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Open Access Highly Accessed Research article

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

J Arvid Ågren1*, Wei Wang1, Daniel Koenig2, Barbara Neuffer3, Detlef Weigel2 and Stephen I Wright1

Author Affiliations

1 Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada

2 Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany

3 Department of Botany, University of Osnabrück, Osnabrück 49076, Germany

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BMC Genomics 2014, 15:602  doi:10.1186/1471-2164-15-602

Published: 16 July 2014

Abstract

Background

Despite 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.

Results

We 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.

Conclusion

Overall, 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.

Keywords:
Transposable elements; Mating system; Brassicaceae; Capsella; Reference genome bias