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.

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.

Figure 1

Phylogenetic relationships within the Capsella genus. For an comprehensive review of the evolutionary history of the genus, see [38].

Figure 2

Venn diagram with the number of unique and shared TE insertion sites in three Capsella species.

Figure 3

Average TE copy number in the three Capsella species genome wide (a), on chromosome arms (b), and in centromeric regions (c). Error bars are ± 1 standard error.

Figure 4

Average TE copy number in 100 bp bins near their closest gene in the three Capsella species. Error bars are ± 1 standard error.

Figure 5

Histogram of population frequencies of TEs in the three Capsella species genome wide (a), on chromosome arms (b), and in centromeric regions (c). 95% confidence intervals based on 200 bootstraps are plotted but too small to be seen.