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Hofmeister, B.T.* ; Denkena, J. ; Colomé-Tatché, M. ; Shahryary, Y.* ; Hazarika, R.* ; Grimwood, J.* ; Mamidi, S.* ; Jenkins, J.* ; Grabowski, P.P.* ; Sreedasyam, A.* ; Shu, S.* ; Barry, K.* ; Lail, K.* ; Adam, C.* ; Lipzen, A.* ; Sorek, R.* ; Kudrna, D.* ; Talag, J.* ; Wing, R.* ; Hall, D.W.* ; Jacobsen, D.* ; Tuskan, G.A.* ; Schmutz, J.* ; Johannes, F.* ; Schmitz, R.J.*

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

Genome Biol. 21:259 (2020)

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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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Publication type Article: Journal article

Document type Scientific Article

Corresponding Author

Keywords Mutation Rate ; Epimutation Rate ; Epigenetics ; Poplar ; Dna Methylation; Dna Methylation; Natural Variation; Patterns; Plants; Annotation; Mosaicism; Discovery; Spectrum; Number; Fruit

ISSN (print) / ISBN 1474-760X

e-ISSN 1465-6906

Journal Genome Biology

Quellenangaben Volume: 21, Issue: 1, Article Number: 259

Publisher BioMed Central

Publishing Place Campus, 4 Crinan St, London N1 9xw, England

Non-patent literature Publications

Reviewing status Peer reviewed

Institute(s) Institute of Computational Biology (ICB)

Grants JGI community sequencing project
Office of Science of the U.S. Department of Energy
National Institute of General Medical Sciences of the National Institutes of Health
Pew Charitable Trusts
Deutsche Forschungsgemeinschaft (DFG)
European Seventh Framework Programme
Technical University of MunichInstitute for Advanced Study - German Excellent Initiative
National Institutes of Health
National Science Foundation