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Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen
Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.ORCID iD: 0000-0002-3793-3264
Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
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2018 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, no 46, p. E10970-E10978Article in journal (Refereed) Published
Abstract [en]

The Populus genus is one of the major plant model systems, but genomic resources have thus far primarily been available for poplar species, and primarily Populus trichocarpa (Torr. & Gray), which was the first tree with a whole-genome assembly. To further advance evolutionary and functional genomic analyses in Populus, we produced genome assemblies and population genetics resources of two aspen species, Populus tremula L. and Populus tremuloides Michx. The two aspen species have distributions spanning the Northern Hemisphere, where they are keystone species supporting a wide variety of dependent communities and produce a diverse array of secondary metabolites. Our analyses show that the two aspens share a similar genome structure and a highly conserved gene content with P. trichocarpa but display substantially higher levels of heterozygosity. Based on population resequencing data, we observed widespread positive and negative selection acting on both coding and noncoding regions. Furthermore, patterns of genetic diversity and molecular evolution in aspen are influenced by a number of features, such as expression level, coexpression network connectivity, and regulatory variation. To maximize the community utility of these resources, we have integrated all presented data within the PopGenIE web resource (PopGenIE.org).

Place, publisher, year, edition, pages
NATL ACAD SCIENCES , 2018. Vol. 115, no 46, p. E10970-E10978
Keywords [en]
genome assembly, natural selection, coexpression, population genetics, Populus
National Category
Genetics
Identifiers
URN: urn:nbn:se:umu:diva-154950DOI: 10.1073/pnas.1801437115ISI: 000449934400020PubMedID: 30373829Scopus ID: 2-s2.0-85056516875OAI: oai:DiVA.org:umu-154950DiVA, id: diva2:1275944
Available from: 2019-01-07 Created: 2019-01-07 Last updated: 2019-01-07Bibliographically approved

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Wang, JingSchiffthaler, BastianHvidsten, Torgeir R.de la Torre, AmandaScofield, Douglas G.Mannapperuma, ChanakaRobinson, Kathryn M.Mähler, NiklasJansson, StefanIngvarsson, Pär K.Street, Nathaniel R.

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Lin, Yao-ChengWang, JingSchiffthaler, BastianZuccolo, AndreaHvidsten, Torgeir R.de la Torre, AmandaScofield, Douglas G.Mannapperuma, ChanakaRobinson, Kathryn M.Mähler, NiklasJansson, StefanIngvarsson, Pär K.Street, Nathaniel R.
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Department of Ecology and Environmental SciencesUmeå Plant Science Centre (UPSC)Department of Plant Physiology
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Proceedings of the National Academy of Sciences of the United States of America
Genetics

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