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Background  Of the major families of long terminal repeat (LTR) retrotransposons, the  Pao / BEL  family is probably the least well studied. It is becoming apparent that numerous LTR retrotransposons and other mobile genetic elements have colonized the genome of the human blood fluke,  Schistosoma mansoni .    Results  A proviral form of  Sinbad , a new LTR retrotransposon, was identified in the genome of  S. mansoni . Phylogenetic analysis indicated that  Sinbad  belongs to one of five discreet subfamilies of  Pao/BEL  like elements. BLAST searches of whole genomes and EST databases indicated that members of this clade occurred in species of the Insecta, Nematoda, Echinodermata and Chordata, as well as Platyhelminthes, but were absent from all plants, fungi and lower eukaryotes examined. Among the deuterostomes examined, only aquatic species harbored these types of elements. All four species of nematode examined were positive for  Sinbad  sequences, although among insect and vertebrate genomes, some were positive and some negative. The full length, consensus  Sinbad  retrotransposon was 6,287 bp long and was flanked at its 5'- and 3'-ends by identical LTRs of 386 bp.  Sinbad  displayed a triple Cys-His RNA binding motif characteristic of Gag of  Pao / BEL -like elements, followed by the enzymatic domains of protease, reverse transcriptase (RT), RNAseH, and integrase, in that order. A phylogenetic tree of deduced RT sequences from 26 elements revealed that  Sinbad  was most closely related to an unnamed element from the zebrafish  Danio rerio  and to  Saci-1 , also from  S. mansoni . It was also closely related to  Pao  from  Bombyx mori  and to  Ninja  of  Drosophila simulans .  Sinbad  was only distantly related to the other schistosome LTR retrotransposons  Boudicca ,  Gulliver ,  Saci-2 ,  Saci-3 , and  Fugitive , which are  gypsy -like. Southern hybridization and bioinformatics analyses indicated that there were about 50 copies of  Sinbad  in the  S. mansoni  genome. The presence of ESTs representing transcripts of  Sinbad  in numerous developmental stages of  S. mansoni  along with the identical 5'- and 3'-LTR sequences suggests that  Sinbad  is an active retrotransposon.    Conclusion   Sinbad  is a  Pao/BEL  type retrotransposon from the genome of  S. mansoni . The  Pao/BEL  group appears to be comprised of at least five discrete subfamilies, which tend to cluster with host species phylogeny.  Pao/BEL  type elements appear to have colonized only the genomes of the Animalia. The distribution of these elements in the Ecdysozoa, Deuterostomia, and Lophotrochozoa is discontinuous, suggesting horizontal transmission and/or efficient elimination of  Pao -like mobile genetic elements from some genomes.

The Sinbad retrotransposon from the genome of the human blood fluke, Schistosoma mansoni, and the distribution of related Pao-like elements.