Impact of Transposable Elements on the Evolution of Coffea arabica (Rubiaceae)

Transposable elements (TEs) are able to promote not only point mutations at the locus level but also large genomic rearrangements. They are prone to contribute to duplications, deletions, inversions and/or translocations, resulting in genomic structural changes, and sometimes, functional modifications. LTR-retrotransposons (RTs) are particularly involved in these kinds of modifications, and because of their mode of transposition following the "copy and paste" model, they may also be responsible for changes in genome sizes. We investigated the transcriptional activity and diversity of insertion sites for nine RTs, two belong to the Copia superfamily and seven to the Gypsy, using RT-PCR, IRAP and REMAP on 22 genotypes of the tetraploid C. arabica, and 10 of C. canephora and 2 of C. eugenioides, the C. arabica parental species. A differential transcriptional activity of the RTs was observed, being some of them active in the three species and others only in the hybrid. Exclusive insertion sites were observed in C. arabica suggesting that these RTs could have mobilized recently, less than 0.6 Mya (time of species origin). Additionally, the different patterns of band distribution comparing the parental species to the hybrid suggests that C. arabica could have undergone genomic structural changes associated to rearrangements mediated by some of these TEs, involving gains and losses of copies. In summary, the results show that TEs could be related to a structural genome evolution of C. arabica in a short time. Further analysis may reveal their potential to impact on some genome functions of this species.