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

Hofmeister, Brigitte; Denkena, Johanna; Colome-Tatche, Maria; Shahryary, Yadollah; Hazarika, Rashmi; Grimwood, Jane; Mamidi, Sujan; Jenkins, Jerry; Grabowsk, Paul; Sreedasyam, Avinash; Shu, Shengqiang; Barry, Kerrie; Lail, Kathleen; Adams, Catherine; Lipzen, Anna; Sorek, Rotem; Kudrna, Dave; Talag, Jayson; Wing, Rod; Hall, David; Jacobsen, Daniel; Tuskan, Gerald A.; Schmutz, Jeremy; Johannes, Frank; Schmitz, Robert J.

doi:10.1186/s13059-020-02162-5

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

Journal Article · 06 October 2020 · Genome Biology (Online)

DOI: https://doi.org/10.1186/s13059-020-02162-5 · OSTI ID:1670495

Hofmeister, Brigitte ^[1]; Denkena, Johanna ^[2]; Colome-Tatche, Maria ^[3]; Shahryary, Yadollah ^[4]; Hazarika, Rashmi ^[4]; Grimwood, Jane ^[5]; Mamidi, Sujan ^[6]; Jenkins, Jerry ^[6]; Grabowsk, Paul ^[6]; Sreedasyam, Avinash ^[6]; Shu, Shengqiang ^[7]; Barry, Kerrie ^[7]; Lail, Kathleen ^[7]; Adams, Catherine ^[7]; Lipzen, Anna ^[7]; Sorek, Rotem ^[8]; Kudrna, Dave ^[9]; Talag, Jayson ^[9]; Wing, Rod ^[9]; Hall, David ^[1] more »

Univ. of Georgia, Athens, GA (United States)
Helmholtz Zentrum München (Germany)
Helmholtz Zentrum München (Germany); Univ. of Groningen (Netherlands); Technical Univ. of Munich (Germany)
Technical Univ. of Munich (Germany)
Hudson Alpha Inst. of Biotechnology, Huntsville, AL (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Hudson Alpha Inst. of Biotechnology, Huntsville, AL (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Weizmann Inst. of Science, Rehovot (Israel)
Univ. of Arizona, Tucson, AZ (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

Background: Plants 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. Results: Here, 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. Conclusion: Taken together, our study provides unprecedented insights into the origin of nucleotide and functional variation in a long-lived perennial plant.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Energy Efficiency and Renewable Energy (EERE); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC05-00OR22725; AC02-05CH11231

OSTI ID:: 1670495

Alternate ID(s):: OSTI ID: 1684685; OSTI ID: 1765576

Journal Information:: Genome Biology (Online), Vol. 21, Issue 1; ISSN 1474-760X

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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