Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen

Yao Cheng Lin, Jing Wang, Nicolas Delhomme, Bastian Schiffthaler, Görel Sundström, Andrea Zuccolo, Björn Nystedt, Torgeir R. Hvidsten, Amanda de la Torre, Rosa M. Cossu, Marc P. Hoeppner, Henrik Lantz, Douglas G. Scofield, Neda Zamani, Anna Johansson, Chanaka Mannapperuma, Kathryn M. Robinson, Niklas Mähler, Ilia J. Leitch, Jaume PellicerEung Jun Park, Marc Van Montagu, Yves Van de Peer, Manfred Grabherr, Stefan Jansson, Pär K. Ingvarsson, Nathaniel R. Street

Research output: Contribution to journalArticlepeer-review

41 Scopus citations

Abstract

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).

Original languageEnglish (US)
Pages (from-to)E10970-E10978
JournalProceedings of the National Academy of Sciences of the United States of America
Volume115
Issue number46
DOIs
StatePublished - Nov 13 2018

Keywords

  • Coexpression
  • Genome assembly
  • Natural selection
  • Population genetics
  • Populus

ASJC Scopus subject areas

  • General

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