The Ancestral Repetitive Nature of Some Genomic "Dark Matter"

Most eukaryotic genomes undergo recurrent waves of transposable elements (TEs) amplifications. These events can be interspersed by periods of low TE activity accompanied by genome size reduction. During these era, extensive sequence drift and physical genome purification can lead to a loss the repetitive nature of several TE families. Furthermore, the high birth and death rates of TE families is in theory sufficient to exhaust the repetitive nature of repeated sequences, even in inflating genomes. Therefore, it is expected that some genomic segments that derive from ancestral repeated sequences do not appear as such and can be considered as genomic "dark matter" in the context of single species. However the differential loss/activity of TE families in the genomes of groups of species and subspecies supposes that TE families under extinction in one species may have close counterparts that are still active or have been active more recently in other species.
Similar to archeologist, we use different tools and approaches to detect successive layers of repeated sequences in the genome of Arabidopsis thaliana. We show that taking advantage of information pulled out from seven different Brassicaceae genomes enables to excavate a substantial quantity of otherwise cryptic repeat remnants in the A. thaliana genome. A similar approach has been used to re-annotate the genome of Drosophila melanogaster with a repeat library comprising sequences from eleven Drosophila secies. Our work supports the relevance of such "group" approaches to scrape an additional layer of ancestral repeated sequences thereby adding to our knowledge of the nature and evolution of eukaryotic genomes.