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

Brigitte T. Hofmeister, Johanna Denkena, Maria Colomé-Tatché, Yadollah Shahryary, Rashmi Hazarika, Jane Grimwood, Sujan Mamidi, Jerry Jenkins, Paul P. Grabowski, Avinash Sreedasyam, Shengqiang Shu, Kerrie Barry, Kathleen Lail, Catherine Adam, Anna Lipzen, Rotem Sorek, Dave Kudrna, Jayson Talag, Rod Wing, David W. HallDaniel Jacobsen, Gerald A. Tuskan, Jeremy Schmutz, Frank Johannes, Robert J. Schmitz

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

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.

Original languageEnglish (US)
Article number259
JournalGenome biology
Volume21
Issue number1
DOIs
StatePublished - Oct 6 2020

Keywords

  • DNA methylation
  • Epigenetics
  • Epimutation rate
  • Mutation rate
  • Poplar

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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