Genome-wide identification and evolution of TC1 / Mariner in the silkworm ( Bombyx mori ) genome

TC1 / Mariner transposons belong to class II transposable elements (TEs) that use DNA-mediated “cut and paste” mechanism to transpose, and they have been identified in almost all organisms. Although silkworm ( Bombyx mori ) has a large amount of TC1 / Mariner elements, the genome wide information of this superfamily in the silkworm is unknown. In this study, we have identified 2670 TC1 / Mariner ( Bmmar ) elements in the silkworm genome. All the TEs were classified into 22 families by means of fgclust, a tool of repetitive sequence classification, seven of which was first reported in this study. Phylogenetic and structure analyses based on the catalytic domain (DDxD/E) of transposase sequences indicated that all members of TC1 / Mariner were grouped into five subgroups: Mariner, Tc1, maT , DD40D and DD41D/E. Of these five subgroups, maT rather than Mariner possessed most members of TC1 / Mariner (51.23%) in the silkworm genome. In particular, phylogenetic analysis and structure analysis revealed that Bmmar15 (DD40D) formed a new basal subgroup of TC1 / Mariner element in insects, which was referred to as bmori . Furthermore, we concluded that DD40D appeared to intermediate between mariner and Tc1 . Finally, we estimated the insertion time for each copy of TC1 / Mariner in the silkworm and found that most of members were dramatically amplified during a period from 0 to 1 mya. Moreover, the detailed functional data analysis showed that Bmmar1, Bmmar6 and Bmmar9 had EST evidence and intact transposases. These implied that TC1 / Mariner might have potential transpositional activity. In conclusion, this study provides some new insights into the landscape, origin and evolution of TC1 / Mariner in the insect genomes.