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

<italic>TC1</italic>/<italic>Mariner</italic> 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 (<italic>Bombyx mori</italic>) has a large amount of <italic>TC1</italic>/<italic>Mariner</italic> elements, the genome wide information of this superfamily in the silkworm is unknown. In this study, we have identified 2670 <italic>TC1</italic>/<italic>Mariner</italic> (<italic>Bmmar</italic>) 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 <italic>TC1</italic>/<italic>Mariner</italic> were grouped into five subgroups: <italic>Mariner, Tc1, maT</italic>, DD40D and DD41D/E. Of these five subgroups, <italic>maT</italic> rather than <italic>Mariner</italic> possessed most members of <italic>TC1</italic>/<italic>Mariner</italic> (51.23%) in the silkworm genome. In particular, phylogenetic analysis and structure analysis revealed that <italic>Bmmar15</italic> (DD40D) formed a new basal subgroup of <italic>TC1</italic>/<italic>Mariner</italic> element in insects, which was referred to as <italic>bmori</italic>. Furthermore, we concluded that DD40D appeared to intermediate between <italic>mariner</italic> and <italic>Tc1</italic>. Finally, we estimated the insertion time for each copy of <italic>TC1</italic>/<italic>Mariner</italic> 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 <italic>Bmmar1, Bmmar6</italic> and <italic>Bmmar9</italic> had EST evidence and intact transposases. These implied that <italic>TC1</italic>/<italic>Mariner</italic> might have potential transpositional activity. In conclusion, this study provides some new insights into the landscape, origin and evolution of <italic>TC1</italic>/<italic>Mariner</italic> in the insect genomes. [ABSTRACT FROM AUTHOR]