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Comparative transcriptome profiling of Arabidopsis lyrata and Arabidopsis thaliana

ABSTRACT: 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).

ORGANISM(S): Arabidopsis thaliana Arabidopsis lyrata subsp. lyrata

PROVIDER: GSE69222 | GEO | 2015/08/01

SECONDARY ACCESSION(S): PRJNA284922

REPOSITORIES: GEO

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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. Arabidopsis lyrata and Arabidopsis thaliana aerial tissues were collected from mock treated plants, total RNA isolated and poly-A RNA populations sequenced

2015-08-01 | E-GEOD-69222 | biostudies-arrayexpress

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Comparative transcriptome analysis in response to heat stress in Arabidopsis thaliana and Arabidopsis lyrata

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. To identify heat stress induced genes, we performed RNA-sequencing of rosette leaves from mock-treated, heat-stressed and heat-stressed-recoved plants of both species. Analysis of genetic element transcriptional changes in response to 6 hours of 37°C heat stress and 48 hours of recovery in Arabidopsis thaliana Col-0 and Arabidopsis lyrata MN47.

2015-08-01 | E-GEOD-69077 | biostudies-arrayexpress

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Project description:Deep sequencing of small RNA from three closely related brassicaceae A. thaliana, A. lyrata and Capsella rubella was done to systematically analyze the evolution of MIRNA genes and their targets.

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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.

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Project description:Gene copy number variation (CNV) is a form of genetic polymorphism that contributes significantly to genome size and function but remains poorly characterized due to technological limitations. Inter-specific comparisons of CNVs in recently diverged plant species are crucial to uncover selection patterns underlying adaptation of a species to stressful environments. Especially given that gene amplifications have long been implicated in emergence of species-specific traits, we conducted a genome-wide survey to identify species-specific gene copy number expansions and deletions in the model extremophile species - Arabidopsis halleri that has diverged in evolutionarily recent time from Arabidopsis thaliana. Cross-species cDNA array based comparative genomic hybridization was employed to compare and identify gene copy number variation in the two sister-species - the metallophyte Arabidopsis halleri and non-metallophyte Arabidopsis lyrata, both relative to Arabidopsis thaliana. We uncovered an unprecedented level of gene copy number polymorphism in Arabidopsis halleri, with a species-specific enrichment of metal homeostasis function in the genes found to be copy number expanded, thus indicating CNV as a mechanism that underlies the key physiological trait of metal hyperaccumulation and hypetolerance in A. halleri.

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