Traces of past transposable element presence in Brassicaceae genome dark matter

Transposable elements (TEs) are mobile, repetitive DNA sequences that have been found in every branch of life. In many organisms TEs are the primary contributors to the genome bulk. They invade genomes recurrently by wave of transposition bursts that ceased rapidly as repressed by host defense mechanisms subsequently triggered. The sequences become immobile and start to degrade, fading away in the genome sequence so that it cannot be recognized as such. It contributes then to the so-called dark matter of the genome, this part of the genome where nothing can be recognized as biologically functional in first instance. We developed a new method able to find these old and degenerated TE sequences. With the new algorithm we implemented, we detect up to 10% of the A. thaliana genome deriving from TEs not yet identified. Altogether we bring to 50% the part of the genome deriving from TE in this species. Interestingly these sequences are generally very short, about 500bp, and found in the upstream 500pb of genes. Their epigenetic status and their nucleotide composition suggest an old TE origin.