Ty3/Gypsy retrotransposons:: Description of new Arabidopsis thaliana elements and evolutionary perspectives derived from comparative genomic data

We performed a comprehensive analysis of the evolution of the Ty3/Gypsy group of long-terminal-repeat retrotransposons (also known as Metaviridae). Exhaustive database searches allowed us to detect novel, elements of this group. In particular, the Arabidopsis thaliana and Drosophila melanogaster genome sequencing projects have recently disclosed a large number of new Ty3/Gypsy sequences. So far, elements of three different Ty3/Gypsy lineages had been described for A. thaliana. Here, we describe six new lineages, which we have called Tit-for-tat1, Tit-for-tat2, Gimli, Gloin, Legolas, and Little Athila. We confirm that plant Ty3/Gypsy elements form two main monophyletic groups. Moreover, our results suggest that at least four independent ancestral lineages existed before the monocot-dicot split, about 200 MYA. Twelve sequences from D. melanogaster that may correspond to new elements are also described. Some of these sequences are similar to those of Osvaldo and UIysses, two elements of the Osvaldo clade that had never before been described for D. melanogaster. Comparative analyses of multiple organisms, some of them with completely sequenced genomes, show that the number of lineages of Ty3/Gypsy elements is very variable. Thus, while only 1 lineage is present in Saccharomyces cerevisiae, at least 6 exist in Caenorhabditis elegans, at least 9 are present in the A. thaliana, and perhaps 20 are present in D. melanogaster. Finally, we suggest that the presence of a chromodomain-containing integrase, a feature of some closely related Ty3/Gypsy elements of fungi, plants, and animals, may be used to define a new Metaviridae genus.