A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa

Genome Biology

Dave Kudrna¹  Jayson Talag¹  Rod Wing¹  Kathleen Lail²  Catherine Adam²  Anna Lipzen²  Kerrie Barry²  Shengqiang Shu²  David W. Hall³  Rotem Sorek⁴  Yadollah Shahryary⁵  Rashmi Hazarika⁶  Frank Johannes⁶  Johanna Denkena⁷  Maria Colomé-Tatché⁸  Sujan Mamidi⁹  Avinash Sreedasyam⁹  Jerry Jenkins⁹  Paul P. Grabowski⁹  Jeremy Schmutz^1,10  Jane Grimwood^1,10  Robert J. Schmitz^1,11  Brigitte T. Hofmeister^1,12  Gerald A. Tuskan^1,13  Daniel Jacobsen^1,13 

[1] Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA;Department of Energy Joint Genome Institute, Walnut Creek, CA, USA;Department of Genetics, University of Georgia, Athens, GA, USA;Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel;Department of Plant Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, Freising, Germany;Department of Plant Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, Freising, Germany;Institute for Advanced Study (IAS), Technical University of Munich, Lichtenbergstr. 2a, Garching, Germany;Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany;Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany;European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands;TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany;HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA;HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA;Department of Energy Joint Genome Institute, Walnut Creek, CA, USA;Institute for Advanced Study (IAS), Technical University of Munich, Lichtenbergstr. 2a, Garching, Germany;Department of Genetics, University of Georgia, Athens, GA, USA;Institute of Bioinformatics, University of Georgia, Athens, GA, USA;The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA;

关键词: Mutation rate;    Epimutation rate;    Epigenetics;    Poplar;    DNA methylation;   

DOI  :  10.1186/s13059-020-02162-5

来源: Springer

【 摘 要 】

BackgroundPlants can transmit somatic mutations and epimutations to offspring, which in turn can affect fitness. Knowledge of the rate at which these variations arise is necessary to understand how plant development contributes to local adaption in an ecoevolutionary context, particularly in long-lived perennials.ResultsHere, we generate a new high-quality reference genome from the oldest branch of a wild Populus trichocarpa tree with two dominant stems which have been evolving independently for 330 years. By sampling multiple, age-estimated branches of this tree, we use a multi-omics approach to quantify age-related somatic changes at the genetic, epigenetic, and transcriptional level. We show that the per-year somatic mutation and epimutation rates are lower than in annuals and that transcriptional variation is mainly independent of age divergence and cytosine methylation. Furthermore, a detailed analysis of the somatic epimutation spectrum indicates that transgenerationally heritable epimutations originate mainly from DNA methylation maintenance errors during mitotic rather than during meiotic cell divisions.ConclusionTaken together, our study provides unprecedented insights into the origin of nucleotide and functional variation in a long-lived perennial plant.

【 授权许可】

CC BY