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The Capsella rubella genome and the genomic consequences of rapid mating system evolution

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

ORGANISM(S): Arabidopsis thaliana Arabidopsis lyrata Capsella rubella Capsella grandiflora

PROVIDER: GSE45687 | GEO | 2013/04/02

SECONDARY ACCESSION(S): PRJNA195606

REPOSITORIES: GEO

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The Capsella rubella genome and the genomic consequences of rapid mating system evolution

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-04-02 | E-GEOD-45687 | biostudies-arrayexpress

The consequences of rapid mating system evolution in crucifer genomes

Project description:We compare RNA expression and polymorphism patterns between C. rubella and its outcrossing progenitor C. grandiflora. There is a clear shift in the expression of genes associated with flowering phenotypes; a similar shift is seen in the related genus Arabidopsis, where self-fertilization evolved about 1 million years ago. This is a two group comparison of gene expression between the self-compatible Capsella Rubella and out-crossing Capsella Grandiflora mixed stage flowerbuds. Leaf expression is also provided as an annotation reference dataset.

2013-03-28 | E-GEOD-45518 | biostudies-arrayexpress

The consequences of rapid mating system evolution in crucifer genomes

2013-03-28 | GSE45518 | GEO

Transposable elements drive rapid phenotypic variation in Capsella rubella.

Project description:Rapid phenotypic changes in traits of adaptive significance are crucial for organisms to thrive in changing environments. How such phenotypic variation is achieved rapidly, despite limited genetic variation in species that experience a genetic bottleneck is unknown. Capsella rubella, an annual and inbreeding forb (Brassicaceae), is a great system for studying this basic question. Its distribution is wider than those of its congeneric species, despite an extreme genetic bottleneck event that severely diminished its genetic variation. Here, we demonstrate that transposable elements (TEs) are an important source of genetic variation that could account for its high phenotypic diversity. TEs are (i) highly enriched in C. rubella compared with its outcrossing sister species Capsella grandiflora, and (ii) 4.2% of polymorphic TEs in C. rubella are associated with variation in the expression levels of their adjacent genes. Furthermore, we show that frequent TE insertions at FLOWERING LOCUS C (FLC) in natural populations of C. rubella could explain 12.5% of the natural variation in flowering time, a key life history trait correlated with fitness and adaptation. In particular, we show that a recent TE insertion at the 3' UTR of FLC affects mRNA stability, which results in reducing its steady-state expression levels, to promote the onset of flowering. Our results highlight that TE insertions can drive rapid phenotypic variation, which could potentially help with adaptation to changing environments in a species with limited standing genetic variation.

| S-EPMC6452725 | biostudies-literature

Mating system shifts and transposable element evolution in the plant genus Capsella.

Project description:BackgroundDespite having predominately deleterious fitness effects, transposable elements (TEs) are major constituents of eukaryote genomes in general and of plant genomes in particular. Although the proportion of the genome made up of TEs varies at least four-fold across plants, the relative importance of the evolutionary forces shaping variation in TE abundance and distributions across taxa remains unclear. Under several theoretical models, mating system plays an important role in governing the evolutionary dynamics of TEs. Here, we use the recently sequenced Capsella rubella reference genome and short-read whole genome sequencing of multiple individuals to quantify abundance, genome distributions, and population frequencies of TEs in three recently diverged species of differing mating system, two self-compatible species (C. rubella and C. orientalis) and their self-incompatible outcrossing relative, C. grandiflora.ResultsWe detect different dynamics of TE evolution in our two self-compatible species; C. rubella shows a small increase in transposon copy number, while C. orientalis shows a substantial decrease relative to C. grandiflora. The direction of this change in copy number is genome wide and consistent across transposon classes. For insertions near genes, however, we detect the highest abundances in C. grandiflora. Finally, we also find differences in the population frequency distributions across the three species.ConclusionOverall, our results suggest that the evolution of selfing may have different effects on TE evolution on a short and on a long timescale. Moreover, cross-species comparisons of transposon abundance are sensitive to reference genome bias, and efforts to control for this bias are key when making comparisons across species.

| S-EPMC4112209 | biostudies-literature