Figure 2

Phylogeny of Transib transposase core sequences. The Transib superfamily is composed of four clades: Transib, TransibSU, Chapaev and Chapaev3. The vertebrate RAG1 proteins cluster with the TransibSU clade. Species name abbreviations: HM - Hydra magnipapillata, NV - Nematostella vectensis, SP - Strongylocentrotus purpuratus, BF - Branchiostoma floridae, PM - Petromyzon marinus, CE - Caenorhabditis elegans, XL – Xenopus laevis, HS - Homo sapiens, FR - Takifugu rubripes, CL - Carcharhinus leucas, GG - Gallus gallus, AA - Aedes aegypti, AG - Anopheles gambiae, DP - Drosophila pseudoobscura, HR - Helobdella robusta, AC - Anolis carolinensis, ACa - Aplysia californica, Transib1-Transib5 are from Drosophila melanogaster. PMRAG1L is encoded by the Bat star TransibSU-1_PM transposon, SPRAG1L, ECRAG1L, AFRAG1L are TransibSU transposases from Strongylocentrotus purpuratus, Evechinus chloroticus sea urchin (encoded by the GenBank: GAPB01003278.1 transcribed RNA sequence) and Asterias forbesi starfish (GenBank: GAUS01036390.1 transcribed RNA sequence), respectively. In addition to Echinoderms, the TransibSU clade includes also a transposon from Pacific oyster (see Additional file 4; the oyster transposase core is ~40% identical to its homologues in Echinodermata). The tree was obtained using the PhyML: RtREV model, discrete gamma model with 10 categories and estimated gamma shape parameter, best of NNIs and SPRs tree topology search. Statistical support is indicated by aLRT-SH values above 95% [27]. Domain structure of RAG1 and transposases encoded by known members of the Transib superfamily was used to infer the domain structure of the transposase encoded by the TransibVDJ transposon, the hypothetical direct ancestor of the vertebrate RAG1-RAG2 locus. The losses of the CHAPA, RING and C2H2 domains in different clades that were inferred under the parsimony principle are indicated by “L:”.