{tab=Research} Nathaniel Street in the UPSC bioinformatics office Photo: Fredrik Larsson

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.

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.

Five photos of aspen buds showing a closed bud on the left followed by different stages of bud burst towards the right side.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.

Collection of differently formed leavesRepresentative 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 You can find out more about us at the group web site
{tab=Team}
  • Personnel Image
    Ahlgren Kalman, Teitur
    PhD Student
    E-mail
    Room: B3-48-51
  • Personnel Image
    Canovi, Camilla
    PhD Student
    E-mail
    Room: B3-48-51
  • Personnel Image
    Delhomme, Nicolas
    Staff scientist
    E-mail
    Room: B3-48-51
  • Personnel Image
    Kochakarn, Theerarat Fai
    Research Engineer
    E-mail
    Room: B3-48-51
  • Personnel Image
    Kumar, Vikash
    Staff scientist
    E-mail
    Room: B3-26-50
  • Personnel Image
    Mccann, Jamie
    Staff scientist
    E-mail
    Room: B3-48-51
  • Personnel Image
    Piombo, Edoardo
    Research Engineer
    E-mail
    Room: B3-48-51
  • Personnel Image
    Rodriguez, Eduardo
    PhD Student
    E-mail
    Room: B3-34-45
  • Personnel Image
    Rydman, Sara
    PhD Student
    E-mail
    Room: B3-48-51
  • Personnel Image
    Sharma, Ashish
    PostDoc
    E-mail
    Room: B3-48-51
  • Personnel Image
    Street, Nathaniel
    Professor
    E-mail
    Room: B3-44-45
    Website
  • Personnel Image
    Van Zalen, Elena
    PhD Student
    E-mail
    Room: B3-48-51

{tab=Publications}
  2024 (9)
A resource of identified and annotated lincRNAs expressed during somatic embryogenesis development in Norway spruce. Canovi, C., Stojkovič, K., Benítez, A. A., Delhomme, N., Egertsdotter, U., & Street, N. R. Physiologia Plantarum, 176(5): e14537. 2024. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.14537
A resource of identified and annotated lincRNAs expressed during somatic embryogenesis development in Norway spruce [link]Paper   doi   link   bibtex   abstract  
An Improved Chromosome-scale Genome Assembly and Population Genetics resource for Populus tremula. Robinson, K. M., Schiffthaler, B., Liu, H., Rydman, S. M., Rendón-Anaya, M., Kalman, T. A., Kumar, V., Canovi, C., Bernhardsson, C., Delhomme, N., Jenkins, J., Wang, J., Mähler, N., Richau, K. H., Stokes, V., A'Hara, S., Cottrell, J., Coeck, K., Diels, T., Vandepoele, K., Mannapperuma, C., Park, E., Plaisance, S., Jansson, S., Ingvarsson, P. K., & Street, N. R. Physiologia Plantarum, 176(5): e14511. 2024. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.14511
An Improved Chromosome-scale Genome Assembly and Population Genetics resource for Populus tremula. [link]Paper   doi   link   bibtex   abstract  
Effects of small-scale outplanting fertilization on conifer seedling growth and fungal community establishment. Schneider, A. N., Castro, D., Holmlund, M., Näsholm, T., Hurry, V., & Street, N. R. Trees, Forests and People, 16: 100568. June 2024.
Effects of small-scale outplanting fertilization on conifer seedling growth and fungal community establishment [link]Paper   doi   link   bibtex   abstract  
Genomic basis of seed colour in quinoa inferred from variant patterns using extreme gradient boosting. Sandell, F. L., Holzweber, T., Street, N. R., Dohm, J. C., & Himmelbauer, H. Plant Biotechnology Journal, 22(5): 1312–1324. 2024. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pbi.14267
Genomic basis of seed colour in quinoa inferred from variant patterns using extreme gradient boosting [link]Paper   doi   link   bibtex   abstract  
Genomic basis of the distinct biosynthesis of β-glucogallin, a biochemical marker for hydrolyzable tannin production, in three oak species. Yang, Q., Li, J., Wang, Y., Wang, Z., Pei, Z., Street, N. R., Bhalerao, R. P., Yu, Z., Gao, Y., Ni, J., Jiao, Y., Sun, M., Yang, X., Chen, Y., Liu, P., Wang, J., Liu, Y., & Li, G. New Phytologist, 242(6): 2702–2718. 2024. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.19711
Genomic basis of the distinct biosynthesis of β-glucogallin, a biochemical marker for hydrolyzable tannin production, in three oak species [link]Paper   doi   link   bibtex   abstract  
High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar. Shi, T., Jia, K., Bao, Y., Nie, S., Tian, X., Yan, X., Chen, Z., Li, Z., Zhao, S., Ma, H., Zhao, Y., Li, X., Zhang, R., Guo, J., Zhao, W., El-Kassaby, Y. A., Müller, N., Van de Peer, Y., Wang, X., Street, N. R., Porth, I., An, X., & Mao, J. Plant Physiology, 195(1): 652–670. May 2024.
High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar [link]Paper   doi   link   bibtex   abstract  
Systems genetic analysis of lignin biosynthesis in Populus tremula. Luomaranta, M., Grones, C., Choudhary, S., Milhinhos, A., Kalman, T. A., Nilsson, O., Robinson, K. M., Street, N. R., & Tuominen, H. New Phytologist, 243(6): 2157–2174. September 2024.
Systems genetic analysis of lignin biosynthesis in <i>Populus tremula</i> [link]Paper   doi   link   bibtex   abstract  
The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees. Shi, T., Zhang, X., Hou, Y., Jia, C., Dan, X., Zhang, Y., Jiang, Y., Lai, Q., Feng, J., Feng, J., Ma, T., Wu, J., Liu, S., Zhang, L., Long, Z., Chen, L., Street, N. R., Ingvarsson, P. K., Liu, J., Yin, T., & Wang, J. Molecular Plant, 17(5): 725–746. May 2024. Publisher: Elsevier
The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees [link]Paper   doi   link   bibtex   abstract  
Whole-genome resequencing facilitates the development of a 50K single nucleotide polymorphism genotyping array for Scots pine (Pinus sylvestris L.) and its transferability to other pine species. Estravis Barcala, M., van der Valk, T., Chen, Z., Funda, T., Chaudhary, R., Klingberg, A., Fundova, I., Suontama, M., Hallingbäck, H., Bernhardsson, C., Nystedt, B., Ingvarsson, P. K., Sherwood, E., Street, N., Gyllensten, U., Nilsson, O., & Wu, H. X. The Plant Journal, 117(3): 944–955. 2024. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.16535
Whole-genome resequencing facilitates the development of a 50K single nucleotide polymorphism genotyping array for Scots pine (Pinus sylvestris L.) and its transferability to other pine species [link]Paper   doi   link   bibtex   abstract  
  2023 (3)
Flexure wood formation via growth reprogramming in hybrid aspen involves jasmonates and polyamines and transcriptional changes resembling tension wood development. Urbancsok, J., Donev, E. N., Sivan, P., van Zalen, E., Barbut, F. R., Derba-Maceluch, M., Šimura, J., Yassin, Z., Gandla, M. L., Karady, M., Ljung, K., Winestrand, S., Jönsson, L. J., Scheepers, G., Delhomme, N., Street, N. R., & Mellerowicz, E. J. New Phytologist. October 2023. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.19307
Flexure wood formation via growth reprogramming in hybrid aspen involves jasmonates and polyamines and transcriptional changes resembling tension wood development [link]Paper   doi   link   bibtex   abstract  
Genetic markers and tree properties predicting wood biorefining potential in aspen (Populus tremula) bioenergy feedstock. Escamez, S., Robinson, K. M., Luomaranta, M., Gandla, M. L., Mähler, N., Yassin, Z., Grahn, T., Scheepers, G., Stener, L., Jansson, S., Jönsson, L. J., Street, N. R., & Tuominen, H. Biotechnology for Biofuels and Bioproducts, 16(1): 65. April 2023.
Genetic markers and tree properties predicting wood biorefining potential in aspen (Populus tremula) bioenergy feedstock [link]Paper   doi   link   bibtex   abstract  
Seiðr: Efficient calculation of robust ensemble gene networks. Schiffthaler, B., van Zalen, E., Serrano, A. R., Street, N. R., & Delhomme, N. Heliyon, 9(6): e16811. June 2023.
Seiðr: Efficient calculation of robust ensemble gene networks [link]Paper   doi   link   bibtex   abstract  
  2022 (5)
Cone-setting in spruce is regulated by conserved elements of the age-dependent flowering pathway. Akhter, S., Westrin, K. J., Zivi, N., Nordal, V., Kretzschmar, W. W., Delhomme, N., Street, N. R., Nilsson, O., Emanuelsson, O., & Sundström, J. F. New Phytologist, 236(5): 1951–1963. December 2022.
Cone-setting in spruce is regulated by conserved elements of the age-dependent flowering pathway [link]Paper   doi   link   bibtex   abstract  
Demographic history and natural selection shape patterns of deleterious mutation load and barriers to introgression across Populus genome. Liu, S., Zhang, L., Sang, Y., Lai, Q., Zhang, X., Jia, C., Long, Z., Wu, J., Ma, T., Mao, K., Street, N. R, Ingvarsson, P. K, Liu, J., & Wang, J. Molecular Biology and Evolution, 39(2): msac008. January 2022.
Demographic history and natural selection shape patterns of deleterious mutation load and barriers to introgression across Populus genome [link]Paper   doi   link   bibtex   abstract  
Identification of growth regulators using cross-species network analysis in plants. Curci, P. L., Zhang, J., Mähler, N., Seyfferth, C., Mannapperuma, C., Diels, T., Van Hautegem, T., Jonsen, D., Street, N., Hvidsten, T. R, Hertzberg, M., Nilsson, O., Inzé, D., Nelissen, H., & Vandepoele, K. Plant Physiology, 190(4): 2350–2365. December 2022.
Identification of growth regulators using cross-species network analysis in plants [link]Paper   doi   link   bibtex   abstract  
Metatranscriptomics captures dynamic shifts in mycorrhizal coordination in boreal forests. Law, S. R., Serrano, A. R., Daguerre, Y., Sundh, J., Schneider, A. N., Stangl, Z. R., Castro, D., Grabherr, M., Näsholm, T., Street, N. R., & Hurry, V. Proceedings of the National Academy of Sciences, 119(26): e2118852119. June 2022.
Metatranscriptomics captures dynamic shifts in mycorrhizal coordination in boreal forests [link]Paper   doi   link   bibtex   abstract  
Norway spruce deploys tissue-specific responses during acclimation to cold. Vergara, A., Haas, J. C., Aro, T., Stachula, P., Street, N. R., & Hurry, V. Plant, Cell & Environment, 45(2). February 2022.
Norway spruce deploys tissue-specific responses during acclimation to cold [link]Paper   doi   link   bibtex   abstract  
  2021 (7)
Adaptive introgression facilitate adaptation to high latitudes in European aspen (Populus tremula L.). Rendón-Anaya, M., Wilson, J., Sveinsson, S., Fedorkov, A., Cottrell, J., Bailey, M. E. S., Ruņģis, D., Lexer, C., Jansson, S., Robinson, K. M., Street, N. R., & Ingvarsson, P. K. Molecular Biology and Evolution, 38(11): 5034–5050. July 2021.
Adaptive introgression facilitate adaptation to high latitudes in European aspen (Populus tremula L.) [link]Paper   doi   link   bibtex   abstract   9 downloads  
Candidate regulators and target genes of drought stress in needles and roots of Norway spruce. Haas, J. C, Vergara, A., Serrano, A. R, Mishra, S., Hurry, V., & Street, N. R Tree Physiology, 41(7): 1230–1246. July 2021.
Candidate regulators and target genes of drought stress in needles and roots of Norway spruce [link]Paper   doi   link   bibtex   abstract   17 downloads  
Centromere-Specific Retrotransposons and Very-Long-Chain Fatty Acid Biosynthesis in the Genome of Yellowhorn (Xanthoceras sorbifolium, Sapindaceae), an Oil-Producing Tree With Significant Drought Resistance. Liu, H., Yan, X., Wang, X., Zhang, D., Zhou, Q., Shi, T., Jia, K., Tian, X., Zhou, S., Zhang, R., Yun, Q., Wang, Q., Xiang, Q., Mannapperuma, C., Van Zalen, E., Street, N. R., Porth, I., El-Kassaby, Y. A., Zhao, W., Wang, X., Guan, W., & Mao, J. Frontiers in Plant Science, 12: 2546. 2021.
Centromere-Specific Retrotransposons and Very-Long-Chain Fatty Acid Biosynthesis in the Genome of Yellowhorn (Xanthoceras sorbifolium, Sapindaceae), an Oil-Producing Tree With Significant Drought Resistance [link]Paper   doi   link   bibtex   abstract   3 downloads  
Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce. Schneider, A. N., Sundh, J., Sundström, G., Richau, K., Delhomme, N., Grabherr, M., Hurry, V., & Street, N. R. mSystems, 6(1). February 2021.
Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce [link]Paper   doi   link   bibtex   abstract   15 downloads  
Effects of Early, Small-Scale Nitrogen Addition on Germination and Early Growth of Scots Pine (Pinus sylvestris) Seedlings and on the Recruitment of the Root-Associated Fungal Community. Castro, D., Schneider, A. N., Holmlund, M., Näsholm, T., Street, N. R., & Hurry, V. Forests, 12(11): 1589. November 2021.
Effects of Early, Small-Scale Nitrogen Addition on Germination and Early Growth of Scots Pine (Pinus sylvestris) Seedlings and on the Recruitment of the Root-Associated Fungal Community [link]Paper   doi   link   bibtex   abstract   3 downloads  
The BOP‐type co‐transcriptional regulator NODULE ROOT1 promotes stem secondary growth of the tropical Cannabaceae tree Parasponia andersonii. Shen, D., Holmer, R., Kulikova, O., Mannapperuma, C., Street, N. R., Yan, Z., Maden, T., Bu, F., Zhang, Y., Geurts, R., & Magne, K. The Plant Journal,tpj.15242. April 2021.
The BOP‐type co‐transcriptional regulator NODULE ROOT1 promotes stem secondary growth of the tropical Cannabaceae tree Parasponia andersonii [link]Paper   doi   link   bibtex  
qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE). Christie, N., Mannapperuma, C., Ployet, R., van der Merwe, K., Mähler, N., Delhomme, N., Naidoo, S., Mizrachi, E., Street, N. R., & Myburg, A. A. BMC Bioinformatics, 22(1): 595. December 2021.
qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE) [link]Paper   doi   link   bibtex   abstract   1 download  
  2020 (7)
A metabolite roadmap of the wood‐forming tissue in Populus tremula. Abreu, I. N., Johansson, A. I., Sokołowska, K., Niittylä, T., Sundberg, B., Hvidsten, T. R., Street, N. R., & Moritz, T. New Phytologist, 228(5): 1559–1572. December 2020.
A metabolite roadmap of the wood‐forming tissue in Populus tremula [link]Paper   doi   link   bibtex   2 downloads  
A single gene underlies the dynamic evolution of poplar sex determination. Müller, N. A., Kersten, B., Leite Montalvão, A. P., Mähler, N., Bernhardsson, C., Bräutigam, K., Carracedo Lorenzo, Z., Hoenicka, H., Kumar, V., Mader, M., Pakull, B., Robinson, K. M., Sabatti, M., Vettori, C., Ingvarsson, P. K., Cronk, Q., Street, N. R., & Fladung, M. Nature Plants, 6(6): 630–637. June 2020.
A single gene underlies the dynamic evolution of poplar sex determination [link]Paper   doi   link   bibtex   3 downloads  
Chromosome-level genome assembly of a parent species of widely cultivated azaleas. Yang, F., Nie, S., Liu, H., Shi, T., Tian, X., Zhou, S., Bao, Y., Jia, K., Guo, J., Zhao, W., An, N., Zhang, R., Yun, Q., Wang, X., Mannapperuma, C., Porth, I., El-Kassaby, Y. A., Street, N. R., Wang, X., Van de Peer, Y., & Mao, J. Nature Communications, 11(1): 5269. December 2020.
Chromosome-level genome assembly of a parent species of widely cultivated azaleas [link]Paper   doi   link   bibtex   abstract  
Evidence for widespread selection in shaping the genomic landscape during speciation of Populus. Wang, J., Street, N. R., Park, E., Liu, J., & Ingvarsson, P. K. Molecular Ecology, 29(6): 1120–1136. March 2020.
Evidence for widespread selection in shaping the genomic landscape during speciation of Populus [link]Paper   doi   link   bibtex  
Inferring the Genomic Landscape of Recombination Rate Variation in European Aspen ( Populus tremula ). Apuli, R., Bernhardsson, C., Schiffthaler, B., Robinson, K. M, Jansson, S., Street, N. R, & Ingvarsson, P. K G3 Genes\textbarGenomes\textbarGenetics, 10(1): 299–309. January 2020.
Inferring the Genomic Landscape of Recombination Rate Variation in European Aspen ( Populus tremula ) [link]Paper   doi   link   bibtex   abstract  
Leaf shape in Populus tremula is a complex, omnigenic trait. Mähler, N., Schiffthaler, B., Robinson, K. M., Terebieniec, B. K., Vučak, M., Mannapperuma, C., Bailey, M. E. S., Jansson, S., Hvidsten, T. R., & Street, N. R. Ecology and Evolution, 10(21): 11922–11940. November 2020.
Leaf shape in Populus tremula is a complex, omnigenic trait [link]Paper   doi   link   bibtex   15 downloads  
The Mitogenome of Norway Spruce and a Reappraisal of Mitochondrial Recombination in Plants. Sullivan, A. R, Eldfjell, Y., Schiffthaler, B., Delhomme, N., Asp, T., Hebelstrup, K. H, Keech, O., Öberg, L., Møller, I. M., Arvestad, L., Street, N. R, & Wang, X. Genome Biology and Evolution, 12(1): 3586–3598. January 2020.
The Mitogenome of Norway Spruce and a Reappraisal of Mitochondrial Recombination in Plants [link]Paper   doi   link   bibtex   abstract  
  2019 (8)
An Ultra-Dense Haploid Genetic Map for Evaluating the Highly Fragmented Genome Assembly of Norway Spruce (Picea abies ). Bernhardsson, C., Vidalis, A., Wang, X., Scofield, D. G, Schiffthaler, B., Baison, J., Street, N. R, García-Gil, M R., & Ingvarsson, P. K G3 Genes\textbarGenomes\textbarGenetics, 9(5): 1623–1632. May 2019.
An Ultra-Dense Haploid Genetic Map for Evaluating the Highly Fragmented Genome Assembly of Norway Spruce (Picea abies ) [link]Paper   doi   link   bibtex   abstract  
Cyberinfrastructure to Improve Forest Health and Productivity: The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment. Wegrzyn, J. L., Staton, M. A., Street, N. R., Main, D., Grau, E., Herndon, N., Buehler, S., Falk, T., Zaman, S., Ramnath, R., Richter, P., Sun, L., Condon, B., Almsaeed, A., Chen, M., Mannapperuma, C., Jung, S., & Ficklin, S. Frontiers in Plant Science, 10: 813. June 2019.
Cyberinfrastructure to Improve Forest Health and Productivity: The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment [link]Paper   doi   link   bibtex  
Genomics of forest trees. Street, N. R. In Advances in Botanical Research, volume 89, pages 1–37. Elsevier, 2019.
Genomics of forest trees [link]Paper   doi   link   bibtex   1 download  
High Spatial Resolution Profiling in Tree Species. Giacomello, S., Delhomme, N., Niittylä, T., Tuominen, H., & Street, N. R. In Annual Plant Reviews online, pages 329–360. American Cancer Society, 2019. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/9781119312994.apr0688
High Spatial Resolution Profiling in Tree Species [link]Paper   doi   link   bibtex   abstract   1 download  
Poplar carbohydrate‐active enzymes: whole‐genome annotation and functional analyses based on RNA expression data. Kumar, V., Hainaut, M., Delhomme, N., Mannapperuma, C., Immerzeel, P., Street, N. R., Henrissat, B., & Mellerowicz, E. J. The Plant Journal, 99(4): 589–609. August 2019.
Poplar carbohydrate‐active enzymes: whole‐genome annotation and functional analyses based on RNA expression data [link]Paper   doi   link   bibtex  
Ray Parenchymal Cells Contribute to Lignification of Tracheids in Developing Xylem of Norway Spruce. Blokhina, O., Laitinen, T., Hatakeyama, Y., Delhomme, N., Paasela, T., Zhao, L., Street, N. R., Wada, H., Kärkönen, A., & Fagerstedt, K. Plant Physiology, 181(4): 1552–1572. December 2019.
Ray Parenchymal Cells Contribute to Lignification of Tracheids in Developing Xylem of Norway Spruce [link]Paper   doi   link   bibtex  
Systems and Synthetic Biology of Forest Trees: A Bioengineering Paradigm for Woody Biomass Feedstocks. Myburg, A. A., Hussey, S. G., Wang, J. P., Street, N. R., & Mizrachi, E. Frontiers in Plant Science, 10: 775. June 2019.
Systems and Synthetic Biology of Forest Trees: A Bioengineering Paradigm for Woody Biomass Feedstocks [link]Paper   doi   link   bibtex   1 download  
Why does nitrogen addition to forest soils inhibit decomposition?. Bonner, M. T., Castro, D., Schneider, A. N., Sundström, G., Hurry, V., Street, N. R., & Näsholm, T. Soil Biology and Biochemistry, 137: 107570. October 2019.
Why does nitrogen addition to forest soils inhibit decomposition? [link]Paper   doi   link   bibtex  
  2018 (8)
A major locus controls local adaptation and adaptive life history variation in a perennial plant. Wang, J., Ding, J., Tan, B., Robinson, K. M., Michelson, I. H., Johansson, A., Nystedt, B., Scofield, D. G., Nilsson, O., Jansson, S., Street, N. R., & Ingvarsson, P. K. Genome Biology, 19(1): 72. December 2018.
A major locus controls local adaptation and adaptive life history variation in a perennial plant [link]Paper   doi   link   bibtex   4 downloads  
Downregulating aspen xylan biosynthetic GT43 genes in developing wood stimulates growth via reprograming of the transcriptome. Ratke, C., Terebieniec, B. K., Winestrand, S., Derba-Maceluch, M., Grahn, T., Schiffthaler, B., Ulvcrona, T., Özparpucu, M., Rüggeberg, M., Lundqvist, S., Street, N. R., Jönsson, L. J., & Mellerowicz, E. J. New Phytologist, 219(1): 230–245. July 2018.
Downregulating aspen xylan biosynthetic GT43 genes in developing wood stimulates growth via reprograming of the transcriptome [link]Paper   doi   link   bibtex   1 download  
Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen. Lin, Y., Wang, J., Delhomme, N., Schiffthaler, B., Sundström, G., Zuccolo, A., Nystedt, B., Hvidsten, T. R., de la Torre, A., Cossu, R. M., Hoeppner, M. P., Lantz, H., Scofield, D. G., Zamani, N., Johansson, A., Mannapperuma, C., Robinson, K. M., Mähler, N., Leitch, I. J., Pellicer, J., Park, E., Van Montagu, M., Van de Peer, Y., Grabherr, M., Jansson, S., Ingvarsson, P. K., & Street, N. R. Proceedings of the National Academy of Sciences, 115(46): E10970–E10978. November 2018.
Functional and evolutionary genomic inferences in <i>Populus</i> through genome and population sequencing of American and European aspen [link]Paper   doi   link   bibtex   abstract   3 downloads  
Integrative Analysis of Three RNA Sequencing Methods Identifies Mutually Exclusive Exons of MADS-Box Isoforms During Early Bud Development in Picea abies. Akhter, S., Kretzschmar, W. W., Nordal, V., Delhomme, N., Street, N. R., Nilsson, O., Emanuelsson, O., & Sundström, J. F. Frontiers in Plant Science, 9: 1625. November 2018.
Integrative Analysis of Three RNA Sequencing Methods Identifies Mutually Exclusive Exons of MADS-Box Isoforms During Early Bud Development in Picea abies [link]Paper   doi   link   bibtex  
Microbial community response to growing season and plant nutrient optimisation in a boreal Norway spruce forest. Haas, J. C., Street, N. R., Sjödin, A., Lee, N. M., Högberg, M. N., Näsholm, T., & Hurry, V. Soil Biology and Biochemistry, 125: 197–209. October 2018.
Microbial community response to growing season and plant nutrient optimisation in a boreal Norway spruce forest [link]Paper   doi   link   bibtex   2 downloads  
Storage lipid accumulation is controlled by photoperiodic signal acting via regulators of growth cessation and dormancy in hybrid aspen. Grimberg, Å., Lager, I., Street, N. R., Robinson, K. M., Marttila, S., Mähler, N., Ingvarsson, P. K., & Bhalerao, R. P. New Phytologist, 219(2): 619–630. July 2018.
Storage lipid accumulation is controlled by photoperiodic signal acting via regulators of growth cessation and dormancy in hybrid aspen [link]Paper   doi   link   bibtex   2 downloads  
Transcriptional Roadmap to Seasonal Variation in Wood Formation of Norway Spruce. Jokipii-Lukkari, S., Delhomme, N., Schiffthaler, B., Mannapperuma, C., Prestele, J., Nilsson, O., Street, N. R., & Tuominen, H. Plant Physiology, 176(4): 2851–2870. April 2018.
Transcriptional Roadmap to Seasonal Variation in Wood Formation of Norway Spruce [link]Paper   doi   link   bibtex   2 downloads  
Transcriptome analysis of embryonic domains in Norway spruce reveals potential regulators of suspensor cell death. Reza, S. H., Delhomme, N., Street, N. R., Ramachandran, P., Dalman, K., Nilsson, O., Minina, E. A., & Bozhkov, P. V. PLOS ONE, 13(3): e0192945. March 2018.
Transcriptome analysis of embryonic domains in Norway spruce reveals potential regulators of suspensor cell death [link]Paper   doi   link   bibtex  
  2017 (8)
A Key Role for Apoplastic H2O2 in Norway Spruce Phenolic Metabolism. Laitinen, T., Morreel, K., Delhomme, N., Gauthier, A., Schiffthaler, B., Nickolov, K., Brader, G., Lim, K., Teeri, T. H., Street, N. R., Boerjan, W., & Kärkönen, A. Plant Physiology, 174(3): 1449–1475. July 2017.
A Key Role for Apoplastic H2O2 in Norway Spruce Phenolic Metabolism [link]Paper   doi   link   bibtex  
AspWood: High-Spatial-Resolution Transcriptome Profiles Reveal Uncharacterized Modularity of Wood Formation in Populus tremula. Sundell, D., Street, N. R., Kumar, M., Mellerowicz, E. J., Kucukoglu, M., Johnsson, C., Kumar, V., Mannapperuma, C., Delhomme, N., Nilsson, O., Tuominen, H., Pesquet, E., Fischer, U., Niittylä, T., Sundberg, B., & Hvidsten, T. R. The Plant Cell, 29(7): 1585–1604. July 2017.
AspWood: High-Spatial-Resolution Transcriptome Profiles Reveal Uncharacterized Modularity of Wood Formation in Populus tremula [link]Paper   doi   link   bibtex  
BatchMap: A parallel implementation of the OneMap R package for fast computation of F1 linkage maps in outcrossing species. Schiffthaler, B., Bernhardsson, C., Ingvarsson, P. K., & Street, N. R. PLOS ONE, 12(12): e0189256. December 2017.
BatchMap: A parallel implementation of the OneMap R package for fast computation of F1 linkage maps in outcrossing species [link]Paper   doi   link   bibtex  
Gene co-expression network connectivity is an important determinant of selective constraint. Mähler, N., Wang, J., Terebieniec, B. K., Ingvarsson, P. K., Street, N. R., & Hvidsten, T. R. PLOS Genetics, 13(4): e1006402. April 2017.
Gene co-expression network connectivity is an important determinant of selective constraint [link]Paper   doi   link   bibtex   21 downloads  
Interspecific Plastome Recombination Reflects Ancient Reticulate Evolution in Picea (Pinaceae). Sullivan, A. R., Schiffthaler, B., Thompson, S. L., Street, N. R., & Wang, X. Molecular Biology and Evolution, 34(7): 1689–1701. July 2017.
Interspecific Plastome Recombination Reflects Ancient Reticulate Evolution in Picea (Pinaceae) [link]Paper   doi   link   bibtex  
Landscape relatedness: detecting contemporary fine-scale spatial structure in wild populations. Norman, A. J., Stronen, A. V., Fuglstad, G., Ruiz-Gonzalez, A., Kindberg, J., Street, N. R., & Spong, G. Landscape Ecology, 32(1): 181–194. January 2017.
Landscape relatedness: detecting contemporary fine-scale spatial structure in wild populations [link]Paper   doi   link   bibtex  
NorWood: a gene expression resource for evo‐devo studies of conifer wood development. Jokipii‐Lukkari, S., Sundell, D., Nilsson, O., Hvidsten, T. R., Street, N. R., & Tuominen, H. New Phytologist, 216(2): 482–494. October 2017.
NorWood: a gene expression resource for evo‐devo studies of conifer wood development [link]Paper   doi   link   bibtex  
Spatially resolved transcriptome profiling in model plant species. Giacomello, S., Salmén, F., Terebieniec, B. K., Vickovic, S., Navarro, J. F., Alexeyenko, A., Reimegård, J., McKee, L. S., Mannapperuma, C., Bulone, V., Ståhl, P. L., Sundström, J. F., Street, N. R., & Lundeberg, J. Nature Plants, 3(6): 17061. June 2017.
Spatially resolved transcriptome profiling in model plant species [link]Paper   doi   link   bibtex  
  2016 (4)
Cytokinin and Auxin Display Distinct but Interconnected Distribution and Signaling Profiles to Stimulate Cambial Activity. Immanen, J., Nieminen, K., Smolander, O., Kojima, M., Alonso Serra, J., Koskinen, P., Zhang, J., Elo, A., Mähönen, A., Street, N., Bhalerao, R., Paulin, L., Auvinen, P., Sakakibara, H., & Helariutta, Y. Current Biology, 26(15): 1990–1997. August 2016.
Cytokinin and Auxin Display Distinct but Interconnected Distribution and Signaling Profiles to Stimulate Cambial Activity [link]Paper   doi   link   bibtex  
DNA methylome of the 20-gigabase Norway spruce genome. Ausin, I., Feng, S., Yu, C., Liu, W., Kuo, H. Y., Jacobsen, E. L., Zhai, J., Gallego-Bartolome, J., Wang, L., Egertsdotter, U., Street, N. R., Jacobsen, S. E., & Wang, H. Proceedings of the National Academy of Sciences, 113(50): E8106–E8113. December 2016.
DNA methylome of the 20-gigabase Norway spruce genome [link]Paper   doi   link   bibtex   abstract  
Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species. Wang, J., Street, N. R, Scofield, D. G, & Ingvarsson, P. K Genetics, 202(3): 1185–1200. March 2016.
Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species [link]Paper   doi   link   bibtex   abstract  
Towards integration of population and comparative genomics in forest trees. Ingvarsson, P. K., Hvidsten, T. R., & Street, N. R. New Phytologist, 212(2): 338–344. October 2016.
Towards integration of population and comparative genomics in forest trees [link]Paper   doi   link   bibtex  
  2015 (5)
A resource for characterizing genome-wide binding and putative target genes of transcription factors expressed during secondary growth and wood formation in Populus. Liu, L., Ramsay, T., Zinkgraf, M., Sundell, D., Street, N. R., Filkov, V., & Groover, A. Plant J, 82(5): 887–98. June 2015. Edition: 2015/04/24
A resource for characterizing genome-wide binding and putative target genes of transcription factors expressed during secondary growth and wood formation in Populus [link]Paper   doi   link   bibtex   abstract  
Comparative physiology of allopatric Populus species: geographic clines in photosynthesis, height growth, and carbon isotope discrimination in common gardens. Soolanayakanahally, R. Y., Guy, R. D., Street, N. R., Robinson, K. M., Silim, S. N., Albrectsen, B. R., & Jansson, S. Front Plant Sci, 6: 528. 2015. Edition: 2015/08/04
Comparative physiology of allopatric Populus species: geographic clines in photosynthesis, height growth, and carbon isotope discrimination in common gardens [link]Paper   doi   link   bibtex   abstract  
Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies). Delhomme, N., Sundstrom, G., Zamani, N., Lantz, H., Lin, Y. C., Hvidsten, T. R., Hoppner, M. P., Jern, P., Van de Peer, Y., Lundeberg, J., Grabherr, M. G., & Street, N. R. PLoS One, 10(9): e0139080. September 2015. Edition: 2015/09/29
Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies) [link]Paper   doi   link   bibtex   abstract  
The Plant Genome Integrative Explorer Resource: PlantGenIE.org. Sundell, D., Mannapperuma, C., Netotea, S., Delhomme, N., Lin, Y. C., Sjodin, A., Van de Peer, Y., Jansson, S., Hvidsten, T. R., & Street, N. R. New Phytol, 208(4): 1149–56. December 2015. Edition: 2015/07/21
The Plant Genome Integrative Explorer Resource: PlantGenIE.org [link]Paper   doi   link   bibtex   abstract  
Variation in linked selection and recombination drive genomic divergence during allopatric speciation of European and American aspens. Wang, J., Street, N. R., Scofield, D. G., & Ingvarsson, P. K. Technical Report Evolutionary Biology, October 2015.
Variation in linked selection and recombination drive genomic divergence during allopatric speciation of European and American aspens [link]Paper   doi   link   bibtex   abstract   1 download  
  2014 (3)
ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa. Netotea, S., Sundell, D., Street, N. R, & Hvidsten, T. R BMC Genomics, 15(1): 106. 2014.
ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa [link]Paper   doi   link   bibtex  
Insights into Conifer Giga-Genomes. De La Torre, A. R., Birol, I., Bousquet, J., Ingvarsson, P. K., Jansson, S., Jones, S. J., Keeling, C. I., MacKay, J., Nilsson, O., Ritland, K., Street, N., Yanchuk, A., Zerbe, P., & Bohlmann, J. Plant Physiology, 166(4): 1724–1732. December 2014.
Insights into Conifer Giga-Genomes [link]Paper   doi   link   bibtex  
Populus tremula (European aspen) shows no evidence of sexual dimorphism. Robinson, K. M, Delhomme, N., Mähler, N., Schiffthaler, B., Önskog, J., Albrectsen, B. R, Ingvarsson, P. K, Hvidsten, T. R, Jansson, S., & Street, N. R BMC Plant Biology, 14(1): 276. December 2014.
Populus tremula (European aspen) shows no evidence of sexual dimorphism [link]Paper   doi   link   bibtex   2 downloads  
  2013 (3)
De Novo SNP Discovery in the Scandinavian Brown Bear (Ursus arctos). Norman, A. J., Street, N. R., & Spong, G. PLoS ONE, 8(11): e81012. November 2013.
De Novo SNP Discovery in the Scandinavian Brown Bear (Ursus arctos) [link]Paper   doi   link   bibtex  
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. Lafon‐Placette, C., Faivre‐Rampant, P., Delaunay, A., Street, N., Brignolas, F., & Maury, S. New Phytologist, 197(2): 416–430. January 2013.
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 [link]Paper   doi   link   bibtex  
The Norway spruce genome sequence and conifer genome evolution. Nystedt, B., Street, N. R., Wetterbom, A., Zuccolo, A., Lin, Y., Scofield, D. G., Vezzi, F., Delhomme, N., Giacomello, S., Alexeyenko, A., Vicedomini, R., Sahlin, K., Sherwood, E., Elfstrand, M., Gramzow, L., Holmberg, K., Hällman, J., Keech, O., Klasson, L., Koriabine, M., Kucukoglu, M., Käller, M., Luthman, J., Lysholm, F., Niittylä, T., Olson, Å., Rilakovic, N., Ritland, C., Rosselló, J. A., Sena, J., Svensson, T., Talavera-López, C., Theißen, G., Tuominen, H., Vanneste, K., Wu, Z., Zhang, B., Zerbe, P., Arvestad, L., Bhalerao, R. P., Bohlmann, J., Bousquet, J., Garcia Gil, R., Hvidsten, T. R., de Jong, P., MacKay, J., Morgante, M., Ritland, K., Sundberg, B., Lee Thompson, S., Van de Peer, Y., Andersson, B., Nilsson, O., Ingvarsson, P. K., Lundeberg, J., & Jansson, S. Nature, 497(7451): 579–584. May 2013.
The Norway spruce genome sequence and conifer genome evolution [link]Paper   doi   link   bibtex   1 download  
  2012 (4)
A collection of INDEL markers for map-based cloning in seven Arabidopsis accessions. Păcurar, D. I., Păcurar, M. L., Street, N., Bussell, J. D., Pop, T. I., Gutierrez, L., & Bellini, C. Journal of Experimental Botany, 63(7): 2491–2501. April 2012.
A collection of INDEL markers for map-based cloning in seven Arabidopsis accessions [link]Paper   doi   link   bibtex  
Improved gap size estimation for scaffolding algorithms. Sahlin, K., Street, N., Lundeberg, J., & Arvestad, L. Bioinformatics, 28(17): 2215–2222. September 2012.
Improved gap size estimation for scaffolding algorithms [link]Paper   doi   link   bibtex  
Paramutation-Like Interaction of T-DNA Loci in Arabidopsis. Xue, W., Ruprecht, C., Street, N., Hematy, K., Chang, C., Frommer, W. B., Persson, S., & Niittylä, T. PLoS ONE, 7(12): e51651. December 2012.
Paramutation-Like Interaction of T-DNA Loci in Arabidopsis [link]Paper   doi   link   bibtex  
The obscure events contributing to the evolution of an incipient sex chromosome in Populus: a retrospective working hypothesis. Tuskan, G. A., DiFazio, S., Faivre-Rampant, P., Gaudet, M., Harfouche, A., Jorge, V., Labbé, J. L., Ranjan, P., Sabatti, M., Slavov, G., Street, N., Tschaplinski, T. J., & Yin, T. Tree Genetics & Genomes, 8(3): 559–571. June 2012.
The obscure events contributing to the evolution of an incipient sex chromosome in Populus: a retrospective working hypothesis [link]Paper   doi   link   bibtex   abstract  
  2011 (2)
A systems biology model of the regulatory network in Populusleaves reveals interacting regulators and conserved regulation. Street, N. R., Jansson, S., & Hvidsten, T. R. BMC Plant Biology, 11(1): 13. January 2011.
A systems biology model of the regulatory network in Populusleaves reveals interacting regulators and conserved regulation [link]Paper   doi   link   bibtex   abstract  
Association genetics of complex traits in plants. Ingvarsson, P. K., & Street, N. R. New Phytologist, 189(4): 909–922. March 2011.
Association genetics of complex traits in plants [link]Paper   doi   link   bibtex  
  2009 (3)
Five QTL hotspots for yield in short rotation coppice bioenergy poplar: The Poplar Biomass Loci. Rae, A. M., Street, N. R., Robinson, K. M., Harris, N., & Taylor, G. BMC Plant Biology, 9(1): 1–13. December 2009. Number: 1 Publisher: BioMed Central
Five QTL hotspots for yield in short rotation coppice bioenergy poplar: The Poplar Biomass Loci [link]Paper   doi   link   bibtex   abstract  
Genome-wide profiling of populus small RNAs. Klevebring, D., Street, N. R., Fahlgren, N., Kasschau, K. D., Carrington, J. C., Lundeberg, J., & Jansson, S. BMC genomics, 10: 620. December 2009.
doi   link   bibtex   abstract  
The Populus Genome Integrative Explorer (PopGenIE): a new resource for exploring the Populus genome. Sjödin, A., Street, N. R., Sandberg, G., Gustafsson, P., & Jansson, S. New Phytologist, 182(4): 1013–1025. June 2009.
The <i>Populus</i> Genome Integrative Explorer (PopGenIE): a new resource for exploring the <i>Populus</i> genome [link]Paper   doi   link   bibtex  
  2008 (2)
A cross-species transcriptomics approach to identify genes involved in leaf development. Street, N., Sjödin, A., Bylesjö, M., Gustafsson, P., Trygg, J., & Jansson, S. BMC Genomics, 9(1): 589. 2008.
A cross-species transcriptomics approach to identify genes involved in leaf development [link]Paper   doi   link   bibtex  
LAMINA: a tool for rapid quantification of leaf size and shape parameters. Bylesjö, M., Segura, V., Soolanayakanahally, R. Y, Rae, A. M, Trygg, J., Gustafsson, P., Jansson, S., & Street, N. R BMC Plant Biology, 8(1): 82. 2008.
LAMINA: a tool for rapid quantification of leaf size and shape parameters [link]Paper   doi   link   bibtex  
  2006 (1)
The genetics and genomics of the drought response in Populus. Street, N. R., Skogström, O., Sjödin, A., Tucker, J., Rodríguez-Acosta, M., Nilsson, P., Jansson, S., & Taylor, G. The Plant Journal, 48(3): 321–341. 2006. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2006.02864.x
The genetics and genomics of the drought response in Populus [link]Paper   doi   link   bibtex   abstract  
  2005 (1)
The transcriptome of Populus in elevated CO2. Taylor, G., Street, N. R., Tricker, P. J., Sjödin, A., Graham, L., Skogström, O., Calfapietra, C., Scarascia-Mugnozza, G., & Jansson, S. New Phytologist, 167(1): 143–154. 2005. _eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-8137.2005.01450.x
The transcriptome of Populus in elevated CO2 [link]Paper   doi   link   bibtex   abstract  
  2004 (1)
Morphological and physiological traits influencing biomass productivity in short-rotation coppice poplar. Rae, A M, Robinson, K M, Street, N R, & Taylor, G Canadian Journal of Forest Research, 34(7): 1488–1498. July 2004. Publisher: NRC Research Press
Morphological and physiological traits influencing biomass productivity in short-rotation coppice poplar [link]Paper   doi   link   bibtex   1 download  
  undefined (1)
A transcriptome atlas of zygotic and somatic embryogenesis in Norway spruce. Stojkovič, K., Canovi, C., Le, K., Ahmad, I., Gaboreanu, I., Johansson, S., Delhomme, N., Egertsdotter, U., & Street, N. R. The Plant Journal, n/a(n/a). . _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.17087
A transcriptome atlas of zygotic and somatic embryogenesis in Norway spruce [link]Paper   doi   link   bibtex   abstract