title: Characterization of multiple lineages of Tc1-like elements within the genome of the amphibian Xenopus tropicalis.
abstract: We have used genomic sequencing data extracted from the first assembly of the Xenopus tropicalis genome combined with a degenerated PCR approach to identify multiple lineages of Tc1 related transposable elements. Full-length elements were isolated in each lineage and were characterized. Most of them exhibit the typical characteristics of Tc1-like elements (TLEs). An open reading frame (ORF) encoding a 340-350 aa transposase containing a [D, D(34)E] signature was found as well as conserved inverted terminal repeats (ITRs) at each extremities. These ITRs could vary in length, depending on the TLE lineage. These new TLEs were named Eagle, Froggy, Jumpy, Maya, Xeminos, XtTXr and XtTXz. Phylogenetic analyses indicate that their closest relatives are present in the genomes of actinopterygian and amphibian. Interestingly, Maya and Xeminos share remarkable characteristics. Maya contains a [D,D(36)E] motif but is not related to any described TLE so far. Xeminos is the first vertebrate TLE strongly related to an invertebrate lineage. Finally, we have identified for most of these TLEs, copies containing an intact transposase ORF suggesting that these elements may still be active.
authors.affiliation: Transgenèse et Génétique des Amphibiens, CNRS UMR 8080, IBAIC, Université Paris-Sud, bât. 447, F-91405 Orsay Cedex, France.
authors.forename: Ludivine
authors.initials: L
authors.lastname: Sinzelle
authors.forename: Nicolas
authors.initials: N
authors.lastname: Pollet
authors.forename: Yves
authors.initials: Y
authors.lastname: Bigot
authors.forename: André
authors.initials: A
authors.lastname: Mazabraud
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000818:Animals; D003001:Cloning, Molecular; D016384:Consensus Sequence; D004251:DNA Transposable Elements; D016678:Genome; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D020079:Terminal Repeat Sequences; D019895:Transposases / Q000737:chemistry / Q000235:genetics; D014981:Xenopus / Q000145:classification / Q000235:genetics*
chemical_list: D004251:DNA Transposable Elements; D019895:Transposases