Characterization of multiple lineages of Tc1-like elements within the genome of the amphibian Xenopus tropicalis

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...

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Bibliographic Details
Published in:Gene 2005-04, Vol.349, p.187-196
Main Authors: Sinzelle, Ludivine, Pollet, Nicolas, Bigot, Yves, Mazabraud, André
Format: Article
Language:English
Subjects:
Amino Acid Motifs
Amino Acid Sequence
Animals
Anoura
Cloning, Molecular
Consensus Sequence
DNA Transposable Elements
Genome
Life Sciences
Mobile DNA
Molecular Sequence Data
Neurons and Cognition
Open Reading Frames
Phylogeny
Polymerase Chain Reaction
Repeat
Sequence Analysis, DNA
Sequence Homology, Amino Acid
Terminal Repeat Sequences
Transposases
Transposases - chemistry
Transposases - genetics
Transposon
Vertebrate
Xenopus
Xenopus - classification
Xenopus - genetics
Xenopus tropicalis
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Summary: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.
ISSN:0378-1119
1879-0038
DOI:10.1016/j.gene.2004.12.023