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

Abstract

AbstractBackgroundTheTc1/marinersuperfamily 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.ResultsHere we identified a new family ofTc1/marinertransposons, namedIncomer(IC), which is close to, but distinct from the known family DD34E/Tc1.ICshave 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). AllICsin bats (Myotis lucifugus,Eptesicus fuscus,Myotis davidii, andMyotis 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 fromICswere also identified in bat genomes. Phylogenetic analysis revealed thatICsare more closely related to DD34E/Tc1than to other families ofTc1/mariner(e.g., DD34D/marinerand DD × D/pogo), and can be classified into four distinct clusters. The host andICphylogenies and pairwise distance comparisons betweenRAG1genes and all consensus sequences ofICssupport the idea that multiple episodes of horizontal transfer (HT) ofICshave occurred in vertebrates. In addition, the discovery of intact transposases, perfect TIRs and target site duplications ofICssuggests that this family may still be active in Insecta, Arachnida, frogs, and fish.ConclusionsExploring the diversity ofTc1/marinertransposons 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) ofTc1/marinertransposons is described in animals. It displays a similar structural organization and close relationship with the known DD34E/Tc1elements, but has a relatively narrow distribution, indicating that DD36E/ICmight have originated from the DD34E/Tc1family. Our data also support the hypothesis of horizontal transfer ofICin vertebrates, even invading one lineage of mammals (bats). This study expands our understanding of the diversity ofTc1/marinertransposons and updates the classification of this superfamily.