title: Ty3/Gypsy retrotransposons: description of new Arabidopsis thaliana elements and evolutionary perspectives derived from comparative genomic data.
abstract: 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 Ulysses, 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.
authors.affiliation: Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Departamento de Genética, Universidad de Valencia, Spain. ignacio.marin@uv.es
authors.forename: I
authors.initials: I
authors.lastname: Marín
authors.forename: C
authors.initials: C
authors.lastname: Lloréns
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D017360:Arabidopsis / Q000235:genetics*; D019143:Evolution, Molecular; D018745:Genome, Plant; D008969:Molecular Sequence Data; D010802:Phylogeny; D018626:Retroelements; D017386:Sequence Homology, Amino Acid
chemical_list: D018626:Retroelements