Although we continue to explain the function of many individual genes within a molecular or functional context, we still know relatively little about how natural variation in complex phenotypes, such as biomass,is determined. QTL studies provide insights into the genetic architecture of complex trait control, revealing that most traits are controlled by a large number of loci and that, in most cases we can only detect loci that together typically explain less than half of the observed variation.

Nathaniel Street 1150
bud sampling
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.
 
nat 1Representative 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.We are interested in identifying the genomic loci involved in controlling natural variation in traits, particularly at the level of gene expression. To do this, we take an approach termed systems genetics where the variation in expression levels, phenotype and genotype within natural populations is utilised in a combinatorial manner to identify polymorphisms underlying key control points, or hubs, within expression networks. Gene expression control is highly complex and involves interacting factors such as genome structure, transcription factor binding, epigenetics and short RNAs. As a result we are interested in integrating all levels of information possible.

Recently next-generation high throughput sequencing has had a profound influence on the nature and scale of data that can be obtained and much of our current effort involves gen-erating, analysing and disseminating 'NGS' data. Our current research focuses on using natural variation in Swedish aspen (Populus tremula) as a model system to explore the control of trait variation. Leaf shape is a particularly suitable trait for study within this species as it is highly heritable and exhibits large- scale variation with little variation in contrasting environments. We are also interested in using cross-species comparison and exploration of regulatory conservation as a means of identifying novel genes involved in trait control.

A more recently developed area of interest involves exploring the extended phenotype of spruce and aspen and how host tree genotype influences the community of fungi and bacteria present living inside host plant cells. We are applying and developing new metatranscriptomics methods alongside traditional metagenomics to explore the dynamics of the fungal community associated with different individuals of aspen and under contrasting forestry management and environmental conditions in spruce.

To support genome-wide association mapping and expression QTL mapping we have produced de novo assemblies of the aspen and spruce genomes, including de novo transcriptome assembly and genome annotation. Associated with this work we develop and maintain the PopGenIE (http://popgenie.org) and ConGenIE (http://ConGenIE.org) (Populus/Conifer Genome Ingerative Explorer) web resources, which include tools for exploring and analysing functional genomics data in both model systems.


Publications list

  1. Storage lipid accumulation is controlled by photoperiodic signal acting via regulators of growth cessation and dormancy in hybrid aspen
    New Phytol. 2018 May 15 [Epub ahead of print]
  2. Downregulating aspen xylan biosynthetic GT43 genes in developing wood stimulates growth via reprograming of the transcriptome
    New Phytol. 2018 Apr 30 [Epub ahead of print]
  3. Transcriptome analysis of embryonic domains in Norway spruce reveals potential regulators of suspensor cell death
    PLoS One. 2018, 13(3):e0192945
  4. Transcriptional roadmap to seasonal variation in wood formation of Norway spruce
    Plant Physiol. 2018, 176(4):2851-2870
  5. 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)
  6. AspWood: High-spatial-resolution transcriptome profiles reveal uncharacterized modularity of wood formation in Populus tremula
    Plant Cell. 2017, 29 (7):1585-1604
  7. A Key Role for Apoplastic H2O2 in Norway Spruce Phenolic Metabolism
    Plant Physiol. 2017;174(3):1449-1475
  8. Spatially resolved transcriptome profiling in model plant species
    Nature Plants. 2017, 3(6)
  9. Gene co-expression network connectivity is an important determinant of selective constraint
    PLoS Genet. 2017, 13(4):e1006402
  10. Interspecific Plastome Recombination Reflects Ancient Reticulate Evolution in Picea (Pinaceae)
    Mol Biol Evol. 2017, 34 (7):1689-1701
  11. NorWood: a gene expression resource for evo-devo studies of conifer wood development
    New Phytol. 2017, 216(2):482-494
  12. Landscape relatedness: detecting contemporary fine-scale spatial structure in wild populations
    LANDSCAPE ECOLOGY, 2017 32 (1):181-194
  13. DNA methylome of the 20-gigabase Norway spruce genome
    Proc Natl Acad Sci U S A. 2016, 113 (50):E8106-E8113
  14. Cytokinin and Auxin Display Distinct but Interconnected Distribution and Signaling Profiles to Stimulate Cambial Activity
    Curr Biol. 2016, 26(15):1990-1997
  15. Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species
    GENETICS 2016, 202 (3):1185
  16. 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
  17. Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies)
    PLoS One. 2015 Sep 28;10(9):e0139080
  18. The Plant Genome Integrative Explorer Resource: PlantGenIE.org
    New Phytol. 2015, 208 (4):1149-1156
  19. 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
  20. 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
  21. Insights into Conifer Giga-Genomes
    Plant Physiol. 2014, 166(4):1724-32
  22. Populus tremula (European aspen) shows no evidence of sexual dimorphism
    BMC Plant Biol. 2014; 14(1):276
  23. ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa
    BMC Genomics. 2014; 15(1):106
  24. De Novo SNP Discovery in the Scandinavian Brown Bear (Ursus arctos)
    PLoS One. 2013; 8(11):e81012
  25. The Norway spruce genome sequence and conifer genome evolution
    Nature 2013; 497(7451):579-584
  26. 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

  27. 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
  28. Sahlin K, Street N, Lundeberg J, Arvestad L
    Improved gap size estimation for scaffolding algorithms
    Bioinformatics. 2012 Sep 1;28(17):2215-22
  29. 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
  30. 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
  31. 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
  32. Ingvarsson PK, Street NR
    Association genetics of complex traits in plants
    New Phytologist: 2011 189:909-922
  33. 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.
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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