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

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

PROVIDER: PRJNA549492 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9321780_1.fastq.gz	Fastqsanger.gz
	SRR9321780_2.fastq.gz	Fastqsanger.gz
	SRR9321772_1.fastq.gz	Fastqsanger.gz
	SRR9321772_2.fastq.gz	Fastqsanger.gz
	SRR9321802.fastq.gz	Fastqsanger.gz

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

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

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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]

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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]

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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:This SuperSeries is composed of the SubSeries listed below.

2020-08-19 | GSE132939 | GEO

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.

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Somatic Mutational Landscape of Wild Populus trichocarpa tree [ncRNA-seq]

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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.

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