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Background  It is becoming apparent that perhaps as much as half of the genome of the human blood fluke  Schistosoma mansoni  is constituted of mobile genetic element-related sequences. Non-long terminal repeat (LTR) retrotransposons, related to the LINE elements of mammals, comprise much of this repetitive component of the schistosome genome. Of more than 12 recognized clades of non-LTR retrotransposons, only members of the CR1, RTE, and R2 clades have been reported from the schistosome genome.    Results  Inspection of the nucleotide sequence of bacterial artificial chromosome number 49_J_14 from chromosome 1 of the genome of  Schistosoma mansoni  (GenBank  AC093105 ) revealed the likely presence of several RTE-like retrotransposons. Among these, a new non-LTR retrotransposon designated  SR3  was identified and is characterized here. Analysis of gene structure and phylogenetic analysis of both the reverse transcriptase and endonuclease domains of the mobile element indicated that  SR3  represented a new family of RTE-like non-LTR retrotransposons. Remarkably, two full-length copies of  SR3 -like elements were present in BAC 49-J-14, and one of 3,211 bp in length appeared to be intact, indicating  SR3  to be an active non-LTR retrotransposon. Both were flanked by target site duplications of 10–12 bp. Southern hybridization and bioinformatics analyses indicated the presence of numerous copies (probably >1,000) of  SR3  interspersed throughout the genome of  S. mansoni . Bioinformatics analyses also revealed  SR3  to be transcribed in both larval and adult developmental stages of  S. mansoni  and to be also present in the genomes of the other major schistosome parasites of humans,  Schistosoma haematobium  and  S. japonicum .    Conclusion  Numerous copies of  SR3 , a novel non-LTR retrotransposon of the RTE clade are present in the genome of  S. mansoni . Non-LTR retrotransposons of the RTE clade including  SR3  appear to have been remarkably successful in colonizing, and proliferation within the schistosome genome.

Characterization of SR3 reveals abundance of non-LTR retrotransposons of the RTE clade in the genome of the human blood fluke, Schistosoma mansoni