabolism during wood formation.
Mähler, Niklas; Schiffthaler, Bastian; Robinson, Kathryn M.; Terebieniec, Barbara K.; Vučak, Matej; Mannapperuma, Chanaka; Bailey, Mark E. S. S.; Jansson, Stefan; Hvidsten, Torgeir R.; Street, Nathaniel R.
Leaf shape in Populus tremula is a complex, omnigenic trait Journal Article
In: Ecology and Evolution, vol. 10, no. 21, pp. 11922–11940, 2020, ISSN: 2045-7758.
@article{Mahler2020,
title = {Leaf shape in Populus tremula is a complex, omnigenic trait},
author = {Niklas Mähler and Bastian Schiffthaler and Kathryn M. Robinson and Barbara K. Terebieniec and Matej Vučak and Chanaka Mannapperuma and Mark E. S. S. Bailey and Stefan Jansson and Torgeir R. Hvidsten and Nathaniel R. Street},
url = {https://onlinelibrary.wiley.com/doi/full/10.1002/ece3.6691 https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.6691 https://onlinelibrary.wiley.com/doi/10.1002/ece3.6691},
doi = {10.1002/ece3.6691},
issn = {2045-7758},
year = {2020},
date = {2020-11-01},
journal = {Ecology and Evolution},
volume = {10},
number = {21},
pages = {11922--11940},
publisher = {John Wiley and Sons Ltd},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Müller, Niels A.; Kersten, Birgit; Montalvão, Ana P. Leite; Mähler, Niklas; Bernhardsson, Carolina; Bräutigam, Katharina; Lorenzo, Zulema Carracedo; Hoenicka, Hans; Kumar, Vikash; Mader, Malte; Pakull, Birte; Robinson, Kathryn M.; Sabatti, Maurizio; Vettori, Cristina; Ingvarsson, Pär K.; Cronk, Quentin; Street, Nathaniel R.; Fladung, Matthias
A single gene underlies the dynamic evolution of poplar sex determination Journal Article
In: Nature Plants, pp. 1–8, 2020, ISSN: 2055-0278.
@article{Muller2020,
title = {A single gene underlies the dynamic evolution of poplar sex determination},
author = {Niels A. Müller and Birgit Kersten and Ana P. Leite Montalvão and Niklas Mähler and Carolina Bernhardsson and Katharina Bräutigam and Zulema Carracedo Lorenzo and Hans Hoenicka and Vikash Kumar and Malte Mader and Birte Pakull and Kathryn M. Robinson and Maurizio Sabatti and Cristina Vettori and Pär K. Ingvarsson and Quentin Cronk and Nathaniel R. Street and Matthias Fladung},
url = {http://www.nature.com/articles/s41477-020-0672-9},
doi = {10.1038/s41477-020-0672-9},
issn = {2055-0278},
year = {2020},
date = {2020-06-01},
journal = {Nature Plants},
pages = {1--8},
publisher = {Nature Publishing Group},
abstract = {Although hundreds of plant lineages have independently evolved dioecy (that is, separation of the sexes), the underlying genetic basis remains largely elusive1. Here we show that diverse poplar species carry partial duplicates of the ARABIDOPSIS RESPONSE REGULATOR 17 (ARR17) orthologue in the male-specific region of the Y chromosome. These duplicates give rise to small RNAs apparently causing male-specific DNA methylation and silencing of the ARR17 gene. CRISPR–Cas9-induced mutations demonstrate that ARR17 functions as a sex switch, triggering female development when on and male development when off. Despite repeated turnover events, including a transition from the XY system to a ZW system, the sex-specific regulation of ARR17 is conserved across the poplar genus and probably beyond. Our data reveal how a single-gene-based mechanism of dioecy can enable highly dynamic sex-linked regions and contribute to maintaining recombination and integrity of sex chromosomes. Populus has young sex chromosomes despite ancient dioecy. This study shows that the ARR17 gene functions as a sex switch, triggering female development when on and male development when off. This single-gene system enables dynamic evolution of poplar sex chromosomes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Although hundreds of plant lineages have independently evolved dioecy (that is, separation of the sexes), the underlying genetic basis remains largely elusive1. Here we show that diverse poplar species carry partial duplicates of the ARABIDOPSIS RESPONSE REGULATOR 17 (ARR17) orthologue in the male-specific region of the Y chromosome. These duplicates give rise to small RNAs apparently causing male-specific DNA methylation and silencing of the ARR17 gene. CRISPR–Cas9-induced mutations demonstrate that ARR17 functions as a sex switch, triggering female development when on and male development when off. Despite repeated turnover events, including a transition from the XY system to a ZW system, the sex-specific regulation of ARR17 is conserved across the poplar genus and probably beyond. Our data reveal how a single-gene-based mechanism of dioecy can enable highly dynamic sex-linked regions and contribute to maintaining recombination and integrity of sex chromosomes. Populus has young sex chromosomes despite ancient dioecy. This study shows that the ARR17 gene functions as a sex switch, triggering female development when on and male development when off. This single-gene system enables dynamic evolution of poplar sex chromosomes.
Haas, Julia C.; Vergara, Alexander; Hurry, Vaughan; Street., Nathaniel R.
Candidate regulators and target genes of drought stress in needles and roots of Norway spruce. Journal Article
In: Biorxiv, 2020.
@article{Haas2020,
title = {Candidate regulators and target genes of drought stress in needles and roots of Norway spruce. },
author = {Julia C. Haas and Alexander Vergara and Vaughan Hurry and Nathaniel R. Street.},
doi = {10.1101/517151},
year = {2020},
date = {2020-01-20},
journal = {Biorxiv},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Vergara, Alexander; Haas, Julia Christa; Stachula, Paulina; Street, Nathaniel R.; Hurry, Vaughan
Norway spruce deploys tissue specific canonical responses to acclimate to cold. Journal Article
In: Biorxiv, 2020.
@article{Vergara2020,
title = { Norway spruce deploys tissue specific canonical responses to acclimate to cold. },
author = {Alexander Vergara and Julia Christa Haas and Paulina Stachula and Nathaniel R. Street and Vaughan Hurry},
doi = {10.1101/2020.01.13.904805},
year = {2020},
date = {2020-01-17},
journal = {Biorxiv},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Lin, Yao-Cheng; Wang, Jing; Delhomme, Nicolas; Schiffthaler, Bastian; Sundström, Görel; Zuccolo, Andrea; Nystedt, Björn; Hvidsten, Torgeir R.; Torre, Amanda; Cossu, Rosa M.; Hoeppner, Marc P.; Lantz, Henrik; Scofield, Douglas G.; Zamani, Neda; Johansson, Anna; Mannapperuma, Chanaka; Robinson, Kathryn M.; Mähler, Niklas; Leitch, Ilia J.; Pellicer, Jaume; Park, Eung-Jun; Montagu, Marc Van; de Peer, Yves Van; Grabherr, Manfred; Jansson, Stefan; Ingvarsson, Pär K.; Street, Nathaniel R.
Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen Journal Article
In: Proceedings of the National Academy of Sciences, vol. 115, no. 46, pp. E10970–E10978, 2018, ISSN: 0027-8424.
@article{Lin2018,
title = {Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen},
author = {Yao-Cheng Lin and Jing Wang and Nicolas Delhomme and Bastian Schiffthaler and Görel Sundström and Andrea Zuccolo and Björn Nystedt and Torgeir R. Hvidsten and Amanda Torre and Rosa M. Cossu and Marc P. Hoeppner and Henrik Lantz and Douglas G. Scofield and Neda Zamani and Anna Johansson and Chanaka Mannapperuma and Kathryn M. Robinson and Niklas Mähler and Ilia J. Leitch and Jaume Pellicer and Eung-Jun Park and Marc Van Montagu and Yves Van de Peer and Manfred Grabherr and Stefan Jansson and Pär K. Ingvarsson and Nathaniel R. Street},
url = {http://www.ncbi.nlm.nih.gov/pubmed/30373829 http://www.pnas.org/lookup/doi/10.1073/pnas.1801437115},
doi = {10.1073/pnas.1801437115},
issn = {0027-8424},
year = {2018},
date = {2018-11-01},
journal = {Proceedings of the National Academy of Sciences},
volume = {115},
number = {46},
pages = {E10970--E10978},
publisher = {National Academy of Sciences},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Haas, Julia C.; Street, Nathaniel R.; Sjödin, Andreas; Lee, Natuschka M.; Högberg, Mona N.; Näsholm, Torgny; Hurry, Vaughan
Microbial community response to growing season and plant nutrient optimisation in a boreal Norway spruce forest Journal Article
In: Soil Biology and Biochemistry, vol. 125, pp. 197–209, 2018, ISSN: 00380717.
@article{Haas2018,
title = {Microbial community response to growing season and plant nutrient optimisation in a boreal Norway spruce forest},
author = {Julia C. Haas and Nathaniel R. Street and Andreas Sjödin and Natuschka M. Lee and Mona N. Högberg and Torgny Näsholm and Vaughan Hurry},
url = {https://www.sciencedirect.com/science/article/pii/S0038071718302335?_rdoc=1&_fmt=high&_origin=gateway&_docanchor=&md5=b8429449ccfc9c30159a5f9aeaa92ffb#.W08E0tWNvoM.twitter https://www.sciencedirect.com/science/article/pii/S0038071718302335 https://linking},
doi = {10.1016/j.soilbio.2018.07.005},
issn = {00380717},
year = {2018},
date = {2018-10-01},
journal = {Soil Biology and Biochemistry},
volume = {125},
pages = {197--209},
publisher = {Pergamon},
abstract = {Interactions between Norway spruce trees and bacteria and fungi in nutrient limited boreal forests can be beneficial for tree growth and fitness. Tree-level effects of anthropogenic nutrient addition have been well studied, however understanding of the long-term effects on the associated microbiota is limited. Here, we report on the sensitivity of microbial community composition to the growing season and nutrient additions. High-throughput sequencing of the bacterial 16S rRNA gene and fungal ITS1 region was used to characterise changes in the microbial community after application of a complete mineral nutrient mixture for five and 25 years. The experiment was conducted using the Flakaliden forest research site in northern boreal Sweden and included naturally low nutrient control plots. Needle and fine root samples of Norway spruce were sampled in addition to bulk soil during one growing season to provide comprehensive insight into phyllosphere and belowground microbiota community changes. The phyllosphere microbiota was compositionally distinct from the belowground communities and phyllosphere diversity increased significantly over the growing season but was not influenced by the improved nutrient status of the trees. In both root and soil samples, alpha diversity of fungal, in particular ectomycorrhizal fungi (EMF), and bacterial communities increased after long-term nutrient optimisation, and with increasing years of treatment the composition of the fungal and bacterial communities changed toward a community with a higher relative abundance of nitrophilic EMF and bacterial species but did not cause complete loss of nitrophobic species from the ecosystem. From this, we conclude that 25 years of continuous nutrient addition to a boreal spruce stand increased phylotype richness and diversity of the microbiota in the soil, and at the root-soil interface, suggesting that long-term anthropogenic nutrient inputs can have positive effects on belowground biodiversity that may enhance ecosystem robustness. Future studies are needed to assess the impact of these changes to the microbiota on ecosystem carbon storage and nitrogen cycling in boreal forests.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Interactions between Norway spruce trees and bacteria and fungi in nutrient limited boreal forests can be beneficial for tree growth and fitness. Tree-level effects of anthropogenic nutrient addition have been well studied, however understanding of the long-term effects on the associated microbiota is limited. Here, we report on the sensitivity of microbial community composition to the growing season and nutrient additions. High-throughput sequencing of the bacterial 16S rRNA gene and fungal ITS1 region was used to characterise changes in the microbial community after application of a complete mineral nutrient mixture for five and 25 years. The experiment was conducted using the Flakaliden forest research site in northern boreal Sweden and included naturally low nutrient control plots. Needle and fine root samples of Norway spruce were sampled in addition to bulk soil during one growing season to provide comprehensive insight into phyllosphere and belowground microbiota community changes. The phyllosphere microbiota was compositionally distinct from the belowground communities and phyllosphere diversity increased significantly over the growing season but was not influenced by the improved nutrient status of the trees. In both root and soil samples, alpha diversity of fungal, in particular ectomycorrhizal fungi (EMF), and bacterial communities increased after long-term nutrient optimisation, and with increasing years of treatment the composition of the fungal and bacterial communities changed toward a community with a higher relative abundance of nitrophilic EMF and bacterial species but did not cause complete loss of nitrophobic species from the ecosystem. From this, we conclude that 25 years of continuous nutrient addition to a boreal spruce stand increased phylotype richness and diversity of the microbiota in the soil, and at the root-soil interface, suggesting that long-term anthropogenic nutrient inputs can have positive effects on belowground biodiversity that may enhance ecosystem robustness. Future studies are needed to assess the impact of these changes to the microbiota on ecosystem carbon storage and nitrogen cycling in boreal forests.
Jokipii-Lukkari, Soile; Sundell, David; Nilsson, Ove; Hvidsten, Torgeir R.; Street, Nathaniel R. N. R.; Tuominen, Hannele
NorWood: a gene expression resource for evo-devo studies of conifer wood development Journal Article
In: New Phytologist, vol. 216, no. 2, pp. 482–494, 2017, ISSN: 0028646X.
@article{Jokipii-Lukkari2017,
title = {NorWood: a gene expression resource for evo-devo studies of conifer wood development},
author = {Soile Jokipii-Lukkari and David Sundell and Ove Nilsson and Torgeir R. Hvidsten and Nathaniel R. N. R. Street and Hannele Tuominen},
url = {http://doi.wiley.com/10.1111/nph.14458},
doi = {10.1111/nph.14458},
issn = {0028646X},
year = {2017},
date = {2017-10-01},
journal = {New Phytologist},
volume = {216},
number = {2},
pages = {482--494},
abstract = {The secondary xylem of conifers is composed mainly of tracheids that differ anatomically and chemically from angiosperm xylem cells. There is currently no high-spatial-resolution data available profiling gene expression during wood formation for any coniferous species, which limits insight into tracheid development. RNA-sequencing data from replicated, high-spatial-resolution section series throughout the cambial and woody tissues of Picea abies were used to generate the NorWood.conGenIE.org web resource, which facilitates exploration of the associated gene expression profiles and co-expression networks. Integration within PlantGenIE.org enabled a comparative regulomics analysis, revealing divergent co-expression networks between P. abies and the two angiosperm species Arabidopsis thaliana and Populus tremula for the secondary cell wall (SCW) master regulator NAC Class IIB transcription factors. The SCW cellulose synthase genes (CesAs) were located in the neighbourhoods of the NAC factors in A. thaliana and P. tremula, but not in P. abies. The NorWood co-expression network enabled identification of potential SCW CesA regula-tors in P. abies. The NorWood web resource represents a powerful community tool for generating evo-devo insights into the divergence of wood formation between angiosperms and gymnosperms and for advancing understanding of the regulation of wood development in P. abies.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The secondary xylem of conifers is composed mainly of tracheids that differ anatomically and chemically from angiosperm xylem cells. There is currently no high-spatial-resolution data available profiling gene expression during wood formation for any coniferous species, which limits insight into tracheid development. RNA-sequencing data from replicated, high-spatial-resolution section series throughout the cambial and woody tissues of Picea abies were used to generate the NorWood.conGenIE.org web resource, which facilitates exploration of the associated gene expression profiles and co-expression networks. Integration within PlantGenIE.org enabled a comparative regulomics analysis, revealing divergent co-expression networks between P. abies and the two angiosperm species Arabidopsis thaliana and Populus tremula for the secondary cell wall (SCW) master regulator NAC Class IIB transcription factors. The SCW cellulose synthase genes (CesAs) were located in the neighbourhoods of the NAC factors in A. thaliana and P. tremula, but not in P. abies. The NorWood co-expression network enabled identification of potential SCW CesA regula-tors in P. abies. The NorWood web resource represents a powerful community tool for generating evo-devo insights into the divergence of wood formation between angiosperms and gymnosperms and for advancing understanding of the regulation of wood development in P. abies.
Giacomello, Stefania; Salmén, Fredrik; Terebieniec, Barbara K.; Vickovic, Sanja; Navarro, José Fernandez; Alexeyenko, Andrey; Reimegård, Johan; McKee, Lauren S.; Mannapperuma, Chanaka; Bulone, Vincent; Ståhl, Patrik L.; Sundström, Jens F.; Street, Nathaniel R.; Lundeberg, Joakim
Spatially resolved transcriptome profiling in model plant species Journal Article
In: Nature Plants, vol. 3, no. 6, pp. 17061, 2017, ISSN: 2055-0278.
@article{Giacomello2017,
title = {Spatially resolved transcriptome profiling in model plant species},
author = {Stefania Giacomello and Fredrik Salmén and Barbara K. Terebieniec and Sanja Vickovic and José Fernandez Navarro and Andrey Alexeyenko and Johan Reimegård and Lauren S. McKee and Chanaka Mannapperuma and Vincent Bulone and Patrik L. Ståhl and Jens F. Sundström and Nathaniel R. Street and Joakim Lundeberg},
url = {http://www.nature.com/articles/nplants201761},
doi = {10.1038/nplants.2017.61},
issn = {2055-0278},
year = {2017},
date = {2017-05-01},
journal = {Nature Plants},
volume = {3},
number = {6},
pages = {17061},
abstract = {textcopyright 2017 Macmillan Publishers Limited. All rights reserved. Understanding complex biological systems requires functional characterization of specialized tissue domains. However, existing strategies for generating and analysing high-throughput spatial expression profiles were developed for a limited range of organisms, primarily mammals. Here we present the first available approach to generate and study high-resolution, spatially resolved functional profiles in a broad range of model plant systems. Our process includes high-throughput spatial transcriptome profiling followed by spatial gene and pathway analyses. We first demonstrate the feasibility of the technique by generating spatial transcriptome profiles from model angiosperms and gymnosperms microsections. In Arabidopsis thaliana we use the spatial data to identify differences in expression levels of 141 genes and 189 pathways in eight inflorescence tissue domains. Our combined approach of spatial transcriptomics and functional profiling offers a powerful new strategy that can be applied to a broad range of plant species, and is an approach that will be pivotal to answering fundamental questions in developmental and evolutionary biology.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
textcopyright 2017 Macmillan Publishers Limited. All rights reserved. Understanding complex biological systems requires functional characterization of specialized tissue domains. However, existing strategies for generating and analysing high-throughput spatial expression profiles were developed for a limited range of organisms, primarily mammals. Here we present the first available approach to generate and study high-resolution, spatially resolved functional profiles in a broad range of model plant systems. Our process includes high-throughput spatial transcriptome profiling followed by spatial gene and pathway analyses. We first demonstrate the feasibility of the technique by generating spatial transcriptome profiles from model angiosperms and gymnosperms microsections. In Arabidopsis thaliana we use the spatial data to identify differences in expression levels of 141 genes and 189 pathways in eight inflorescence tissue domains. Our combined approach of spatial transcriptomics and functional profiling offers a powerful new strategy that can be applied to a broad range of plant species, and is an approach that will be pivotal to answering fundamental questions in developmental and evolutionary biology.
Mähler, Niklas; Wang, Jing; Terebieniec, Barbara K. B. K.; Ingvarsson, Pär K. P. K.; Street, N. R. Nathaniel R.; Hvidsten, Torgeir R.
Gene co-expression network connectivity is an important determinant of selective constraint Journal Article
In: PLOS Genetics, vol. 13, no. 4, pp. e1006402, 2017, ISSN: 1553-7404.
@article{Mahler2017,
title = {Gene co-expression network connectivity is an important determinant of selective constraint},
author = {Niklas Mähler and Jing Wang and Barbara K. B. K. Terebieniec and Pär K. P. K. Ingvarsson and N. R. Nathaniel R. Street and Torgeir R. Hvidsten},
editor = {Nathan M. Springer},
url = {http://dx.plos.org/10.1371/journal.pgen.1006402},
doi = {10.1371/journal.pgen.1006402},
issn = {1553-7404},
year = {2017},
date = {2017-04-01},
journal = {PLOS Genetics},
volume = {13},
number = {4},
pages = {e1006402},
publisher = {Public Library of Science},
abstract = {While several studies have investigated general properties of the genetic architecture of natural variation in gene expression, few of these have considered natural, outbreeding populations. In parallel, systems biology has established that a general feature of biological networks is that they are scale-free, rendering them buffered against random mutations. To date, few studies have attempted to examine the relationship between the selective processes acting to maintain natural variation of gene expression and the associated co-expression network structure. Here we utilised RNA-Sequencing to assay gene expression in winter buds undergoing bud flush in a natural population of Populus tremula, an outbreeding forest tree species. We performed expression Quantitative Trait Locus (eQTL) mapping and identified 164,290 significant eQTLs associating 6,241 unique genes (eGenes) with 147,419 unique SNPs (eSNPs). We found approximately four times as many local as distant eQTLs, with local eQTLs having significantly higher effect sizes. eQTLs were primarily located in regulatory regions of genes (UTRs or flanking regions), regardless of whether they were local or distant. We used the gene expression data to infer a co-expression network and investigated the relationship between network topology, the genetic architecture of gene expression and signatures of selection. Within the co-expression network, eGenes were underrepresented in network module cores (hubs) and overrepresented in the periphery of the network, with a negative correlation between eQTL effect size and network connectivity. We additionally found that module core genes have experienced stronger selective constraint on coding and non-coding sequence, with connectivity associated with signatures of selection. Our integrated genetics and genomics results suggest that purifying selection is the primary mechanism underlying the genetic architecture of natural variation in gene expression assayed in flushing leaf buds of P. tremula and that connectivity within the co-expression network is linked to the strength of purifying selection.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
While several studies have investigated general properties of the genetic architecture of natural variation in gene expression, few of these have considered natural, outbreeding populations. In parallel, systems biology has established that a general feature of biological networks is that they are scale-free, rendering them buffered against random mutations. To date, few studies have attempted to examine the relationship between the selective processes acting to maintain natural variation of gene expression and the associated co-expression network structure. Here we utilised RNA-Sequencing to assay gene expression in winter buds undergoing bud flush in a natural population of Populus tremula, an outbreeding forest tree species. We performed expression Quantitative Trait Locus (eQTL) mapping and identified 164,290 significant eQTLs associating 6,241 unique genes (eGenes) with 147,419 unique SNPs (eSNPs). We found approximately four times as many local as distant eQTLs, with local eQTLs having significantly higher effect sizes. eQTLs were primarily located in regulatory regions of genes (UTRs or flanking regions), regardless of whether they were local or distant. We used the gene expression data to infer a co-expression network and investigated the relationship between network topology, the genetic architecture of gene expression and signatures of selection. Within the co-expression network, eGenes were underrepresented in network module cores (hubs) and overrepresented in the periphery of the network, with a negative correlation between eQTL effect size and network connectivity. We additionally found that module core genes have experienced stronger selective constraint on coding and non-coding sequence, with connectivity associated with signatures of selection. Our integrated genetics and genomics results suggest that purifying selection is the primary mechanism underlying the genetic architecture of natural variation in gene expression assayed in flushing leaf buds of P. tremula and that connectivity within the co-expression network is linked to the strength of purifying selection.
Sundell, David; Mannapperuma, Chanaka; Netotea, Sergiu; Delhomme, Nicolas; Lin, Y. -C. Yao-Cheng; Sjödin, Andreas; de Peer, Yves Van; Jansson, Stefan; Hvidsten, Torgeir R.; Street, N. R. Nathaniel R.
The Plant Genome Integrative Explorer Resource: PlantGenIE.org Journal Article
In: New Phytologist, vol. 208, no. 4, pp. 1149–1156, 2015, ISSN: 0028646X.
@article{Sundell2015,
title = {The Plant Genome Integrative Explorer Resource: PlantGenIE.org},
author = {David Sundell and Chanaka Mannapperuma and Sergiu Netotea and Nicolas Delhomme and Y. -C. Yao-Cheng Lin and Andreas Sjödin and Yves Van de Peer and Stefan Jansson and Torgeir R. Hvidsten and N. R. Nathaniel R. Street},
url = {http://www.ncbi.nlm.nih.gov/pubmed/26192091 http://doi.wiley.com/10.1111/nph.13557},
doi = {10.1111/nph.13557},
issn = {0028646X},
year = {2015},
date = {2015-12-01},
journal = {New Phytologist},
volume = {208},
number = {4},
pages = {1149--1156},
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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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.
Delhomme, Nicolas; Sundström, Görel; Zamani, Neda; Lantz, Henrik; Lin, Yao-Cheng; Hvidsten, Torgeir R.; Höppner, Marc P.; Jern, Patric; de Peer, Yves Van; Lundeberg, Joakim; Grabherr, Manfred G.; Street, Nathaniel R.
Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies) Journal Article
In: PLOS ONE, vol. 10, no. 9, pp. e0139080, 2015, ISSN: 1932-6203.
@article{Delhomme2015,
title = {Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies)},
author = {Nicolas Delhomme and Görel Sundström and Neda Zamani and Henrik Lantz and Yao-Cheng Lin and Torgeir R. Hvidsten and Marc P. Höppner and Patric Jern and Yves Van de Peer and Joakim Lundeberg and Manfred G. Grabherr and Nathaniel R. Street},
editor = {Wolfgang Arthofer},
url = {http://dx.plos.org/10.1371/journal.pone.0139080},
doi = {10.1371/journal.pone.0139080},
issn = {1932-6203},
year = {2015},
date = {2015-09-01},
journal = {PLOS ONE},
volume = {10},
number = {9},
pages = {e0139080},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Nystedt, Björn; Street, Nathaniel R.; Wetterbom, Anna; Zuccolo, Andrea; Lin, Yao-Cheng; Scofield, Douglas G.; Vezzi, Francesco; Delhomme, Nicolas; Giacomello, Stefania; Alexeyenko, Andrey; Vicedomini, Riccardo; Sahlin, Kristoffer; Sherwood, Ellen; Elfstrand, Malin; Gramzow, Lydia; Holmberg, Kristina; Hällman, Jimmie; Keech, Olivier; Klasson, Lisa; Koriabine, Maxim; Kucukoglu, Melis; Käller, Max; Luthman, Johannes; Lysholm, Fredrik; Niittylä, Totte; Olson, Åke; Rilakovic, Nemanja; Ritland, Carol; Rosselló, Josep A.; Sena, Juliana; Svensson, Thomas; Talavera-López, Carlos; Theißen, Günter; Tuominen, Hannele; Vanneste, Kevin; Wu, Zhi-Qiang; Zhang, Bo; Zerbe, Philipp; Arvestad, Lars; Bhalerao, Rishikesh; Bohlmann, Joerg; Bousquet, Jean; Gil, Rosario Garcia; Hvidsten, Torgeir R.; Jong, Pieter; MacKay, John; Morgante, Michele; Ritland, Kermit; Sundberg, Björn; Thompson, Stacey Lee; de Peer, Yves Van; Andersson, Björn; Nilsson, Ove; Ingvarsson, Pär K.; Lundeberg, Joakim; Jansson, Stefan
The Norway spruce genome sequence and conifer genome evolution Journal Article
In: Nature, vol. 497, no. 7451, pp. 579–584, 2013, ISSN: 0028-0836.
@article{Nystedt2013,
title = {The Norway spruce genome sequence and conifer genome evolution},
author = {Björn Nystedt and Nathaniel R. Street and Anna Wetterbom and Andrea Zuccolo and Yao-Cheng Lin and Douglas G. Scofield and Francesco Vezzi and Nicolas Delhomme and Stefania Giacomello and Andrey Alexeyenko and Riccardo Vicedomini and Kristoffer Sahlin and Ellen Sherwood and Malin Elfstrand and Lydia Gramzow and Kristina Holmberg and Jimmie Hällman and Olivier Keech and Lisa Klasson and Maxim Koriabine and Melis Kucukoglu and Max Käller and Johannes Luthman and Fredrik Lysholm and Totte Niittylä and Åke Olson and Nemanja Rilakovic and Carol Ritland and Josep A. Rosselló and Juliana Sena and Thomas Svensson and Carlos Talavera-López and Günter Theißen and Hannele Tuominen and Kevin Vanneste and Zhi-Qiang Wu and Bo Zhang and Philipp Zerbe and Lars Arvestad and Rishikesh Bhalerao and Joerg Bohlmann and Jean Bousquet and Rosario Garcia Gil and Torgeir R. Hvidsten and Pieter Jong and John MacKay and Michele Morgante and Kermit Ritland and Björn Sundberg and Stacey Lee Thompson and Yves Van de Peer and Björn Andersson and Ove Nilsson and Pär K. Ingvarsson and Joakim Lundeberg and Stefan Jansson},
url = {http://www.nature.com/doifinder/10.1038/nature12211},
doi = {10.1038/nature12211},
issn = {0028-0836},
year = {2013},
date = {2013-05-01},
journal = {Nature},
volume = {497},
number = {7451},
pages = {579--584},
abstract = {Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the .100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (.10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding. Gymnosperms are a group of land plants comprising the extant taxa, cycads, Ginkgo, gnetophytes and conifers. Gymnosperms first appeared more than 300 million years ago (Myr ago) 1 , well before the angiosperm lineage separated from the stem group of extant gymnosperms 2 . The major radiation of conifer families occurred 250–65 Myr ago 3 , and during their evolution the morphology of conifers has changed rela-tively little. There are approximately 630 conifer species, representing about 70 currently recognized genera, which dominate many terrestrial ecosystems, especially in the Northern Hemisphere. Conifers also dominated both before and after the major mass extinction events at the end of the Permian and Cretaceous periods, around 250 and 65 Myr ago, respectively. Conifers are of immense ecological and economic value; coniferous forests cover enormous areas in the Northern Hemi-sphere, and conifers are keystone species in many other ecosystems. Conifers contribute a large fraction of terrestrial photosynthesis and biomass, and the cultural and economic values of conifers are also para-mount; early civilizations used conifers for firewood, tools and artefacts and today several national economies depend on commodities produced from conifers. However, despite their abundance and importance, our understanding of conifer genomes is limited. Most conifers have 12 (2n 5 24) chromosomes, probably reflecting the ancestral karyotype 4},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the .100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (.10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding. Gymnosperms are a group of land plants comprising the extant taxa, cycads, Ginkgo, gnetophytes and conifers. Gymnosperms first appeared more than 300 million years ago (Myr ago) 1 , well before the angiosperm lineage separated from the stem group of extant gymnosperms 2 . The major radiation of conifer families occurred 250–65 Myr ago 3 , and during their evolution the morphology of conifers has changed rela-tively little. There are approximately 630 conifer species, representing about 70 currently recognized genera, which dominate many terrestrial ecosystems, especially in the Northern Hemisphere. Conifers also dominated both before and after the major mass extinction events at the end of the Permian and Cretaceous periods, around 250 and 65 Myr ago, respectively. Conifers are of immense ecological and economic value; coniferous forests cover enormous areas in the Northern Hemi-sphere, and conifers are keystone species in many other ecosystems. Conifers contribute a large fraction of terrestrial photosynthesis and biomass, and the cultural and economic values of conifers are also para-mount; early civilizations used conifers for firewood, tools and artefacts and today several national economies depend on commodities produced from conifers. However, despite their abundance and importance, our understanding of conifer genomes is limited. Most conifers have 12 (2n 5 24) chromosomes, probably reflecting the ancestral karyotype 4
If you stand in a forest you can easily differentiate a Norway spruce from a Scots pine tree but, just like humans, not all trees in a species look alike. Understanding why this variation exists can be challenging, as can finding how those differences are caused by variation in the DNA sequence. Nathaniel’s group study how variation in genomes among individuals and between species give rise to this variation. The group focuses on forest trees that are both ecologically essential and economically important in Scandinavia: Norway spruce, Scots pine and aspen. They develop genomic resources for these species, including genome assemblies, and make extensive use of DNA sequencing technologies to study genome structure (the shape of DNA within the cell and how this changes) and gene expression. Nathaniel likes to link the work of the group to trees in the forest so most experimental samples are collected from nature. More recently the group has also started to use RNA sequencing to measure gene expression in both trees and the complex communities of fungal species associated with the trees to explore how both parts of the ecosystem are connected, interact and respond to environmental change. The research approaches used in the group take a holistic approach, studying whole genome or all expressed genes and extracting signal from these large-scale datasets. As this signal is often weak and affected by noise they are interested in applying methods such as machine learning to isolate meaningful patterns from the data linking variation among individuals or between species to changes in genome sequence, gene expression or, for example, changes in species present in microbial communities. The group also develop web resources to let others explore the data they produce, including the Plant Genome Integrative Explorer site (http://plantgenie.org).
Nathaniel did his PhD at the University of Southampton (UK) identifying how variation in the genome and gene expression of poplar trees is linked to differences in their growth rate and responses to abiotic stresses. After a short time working as a research fellow for the UK Energy Research Centre on projects to improve biomass yield of poplar and use biomass for energy production he moved to Sweden. He did a postdoc at the Umeå Plant Science Centre (UPSC) working on leaf shape variation and gene expression in aspen before moving to the Ecology department for a postdoc working on population genomics in aspen. He then moved back to UPSC as an assistant professor and remains there now as an associated professor. Outside of work you will find him running, biking or skiing in forests or mountains.
Current projects:
- Genome assembly of Norway spruce and Scots pine. These two conifer species have genomes of 20 Gbp with most of the genome composed of repetitive DNA element and where gene represent a tiny part of the genome. The repetitive DNA was previous termed junk DNA, but our understanding of this is changing. We are interested to learn how these huge genomes function.
- Identifying genes involved in specialised metabolite production in aspen. Aspen trees produce large amounts of specialised phenolic glycosides (SPGs), which as secondary metabolites important in defence against herbivores. The biochemical pathway producing SPGs is only partly known. We are using natural variation among aspens to identify new genes in the pathway and verifying these using genome editing methods such as CRISPR-Cas9.
- Metatranscriptomics in conifer forests. We are using RNA Sequencing to measure gene expression in Norway spruce and Scots pine roots and the fungal species associated with roots. These fungi provide nutrients to the trees in exchange for carbon. We are using RNA-Seq to gain functional insight into how this exchange is controlled and how it changes in response to environmental factors such as nitrogen fertilisaiton.
Current Projects
Bacteria Cell Wall Systems Biology (Kempe Foundation)
F Cava, N Street, E Libby
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