title: Mating system shifts and transposable element evolution in the plant genus Capsella.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada. arvid.agren@utoronto.ca.
authors.forename: J Ågren
authors.initials: JÅ
authors.lastname: Agren
authors.forename: Wei
authors.initials: W
authors.lastname: Wang
authors.forename: Daniel
authors.initials: D
authors.lastname: Koenig
authors.forename: Barbara
authors.initials: B
authors.lastname: Neuffer
authors.forename: Detlef
authors.initials: D
authors.lastname: Weigel
authors.forename: Stephen I
authors.initials: SI
authors.lastname: Wright
mesh_terms: D005075:Biological Evolution; D029687:Capsella / Q000145:classification / Q000235:genetics*; D004251:DNA Transposable Elements / Q000235:genetics*; D018628:Gene Dosage; D005787:Gene Frequency; D018745:Genome, Plant; D010802:Phylogeny
chemical_list: D004251:DNA Transposable Elements