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

Abstract

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.

AlphaBeta: computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants

“…We found similar accumulation slopes as well as epimutation rates (Fig. 4h, see also co-submission [26]).…”

“…Furthermore, the model fits provided overwhelming evidence that somatic epimutations, in poplar, accumulate in a selectively neutral fashion during aging, both at the genome-wide scale (globally) as well as at the sub-genomic scale (exons, promoters, TEs) ( Fig. 4f, see also co-submission [26]). This was true for CG and CHG contexts (Fig.…”

“…To facilitate the first insights into epimutational processes in long-lived perennials, we applied AlphaBeta to MethylC-seq leaf samples (∼ 41.1X coverage) from 8 separate branches of a single poplar (Populus trichocarpa) tree (see also co-submission, [26]). The tree features two main stems (here referred to as tree 13 and tree 14), which were originally thought to be two separate trees (Fig.…”

“…MethylC-seq reads were aligned using Methylpy v1.3.2 [57]. Alignment was to the new Stettler14 assembly of P. trichocarpa, as described in [26]. Starting from the BAM files (*.bam), the MethylStar pipeline [42] was used for further data processing and methylation state calling.…”

“…1a). By combining this information with contemporary leaf methylome measurements, it is possible to infer the rate of somatic epimutations as a function of age (see also co-submission, [26]).…”