Journal
GENOME BIOLOGY
Volume 21, Issue 1, Pages -Publisher
BMC
DOI: 10.1186/s13059-020-02162-5
Keywords
Mutation rate; Epimutation rate; Epigenetics; Poplar; DNA methylation
Funding
- National Science Foundation [IOS-1546867]
- National Institutes of Health [R01-GM134682]
- Technical University of MunichInstitute for Advanced Study - German Excellent Initiative
- European Seventh Framework Programme [291763]
- Deutsche Forschungsgemeinschaft (DFG) [SFB/Sonderforschungsbereich924]
- Pew Charitable Trusts
- National Institute of General Medical Sciences of the National Institutes of Health [T32GM007103]
- Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231]
- JGI community sequencing project [CSP1678]
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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.
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