Long-Term Impact of Repetitive Elements on Plant Genomes and Biology

Long-term impact of repetitive elements on plant genomes and biology

The characterization of repetitive elements is of primary importance for the analysis of transcriptional and epigenetic regulation as well as for the comprehension of genome evolution. Little is known however about the long-term evolution and consequences of repeats in plants. We show that the majority of repeats found in the model plant Arabidopsis thaliana are remnants of copies that integrated in the genome of a Brassicaceae ancestor. It appears that such old copies have broad current impacts on the regulation of host gene expression and are the target of a rich, diversified population of small RNAs. Ancestral repeats also appear to affect the composition of the intergenic space, being slowly composted into G+C-poor sequences most likely through the deamination of methylcytosines. In addition, a combination of approaches allowed assigning a putative repetitive origin to a substantial amount of otherwise non-annotated sequences (aka genomic “dark matter”). Finally, we show that the ancestral distribution of repetitive elements along chromosomes have present impacts on small and large scale genome dynamics in modern genomes that are for instance associated with selective sweeps and supernumerary centromere wiping following chromosome fusions.