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

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Populus trichocarpa

PROVIDER: GSE132939 | GEO | 2020/08/19

REPOSITORIES: GEO

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

Project description: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 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.ConclusionTaken together, our study provides unprecedented insights into the origin of nucleotide and functional variation in a long-lived perennial plant.

| S-EPMC7539514 | biostudies-literature

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

Project description:This research uses terminal branches from a wild poplar tree to track somatic genetic, epigenetic, and transcriptional changes. Using a multi-omics approach, we aim to identify and describe mutations which arise during the lifetime of a long-lived perennial plant.

2020-08-19 | GSE132934 | GEO

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

2020-08-19 | GSE132937 | GEO

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

2020-08-19 | GSE132935 | GEO

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

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

| PRJNA549492 | ENA

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

Project description:A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa [ATAC-Seq]

| PRJNA549495 | ENA

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

Project description:A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa [RNA-Seq]

| PRJNA549496 | ENA

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

Project description:A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa [Bisulfite-Seq]

| PRJNA549497 | ENA

A phylogenomic approach reveals a low somatic mutation rate in a long-lived plant.

Project description:Somatic mutations can have important effects on the life history, ecology, and evolution of plants, but the rate at which they accumulate is poorly understood and difficult to measure directly. Here, we develop a method to measure somatic mutations in individual plants and use it to estimate the somatic mutation rate in a large, long-lived, phenotypically mosaic Eucalyptus melliodora tree. Despite being 100 times larger than Arabidopsis, this tree has a per-generation mutation rate only ten times greater, which suggests that this species may have evolved mechanisms to reduce the mutation rate per unit of growth. This adds to a growing body of evidence that illuminates the correlated evolutionary shifts in mutation rate and life history in plants.

| S-EPMC7126060 | biostudies-literature

De Novo Genome Assembly of Populus simonii Further Supports That Populus simonii and Populus trichocarpa Belong to Different Sections.

Project description:Populus simonii is an important tree in the genus Populus, widely distributed in the Northern Hemisphere and having a long cultivation history. Although this species has ecologically and economically important values, its genome sequence is currently not available, hindering the development of new varieties with wider adaptive and commercial traits. Here, we report a chromosome-level genome assembly of P. simonii using PacBio long-read sequencing data aided by Illumina paired-end reads and related genetic linkage maps. The assembly is 441.38 Mb in length and contain 686 contigs with a contig N50 of 1.94 Mb. With the linkage maps, 336 contigs were successfully anchored into 19 pseudochromosomes, accounting for 90.2% of the assembled genome size. Genomic integrity assessment showed that 1,347 (97.9%) of the 1,375 genes conserved among all embryophytes can be found in the P. simonii assembly. Genomic repeat analysis revealed that 41.47% of the P. simonii genome is composed of repetitive elements, of which 40.17% contained interspersed repeats. A total of 45,459 genes were predicted from the P. simonii genome sequence and 39,833 (87.6%) of the genes were annotated with one or more related functions. Phylogenetic analysis indicated that P. simonii and Populus trichocarpa should be placed in different sections, contrary to the previous classification according to morphology. The genome assembly not only provides an important genetic resource for the comparative and functional genomics of different Populus species, but also furnishes one of the closest reference sequences for identifying genomic variants in an F1 hybrid population derived by crossing P. simonii with other Populus species.

| S-EPMC7003099 | biostudies-literature

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