PT  - JOURNAL ARTICLE
AU  - Brigitte T. Hofmeister
AU  - Johanna Denkena
AU  - Maria Colomé-Tatché
AU  - Yadollah Shahryary
AU  - Rashmi Hazarika
AU  - Jane Grimwood
AU  - Sujan Mamidi
AU  - Jerry Jenkins
AU  - Paul P. Grabowski
AU  - Avinash Sreedasyam
AU  - Shengqiang Shu
AU  - Kerrie Barry
AU  - Kathleen Lail
AU  - Catherine Adam
AU  - Anna Lipzen
AU  - Rotem Sorek
AU  - Dave Kudrna
AU  - Jayson Talag
AU  - Rod Wing
AU  - David W. Hall
AU  - Gerald A. Tuskan
AU  - Jeremy Schmutz
AU  - Frank Johannes
AU  - Robert J. Schmitz
TI  - The somatic genetic and epigenetic mutation rate in a wild long-lived perennial <em>Populus trichocarpa</em>
AID  - 10.1101/862623
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 862623
4099  - http://biorxiv.org/content/early/2019/12/03/862623.short
4100  - http://biorxiv.org/content/early/2019/12/03/862623.full
AB  - 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 eco-evolutionary context, particularly in long-lived perennials.Results Here, we generated 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 used 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.