Journal Article

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

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

2020

Overview

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.

• Publisher: BioMed Central,Springer Nature B.V,BMC
• Subject: Age / Age Factors / Animal Genetics and Genomics / Annotations / BASIC BIOLOGICAL SCIENCES / Bioinformatics / Biomedical and Life Sciences / Branches / Cell division / Cytosine / Deoxyribonucleic acid / Divergence / DNA / DNA Methylation / Epigenesis, Genetic / Epigenetics / Epimutation rate / Evolutionary Biology / Gene Expression / genome / genome assembly / Genome, Plant / Genomes / Genotype & phenotype / Human Genetics / Life Sciences / Meiosis / Microbial Genetics and Genomics / mitosis / Molecular Sequence Annotation / multiomics / Mutation / Mutation Rate / Mutation rates / perennials / plant development / Plant Genetics and Genomics / Poplar / Populus - genetics / Populus trichocarpa / progeny / somatic mutation / Transcription / transcription (genetics) / Trees