Our group has a focus on genomics research of aspen, Norway spruce and Scots pine. We perform genome assembly, transcriptome and co-expression network analyses with a focus on understanding the genetic architecture of complex traits such as leaf shape variation, wood development and specialised metabolite production and the role of non-coding RNAs in regulation and genome function.
Photo: Fredrik Larsson
Through collaboration with Prof. Vaughan Hurry we are also performing metagenomics and metatranscriptomics analyses to understand functional links between tree hosts, their associated microbiome and abiotic factors. The group have a strong interest in applications of new sequencing technologies and develop the PlantGenIE.org web resource to make their genomics data available to the community.
We make extensive use of bioinformatics and computational approaches including machine learning, GWAS, network inference, differential, network analysis and a plethora of genome assembly and comparative genomics analysis tools. These approaches are implemented using genomic DNA, RNA-Seq, ATAC-Seq, DAP-Seq, Hi-C and other high-throughput based sequencing methods.
Stages of leaf development in aspen. We are performing detailed characterisation of developmental profiles in aspen to support our association mapping project and to further understanding of genes functioning during leaf development.
We are also working to establish wet lab methods for validation of candidate genes and regulatory mechanisms identified from our in-silico work. The group are firm believers in implementing reproducible and transparent analyses through the use of resources such as snakmake/nextflow, git and by developing FAIR compliant tools. We make extensive use of R, python and high performance computing infrastructures.
Representative leaf shapes from the Swedish Aspen collection, a collection of natural aspen genotypes from across Sweden that is grown in a common garden experiment near Umeå.
Publication list
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Candidate regulators and target genes of drought stress in needles and roots of Norway spruce
Tree Physiol. 2021 Jan 8 Epub ahead of print
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Leaf shape in Populus tremulais a complex, omnigenic trait
ECOLOGY AND EVOLUTION 2020, 10(21):11922-11940
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Chromosome-level genome assembly of a parent species of widely cultivated azaleas
Nat Commun. 2020, 11(1):5269
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A metabolite roadmap of the wood-forming tissue in Populus tremula
New Phytol. 2020 Jul 10 [Epub ahead of print]
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A single gene underlies the dynamic evolution of poplar sex determination
Nat Plants. 2020 Jun 1 [Epub ahead of print]
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Evidence for widespread selection in shaping the genomic landscape during speciation of Populus
Mol Ecol. 2020, 29(6):1120-1136
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Inferring the Genomic Landscape of Recombination Rate Variation in European Aspen (Populus tremula)
G3-GENES GENOMES GENETICS 2020, 10(1):299-309
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Genomics of forest trees
Molecular Physiology And Biotechnology Of Trees 2019, 89:1-37
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The mitogenome of Norway spruce and a reappraisal of mitochondrial recombination in plants
Genome Biol Evol. 2020, 12(1):3586-3598
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Why does nitrogen addition to forest soils inhibit decomposition?
SOIL BIOLOGY & BIOCHEMISTRY 2019, 137
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Poplar carbohydrate-active enzymes: whole-genome annotation and functional analyses based on RNA expression data
Plant journal 2019, 99(4):589-609
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Ray parenchymal cells contribute to lignification of tracheids in developing xylem of Norway spruce
Plant Physiol. 2019, 181(4):1552-1572
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Systems and Synthetic Biology of Forest Trees: A Bioengineering Paradigm for Woody Biomass Feedstocks
FRONTIERS IN PLANT SCIENCE 2019, 10
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Cyberinfrastructure to Improve Forest Health and Productivity: The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment
FRONTIERS IN PLANT SCIENCE 2019, 10
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An Ultra-Dense Haploid Genetic Map for Evaluating the Highly Fragmented Genome Assembly of Norway Spruce (Picea abies)
G3 (Bethesda) 2019;9(5):1623-1632
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Poplar carbohydrate-active enzymes - whole genome annotation and functional analyses based on RNA expression data
Plant J. 2019 May 20 [Epub ahead of print]
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High Spatial Resolution Profiling in Tree Species
Annual Plant Reviews Online 2019
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Integrative Analysis of Three RNA Sequencing Methods Identifies Mutually Exclusive Exons of MADS-Box Isoforms During Early Bud Development in Picea abies
FRONTIERS IN PLANT SCIENCE 2018, 8:1625
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Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen
Proc Natl Acad Sci U S A. 2018, 115(46):E10970-E10978
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Microbial community response to growing season and plant nutrient optimisation in a boreal Norway spruce forest
SOIL BIOLOGY & BIOCHEMISTRY 2018, 125:197-209
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A major locus controls local adaptation and adaptive life history variation in a perennial plant
Genome Biol. 2018 Jun 4;19(1):72
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Storage lipid accumulation is controlled by photoperiodic signal acting via regulators of growth cessation and dormancy in hybrid aspen
New Phytol. 2018, 219 (2):619-630
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Downregulating aspen xylan biosynthetic GT43 genes in developing wood stimulates growth via reprograming of the transcriptome
New Phytol. 2018, 219 (1):230-245
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Transcriptome analysis of embryonic domains in Norway spruce reveals potential regulators of suspensor cell death
PLoS One. 2018, 13(3):e0192945
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Transcriptional roadmap to seasonal variation in wood formation of Norway spruce
Plant Physiol. 2018, 176(4):2851-2870
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BatchMap: A parallel implementation of the OneMap R package for fast computation of F-1 linkage maps in outcrossing species
PLOS ONE 2017, 12 (12)
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AspWood: High-spatial-resolution transcriptome profiles reveal uncharacterized modularity of wood formation in Populus tremula
Plant Cell. 2017, 29 (7):1585-1604
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A Key Role for Apoplastic H2O2 in Norway Spruce Phenolic Metabolism
Plant Physiol. 2017;174(3):1449-1475
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Spatially resolved transcriptome profiling in model plant species
Nature Plants. 2017, 3(6)
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Gene co-expression network connectivity is an important determinant of selective constraint
PLoS Genet. 2017, 13(4):e1006402
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Interspecific Plastome Recombination Reflects Ancient Reticulate Evolution in Picea (Pinaceae)
Mol Biol Evol. 2017, 34 (7):1689-1701
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NorWood: a gene expression resource for evo-devo studies of conifer wood development
New Phytol. 2017, 216(2):482-494
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Landscape relatedness: detecting contemporary fine-scale spatial structure in wild populations
LANDSCAPE ECOLOGY, 2017 32 (1):181-194
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DNA methylome of the 20-gigabase Norway spruce genome
Proc Natl Acad Sci U S A. 2016, 113 (50):E8106-E8113
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Cytokinin and Auxin Display Distinct but Interconnected Distribution and Signaling Profiles to Stimulate Cambial Activity
Curr Biol. 2016, 26(15):1990-1997
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Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species
GENETICS 2016, 202 (3):1185
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Variation in linked selection and recombination drive genomic divergence during allopatric speciation of European and American aspens
Mol Biol Evol. 2016, 33(7):1754-1767
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Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies)
PLoS One. 2015 Sep 28;10(9):e0139080
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The Plant Genome Integrative Explorer Resource: PlantGenIE.org
New Phytol. 2015, 208 (4):1149-1156
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Comparative physiology of allopatric Populus species: geographic clines in photosynthesis, height growth, and carbon isotope discrimination in common gardens
Front Plant Sci. 2015, 6:528
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A resource for characterizing genome-wide binding and putative target genes of transcription factors expressed during secondary growth and wood formation in Populus
Plant J. 2015, 82(5):887-98
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Insights into Conifer Giga-Genomes
Plant Physiol. 2014, 166(4):1724-32
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Populus tremula (European aspen) shows no evidence of sexual dimorphism
BMC Plant Biol. 2014; 14(1):276
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ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa
BMC Genomics. 2014; 15(1):106
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De Novo SNP Discovery in the Scandinavian Brown Bear (Ursus arctos)
PLoS One. 2013; 8(11):e81012
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The Norway spruce genome sequence and conifer genome evolution
Nature 2013; 497(7451):579-584
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Lafon-Placette C, Faivre-Rampant P, Delaunay A, Street N, Brignolas F, Maury S
Methylome of DNase I sensitive chromatin in Populus trichocarpa shoot apical meristematic cells: a simplified approach revealing characteristics of gene-body DNA methylation in open chromatin state
New Phytol. 2013; 197(2):416-30
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Xue W, Ruprecht C, Street N, Hematy K, Chang C, Frommer WB, Persson S, Niittylä T
Paramutation-Like Interaction of T-DNA Loci in Arabidopsis
PLoS ONE 2012 7(12): e51651
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Sahlin K, Street N, Lundeberg J, Arvestad L
Improved gap size estimation for scaffolding algorithms
Bioinformatics. 2012 Sep 1;28(17):2215-22
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Tuskan GA, DiFazio S, Faivre-Rampant P, Gaudet M, Harfouche A, Jorge V, Labbé JL, Ranjan P, Sabatti M, Slavov G, Street N, Tschaplinski TJ, Yin T
The obscure events contributing to the evolution of an incipient sex chromosome in Populus: a retrospective working hypothesis
Tree Genetics & Genomes 2012; 8(3):559-571
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Pacurar DI, Pacurar ML, Street N, Bussell JD, Pop TI, Gutierrez L, Bellini C.
A collection of INDEL markers for map-based cloning in seven Arabidopsis accessions
J Exp Bot. 2012;63(7):2491-501
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Street NR, Jansson S, Hvidsten TR
A systems biology model of the regulatory network in Populus leaves reveals interacting regulators and conserved regulation
BMC Plant Biology: 2011 11:13
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Ingvarsson PK, Street NR
Association genetics of complex traits in plants
New Phytologist: 2011 189:909-922
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Klevebring D, Street NR, Fahlgren N, Kasschau KD, Carrington JC, Lundeberg J, Jansson S
Genome-wide profiling of Populus small RNAs
BMC Genomics: 2009 10:620, 18 pp.
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Sjödin A, Street NR, Sandberg G, Gustafsson P, Jansson S
The Populus genome integrative explorer (PopGenIE): a new resource for exploring the Populus genome
New Phytologist: 2009 182:1013-1025
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Sjödin A, Street NR, Sandberg G, Gustafsson P, Jansson S
The Populus genome integrative explorer (PopGenIE): a new resource for exploring the Populus genome
New Phytologist: 2009, publised online
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Street NR, Sjödin A, Bylesjö M, Gustafsson P, Trygg J, Jansson S
A cross-species transcriptomics approach to identify genes involved in leaf development
BMC Genomics: 2008 9:589
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Street NR, Sjödin A, Bylesjö M, Gustafsson P, Trygg J, Jansson S
A cross-species transcriptomics approach to identify genes involved in leaf development
BMC Genomics: 2008 9:589
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Bylesjö M, Segura V, Soolanayakanahally RY, Rae AM, Trygg J, Gustafsson P, Jansson S, Street NR
LAMINA: a tool for rapid quantification of leaf size and shape parameters
BMC Plant Biology: 2008 8:82
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Bylesjö M, Segura V, Soolanayakanahally RY, Rae AM, Trygg J, Gustafsson P, Jansson S, Street NR
LAMINA: a tool for rapid quantification of leaf size and shape parameters
BMC Plant Biology: 2008 8:82
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Street NR, Skogstrom O, Sjodin A, Tucker J, Rodriguez-Acosta M, Nilsson P, Jansson S, Taylor G
The genetics and genomics of the drought response in Populus
Plant Journal: 2006 48:321-341
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Taylor G, Street NR, Tricker PJ, Sjodin A, Graham L, Skogstrom O, Calfapietra C, Mugnozza GS, Jansson S
The transcriptome of Populus in elevated CO2
New Phytol: 2005 167:143-154