Diversity, dynamics and effects of long terminal repeat retrotransposons in the model grass Brachypodium distachyon

Abstract

Transposable elements (TEs) are the main reason for the high plasticity of plant genomes, where they occur as communities of diverse evolutionary lineages. Because research has typically focused on single abundant families or summarized TEs at a coarse taxonomic level, our knowledge about how these lineages differ in their effects on genome evolution is still rudimentary. Here we investigate the community composition and dynamics of 32 long terminal repeat retrotransposon (LTR-RT) families in the 272-Mb genome of the Mediterranean grass Brachypodium distachyon. We find that much of the recent transpositional activity in the B. distachyon genome is due to centromeric Gypsy families and Copia elements belonging to the Angela lineage. With a half-life as low as 66 kyr, the latter are the most dynamic part of the genome and an important source of within-species polymorphisms. Second, GC-rich Gypsy elements of the Retand lineage are the most abundant TEs in the genome. Their presence explains > 20% of the genome-wide variation in GC content and is associated with higher methylation levels. Our study shows how individual TE lineages change the genetic and epigenetic constitution of the host beyond simple changes in genome size.

Impact of Transposable Elements on Methylation and Gene Expression across Natural Accessions of Brachypodium distachyon

“…Methylation spreading was in a second step used to statistically cluster the ten families. Eventually, as young TEs might be more efficiently targeted by silencing mechanisms, we extracted the age of each copy from Stritt et al. (2020) .…”

“…3 A ). It is nonetheless worth noting that RLG_Bdis004 and RLC_Bdis022 are two of the most recently active families in the genome of B. distachyon ( Stritt et al. 2020 ), suggesting a possible scenario where de novo silencing of these two elements may influence nearby-gene regulation.…”

“…Names on the right of the heatmap describe the TE lineage to which each family belongs. Boxplots display the age of each family estimated by Stritt et al. (2020) .…”

“…The differences observed between the two species may result from the nature of their TEs. Notably, the genome of B. distachyon displays a much higher ratio of solo-LTRs: intact copies for both conserved elements and TIPs (up to 14:1 for some families; Stritt et al. 2020 ) compared to A. thaliana , where the number of intact copies approximate the number of solo-LTRs ( Devos et al.…”

“…Furthermore, TEs are much more pervasive than in A. thaliana , and although their dynamics is well characterized in B. distachyon ( Stritt et al. 2018 , 2020 ), little is known about their functional impact. We, therefore, asked to what extent TEs influence DNA methylation and gene expression in B. distachyon , and how these patterns differ from what is observed in A. thaliana.…”