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 gro up of long-terminal-repeat retrotransposons (also known as Metaviridae). Ex haustive database searches allowed us to detect novel, elements of this gro up. In particular, the Arabidopsis thaliana and Drosophila melanogaster gen ome sequencing projects have recently disclosed a large number of new Ty3/G ypsy sequences. So far, elements of three different Ty3/Gypsy lineages had been described for A. thaliana. Here, we describe six new lineages, which w e have called Tit-for-tat1, Tit-for-tat2, Gimli, Gloin, Legolas, and Little Athila. We confirm that plant Ty3/Gypsy elements form two main monophyleti c groups. Moreover, our results suggest that at least four independent ance stral lineages existed before the monocot-dicot split, about 200 MYA. Twelv e sequences from D. melanogaster that may correspond to new elements are al so described. Some of these sequences are similar to those of Osvaldo and U Iysses, two elements of the Osvaldo clade that had never before been descri bed for D. melanogaster. Comparative analyses of multiple organisms, some o f them with completely sequenced genomes, show that the number of lineages of Ty3/Gypsy elements is very variable. Thus, while only 1 lineage is prese nt 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-con taining integrase, a feature of some closely related Ty3/Gypsy elements of fungi, plants, and animals, may be used to define a new Metaviridae genus.