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 Colome-Tatche, 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 journalArticleAcademicpeer-review

66 Citations (Scopus)
121 Downloads (Pure)

Abstract

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 330years. 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.

Original languageEnglish
Article number259
Number of pages27
JournalGenome Biology
Volume21
Issue number1
DOIs
Publication statusPublished - 6-Oct-2020

Keywords

  • Mutation rate
  • Epimutation rate
  • Epigenetics
  • Poplar
  • DNA methylation
  • DNA METHYLATION
  • NATURAL VARIATION
  • PATTERNS
  • PLANTS
  • ANNOTATION
  • MOSAICISM
  • DISCOVERY
  • SPECTRUM
  • NUMBER
  • FRUIT

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