Diversity, dynamics and effects of LTR retrotransposons in the model grass Brachypodium distachyon

Abstract

O_LITransposable 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.\nC_LIO_LIHere 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.\nC_LIO_LIWe 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 ky, 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 more than 20 percent of the genome-wide variation in GC content and is associated to higher methylation levels.\nC_LIO_LIOur study shows how individual TE lineages change the genetic and epigenetic constitution of the host beyond simple changes in genome size.\nC_LI