TROMB, a new retrotransposon of the gypsy-Ty3 group from the fly Megaselia scalaris

We describe TROMB, a new LTR retrotransposon, from the phorid fly Megaselia scalaris. Three full-length copies (4226, 4160 and 4129bp) and a truncated one (319bp) have been isolated. The target site consensus is TATAT, with a 4bp target site duplication TATA. The LTRs are short (142bp) and contain a TATA-box and a polyadenylation signal. The isolated copies are degenerate to different degrees and presumably inactive. The polyprotein coding sequence contains scattered stop codons and deletions/insertions at non-homologous positions. The consensus sequence among the three full-length copies, however, has an uninterrupted open reading frame and, presumably, represents the original sequence of the active element. Southern hybridization experiments showed TROMB to be present at a low copy number in two wild-type strains of M. scalaris and absent in a related species, M. abdita. The order of domains in the polyprotein coding region, the target site specificity for AT-rich sequences, and the protein sequence similarity to blastopia, mdg3 and micropia place TROMB in the gypsy-Ty3 group of LTR retrotransposons.