The Role of Small RNA-Based Epigenetic Silencing for Purifying Selection on Transposable Elements in Capsella grandiflora.

To avoid negative effects of transposable element (TE) proliferation, plants epigenetically silence TEs using a number ofmechanisms, including RNA-directed DNA methylation. These epigenetic modifications can extend outside the boundaries of TE insertions and lead to silencing of nearby genes, resulting in a trade-off between TE silencing and interference with nearby gene regulation. Therefore, purifyingselection is expectedtoremove silencedTE insertions near genesmore efficiently andprevent their accumulation within a population. To explore howeffects of TE silencing on gene regulation shapes purifying selection on TEs,we analyzedwhole genome sequencing data from166 individuals of a large population of the outcrossing species Capsella grandiflora.We found that most TEs are rare, and in chromosome arms, silenced TEs are exposed to stronger purifying selection than those that are not silenced by 24-nucleotide small RNAs, especially with increasing proximity to genes. An age-of-allele test of neutrality on a subset of TEs supports our inference of purifying selection on silenced TEs, suggesting that our results are robust to varying transposition rates.Our results provide newinsights into the processes affecting the accumulation of TEs in an outcrossing species and support the viewthat epigenetic silencing of TEs results in a trade-off between preventing TE proliferation and interference with nearby gene regulation. We also suggest that in the centromeric and pericentromeric regions, the negative aspects of epigenetic TE silencing are missing. [ABSTRACT FROM AUTHOR]