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Background  The  Tc1/mariner  superfamily might represent the most diverse and widely distributed group of DNA transposons. Several families have been identified; however, exploring the diversity of this superfamily and updating its classification is still ongoing in the life sciences.    Results  Here we identified a new family of  Tc1/mariner  transposons, named  Incomer  ( IC ), which is close to, but distinct from the known family DD34E /Tc1 .  ICs  have a total length of about 1.2 kb, and harbor a single open reading frame encoding a ~ 346 amino acid transposase with a DD36E motif and flanked by short terminal inverted repeats (TIRs) (22–32 base pairs, bp). This family is absent from prokaryotes, and is mainly distributed among vertebrates (141 species of four classes), including Agnatha (one species of jawless fish), Actinopterygii (132 species of ray-finned fish), Amphibia (four species of frogs), and Mammalia (four species of bats), but have a restricted distribution in invertebrates (four species in Insecta and nine in Arachnida). All  ICs  in bats ( Myotis lucifugus ,  Eptesicus fuscus ,  Myotis davidii , and  Myotis brandtii ) are present as truncated copies in these genomes, and most of them are flanked by relatively long TIRs (51–126 bp). High copy numbers of miniature inverted-repeat transposable elements (MITEs) derived from  ICs  were also identified in bat genomes. Phylogenetic analysis revealed that  ICs  are more closely related to DD34E /Tc1  than to other families of  Tc1/mariner  (e.g., DD34D /mariner  and DD × D /pogo ), and can be classified into four distinct clusters. The host and  IC  phylogenies and pairwise distance comparisons between  RAG1  genes and all consensus sequences of  ICs  support the idea that multiple episodes of horizontal transfer (HT) of  ICs  have occurred in vertebrates. In addition, the discovery of intact transposases, perfect TIRs and target site duplications of  ICs  suggests that this family may still be active in Insecta, Arachnida, frogs, and fish.    Conclusions  Exploring the diversity of  Tc1/mariner  transposons and revealing their evolutionary profiles will help provide a better understanding of the evolution of DNA transposons and their impact on genomic evolution. Here, a newly discovered family (DD36E/ Incomer ) of  Tc1/mariner  transposons is described in animals. It displays a similar structural organization and close relationship with the known DD34E/ Tc1  elements, but has a relatively narrow distribution, indicating that DD36E/ IC  might have originated from the DD34E/ Tc1  family. Our data also support the hypothesis of horizontal transfer of  IC  in vertebrates, even invading one lineage of mammals (bats). This study expands our understanding of the diversity of  Tc1/mariner  transposons and updates the classification of this superfamily.

Incomer, a DD36E family of Tc1/mariner transposons newly discovered in animals