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Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata

ABSTRACT: Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata

PROVIDER: PRJNA167289 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR072806.fastq.gz	Fastqsanger.gz
	SRR072807.fastq.gz	Fastqsanger.gz
	SRR072808.fastq.gz	Fastqsanger.gz
	SRR072809.fastq.gz	Fastqsanger.gz

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Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata

Project description:This SuperSeries is composed of the following subset Series: GSE24571: Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata [RNA-Seq] GSE38109: Natural variation in Arabidopsis thaliana transcriptomes Refer to individual Series

2012-05-21 | E-GEOD-38113 | biostudies-arrayexpress

Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata [RNA-Seq]

Project description:Transposable elements (TEs) are often the primary determinant of genome size differences among eukaryotes. In plants, the proliferation of TEs is countered through epigenetic silencing mechanisms that prevent transposition. Recent studies using the model plant Arabidopsis thaliana have revealed that methylated TE insertions are often associated with reduced expression of nearby genes, and these insertions may be subject to purifying selection due to their effect on nearby genes. Less is known about the genome-wide patterns of epigenetic silencing of TEs in other plant species. Here, we compare the 24-nt siRNA complement from Arabidopsis thaliana and a closely related congener with a two- to three-fold higher TE copy number, A. lyrata. We show that TEs, and particularly siRNA-targeted TEs, are associated with reduced gene expression within both species and also with gene expression differences between orthologs. In addition, A. lyrata TEs are targeted by a lower fraction of uniquely matching siRNAs, which are associated with more effective silencing of TE expression. Overall, our results suggest that the efficacy of RNA-directed DNA methylation silencing is lower in A. lyrata, a finding that may shed light on the causes of differential TE proliferation among species. 4 A. lyrata mRNA-seq samples

2011-02-11 | E-GEOD-24571 | biostudies-arrayexpress

Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata [RNA-Seq]

2011-02-11 | GSE24571 | GEO

Arabidopsis lyrata

Project description:Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata [RNA-Seq]

| PRJNA132411 | ENA

Arabidopsis lyrata small RNAs

Project description:Small RNA sequences from Arabidopsis lyrata leaves, as isolated from a single sample of rosette leaf tissue. These data were analyzed to 1) examine microRNA processing accuracy in A. lyrata and 2) to examine patterns of 24nt siRNA accumulation in A. lyrata.

2010-03-01 | GSE18077 | GEO

Arabidopsis lyrata flowering tissues small RNAs

Project description:Small RNA sequences from Arabidopsis lyrata flowering tissues, as isolated from flowering tissues of two biological replicates. These data were analyzed to 1) discover new micoRNAs in A. lyrata 2) examine microRNA processing accuary in A. lyrata and 3) to examine patterns of 24nt siRNA accumulation in A. lyrata.

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Arabidopsis lyrata subsp. lyrata

Project description:Arabidopsis lyrata subsp. lyrata Genome sequencing

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Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata.

Project description:Transposable elements (TEs) are often the primary determinant of genome size differences among eukaryotes. In plants, the proliferation of TEs is countered through epigenetic silencing mechanisms that prevent mobility. Recent studies using the model plant Arabidopsis thaliana have revealed that methylated TE insertions are often associated with reduced expression of nearby genes, and these insertions may be subject to purifying selection due to this effect. Less is known about the genome-wide patterns of epigenetic silencing of TEs in other plant species. Here, we compare the 24-nt siRNA complement from A. thaliana and a closely related congener with a two- to threefold higher TE copy number, Arabidopsis lyrata. We show that TEs--particularly siRNA-targeted TEs--are associated with reduced gene expression within both species and also with gene expression differences between orthologs. In addition, A. lyrata TEs are targeted by a lower fraction of uniquely matching siRNAs, which are associated with more effective silencing of TE expression. Our results suggest that the efficacy of RNA-directed DNA methylation silencing is lower in A. lyrata, a finding that may shed light on the causes of differential TE proliferation among species.

| S-EPMC3038775 | biostudies-literature

Arabidopsis lyrata subsp. lyrata

Project description:Arabidopsis lyrata subsp. lyrata Raw sequence reads

| PRJNA339675 | ENA

Comparative transcriptome profiling of Arabidopsis lyrata and Arabidopsis thaliana

Project description:Arabidopsis thaliana and Arabidopsis lyrata are two closely related Brassicaceae species, which are used as models for plant comparative biology. They differ by lifestyle, predominant mating strategy, ecological niches and genome organization. In order to explore molecular basis of specific traits, we performed RNA-sequencing of vegetative rosettes from both species. Additionally, we sequenced apical meristems and inflorescences of A. lyrata that allow for intra-specific transcriptome comparison in several major developmental stages. Please view also related dataset GSE69077 (RNA-sequencing of heat stressed A. lyrata and A. thaliana plants).

2015-08-01 | GSE69222 | GEO

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