Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation

Abstract

Despite evolutionary conserved mechanisms to silence transposable element activity, there are drastic differences in the abundance of transposable elements even among closely related plant species. We conducted a de novo assembly for the 375 Mb genome of the perennial model plant, Arabis alpina. Analysing this genome revealed long-lasting and recent transposable element activity predominately driven by Gypsy long terminal repeat retrotransposons, which extended the low-recombining pericentromeres and transformed large formerly euchromatic regions into repeat-rich pericentromeric regions. This reduced capacity for long terminal repeat retrotransposon silencing and removal in A. alpina co-occurs with unexpectedly low levels of DNA methylation. Most remarkably, the striking reduction of symmetrical CG and CHG methylation suggests weakened DNA methylation maintenance in A. alpina compared with Arabidopsis thaliana. Phylogenetic analyses indicate a highly dynamic evolution of some components of methylation maintenance machinery that might be related to the unique methylation in A. alpina.

CG gene body DNA methylation changes and evolution of duplicated genes in cassava

“…2 G-I), suggesting that methylation of LTR transposons could be especially important for repression of transposon activity. Consistent with this idea, a recent study showed that genome expansion of Arabis alpina was caused in part by the expansion of GYPSY retrotransposons, which could be a result of high transposition activity caused in turn by lower levels of DNA methylation of GYPSY retro-transposons (14). Repeats showed lower methylation levels than transposons (70%, 50%, and 5% methylation levels for CG, CHG, and CHH, respectively), which is consistent with results of Arabidopsis and other plant species (9,10).…”

Epigenetics in natural animal populations

“…Substantial differences in epigenetic mechanisms and patterns can exist between and within taxa experiencing changes in temperature (Feng et al, 2010;Zemach et al, 2010), for example, differences in methylation maintenance machinery (Alonso et al, 2015;Willing et al, 2015), and different strategies to maintain body temperature between ectotherms and endotherms. Epigenetic variation may also be linked to particular life history or habitat features (Herman et al, 2014;Verhoeven & Preite, 2014).…”

Analysis of nuclear mitochondrial DNAs and factors affecting patterns of integration in plant species

“…Young NUMTs may have stronger deleterious effects and their toleration by nuclear genomes may be determined by conditions such as genome architecture and the strength of the genome immune system against foreign DNAs. Genes potentially involved in such epigenetic mechanisms show functional variation within species (Shen et al, 2014) or elevated amino acid substitution rates between species (Willing et al, 2015), suggesting differences in the genome immune system between species (Springer et al, 2016). In contrast, NUMTs that survived in the genome to an older age could have always been or could have become less deleterious, and the cumulative length of those NUMTs might be determined by the size of the nuclear genome.…”