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.

Nathaniel Street 1150

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.

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.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

  1. A single gene underlies the dynamic evolution of poplar sex determination
    Nat Plants. 2020 Jun 1 [Epub ahead of print]
  2. Evidence for widespread selection in shaping the genomic landscape during speciation of Populus
    Mol Ecol. 2020, 29(6):1120-1136
  3. Inferring the Genomic Landscape of Recombination Rate Variation in European Aspen (Populus tremula)
    G3-GENES GENOMES GENETICS 2020, 10(1):299-309
  4. Genomics of forest trees
    Molecular Physiology And Biotechnology Of Trees 2019, 89:1-37
  5. The mitogenome of Norway spruce and a reappraisal of mitochondrial recombination in plants
    Genome Biol Evol. 2020, 12(1):3586-3598
  6. Why does nitrogen addition to forest soils inhibit decomposition?
    SOIL BIOLOGY & BIOCHEMISTRY 2019, 137
  7. Poplar carbohydrate-active enzymes: whole-genome annotation and functional analyses based on RNA expression data
    Plant journal 2019, 99(4):589-609
  8. Ray parenchymal cells contribute to lignification of tracheids in developing xylem of Norway spruce
    Plant Physiol. 2019 Sep 26 [Epub ahead of print]
  9. Systems and Synthetic Biology of Forest Trees: A Bioengineering Paradigm for Woody Biomass Feedstocks
    FRONTIERS IN PLANT SCIENCE 2019, 10
  10. 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
  11. 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
  12. Poplar carbohydrate-active enzymes - whole genome annotation and functional analyses based on RNA expression data
    Plant J. 2019 May 20 [Epub ahead of print]
  13. High Spatial Resolution Profiling in Tree Species
    Annual Plant Reviews Online 2019
  14. 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
  15. 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
  16. Microbial community response to growing season and plant nutrient optimisation in a boreal Norway spruce forest
    SOIL BIOLOGY & BIOCHEMISTRY 2018, 125:197-209
  17. A major locus controls local adaptation and adaptive life history variation in a perennial plant
    Genome Biol. 2018 Jun 4;19(1):72
  18. 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
  19. Downregulating aspen xylan biosynthetic GT43 genes in developing wood stimulates growth via reprograming of the transcriptome
    New Phytol. 2018, 219 (1):230-245
  20. Transcriptome analysis of embryonic domains in Norway spruce reveals potential regulators of suspensor cell death
    PLoS One. 2018, 13(3):e0192945
  21. Transcriptional roadmap to seasonal variation in wood formation of Norway spruce
    Plant Physiol. 2018, 176(4):2851-2870
  22. 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)
  23. AspWood: High-spatial-resolution transcriptome profiles reveal uncharacterized modularity of wood formation in Populus tremula
    Plant Cell. 2017, 29 (7):1585-1604
  24. A Key Role for Apoplastic H2O2 in Norway Spruce Phenolic Metabolism
    Plant Physiol. 2017;174(3):1449-1475
  25. Spatially resolved transcriptome profiling in model plant species
    Nature Plants. 2017, 3(6)
  26. Gene co-expression network connectivity is an important determinant of selective constraint
    PLoS Genet. 2017, 13(4):e1006402
  27. Interspecific Plastome Recombination Reflects Ancient Reticulate Evolution in Picea (Pinaceae)
    Mol Biol Evol. 2017, 34 (7):1689-1701
  28. NorWood: a gene expression resource for evo-devo studies of conifer wood development
    New Phytol. 2017, 216(2):482-494
  29. Landscape relatedness: detecting contemporary fine-scale spatial structure in wild populations
    LANDSCAPE ECOLOGY, 2017 32 (1):181-194
  30. DNA methylome of the 20-gigabase Norway spruce genome
    Proc Natl Acad Sci U S A. 2016, 113 (50):E8106-E8113
  31. Cytokinin and Auxin Display Distinct but Interconnected Distribution and Signaling Profiles to Stimulate Cambial Activity
    Curr Biol. 2016, 26(15):1990-1997
  32. Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species
    GENETICS 2016, 202 (3):1185
  33. 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
  34. Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies)
    PLoS One. 2015 Sep 28;10(9):e0139080
  35. The Plant Genome Integrative Explorer Resource: PlantGenIE.org
    New Phytol. 2015, 208 (4):1149-1156
  36. 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
  37. 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
  38. Insights into Conifer Giga-Genomes
    Plant Physiol. 2014, 166(4):1724-32
  39. Populus tremula (European aspen) shows no evidence of sexual dimorphism
    BMC Plant Biol. 2014; 14(1):276
  40. ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa
    BMC Genomics. 2014; 15(1):106
  41. De Novo SNP Discovery in the Scandinavian Brown Bear (Ursus arctos)
    PLoS One. 2013; 8(11):e81012
  42. The Norway spruce genome sequence and conifer genome evolution
    Nature 2013; 497(7451):579-584
  43. 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

  44. 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
  45. Sahlin K, Street N, Lundeberg J, Arvestad L
    Improved gap size estimation for scaffolding algorithms
    Bioinformatics. 2012 Sep 1;28(17):2215-22
  46. 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
  47. 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
  48. 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
  49. Ingvarsson PK, Street NR
    Association genetics of complex traits in plants
    New Phytologist: 2011 189:909-922
  50. 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.
  51. 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
  52. 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
  53. 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
  54. 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
  55. 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
  56. 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
  57. 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
  58. 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