Genome-wide Identification And Evolution Of Tc1/Mariner In The Silkworm(Bombyx Mori) Genome

Tcl/Mariner transposons belong to class II transposable elements that use DNA-mediated "cut and paste" mechanism to transpose. Tel/Mariner, which was first discovered in Drosophila mauritiana has been identified in almost all organisms. As a model of Lepidopteran insects, the silkworm, Bombyx mori, is the only known economic insect, which is completely domesticated by human. TEs constitute approximately 35% of the silkworm genome and DNA transposons occupy about 3% of the whole genome. Compared with other superfamilies of DNA transposons in the silkworm, Tcl/Mariner elements are almost 90% of the whole DNA transposons. Although, silkworm (Bombyx mori) has a large amount of Tcl/Mariner elements, the genome wide information of this superfamily in the silkworm is unknown. Some Tcl/Mariner families have been identified in the silkworm, e.g. Bmmarl, Bmmar2, Bmmar3, Bmmar4, Bmmar5 and Bmmar6. Meanwhile, previous studies have systematically analyzed Tel/Mariner in the silkworm. However, these studies were incomplete due to lack the silkworm genome sequences. Fortunately, the silkworm genome sequence and a new assemble have been recently completed, and this provides us with a good opportunity for studying Tcl/Mariner transposons of the silkworm at a genome-wide scale. The main results are as follows:1. Identification and phylogenetic analysis of Tcl/Mariner transposons in the silkwormIn this study, we have identified 2670 Tcl/Mariner (Bmmar) elements using homology-based strategy in the silkworm genome. All the TEs were classified into 22 families by means of fgclust which was a tool of repetitive sequence classification. They were designated as Bmmarl to Bmmar22, respectively. Among 22 families, six families were reported previously, nine families were collected by Repbase, and the rest seven families were identified for the first time in this study. Phylogenetic and structure analyses based on the catalytic domain (DDxD/E) of transposase sequences indicated that all members of Tcl/Mariner were grouped into five subgroups:mariner, Tel, maT, DD40D and DD41D/E. Of these five subgroups, maT rather than mariner possessed most members of Tel/Mariner (51.23%) in the silkworm genome through calculating the content of each clade.2. Identification of bmori and a new lineage sister to the rosa subfamilyIn particular, phylogenetic analysis and structure analysis revealed that Bmmarl5 (DD40D) formed a new basal subgroup of Tcl/Mariner element in insects, which was referred to as bmori. Meanwhile, our results showed that there was a new lineage sister to the rosa lineage, which was a new lineage of mariner subgroup in insects was characterized by encoding a DD41D motif in their catalytic domain. Moreover, two clusters had different conservation sites at the amino acid level. It also showed that the members of the rosa subfamily not only existed in insects but also in vertebrate (such as Anolis carolinensis). Furthermore, we concluded that DD40D and DD41D/E appeared to intermediate between mariner and Tcl.3. Analysis of insertion time and possible transposition activity of Tcl/Mariner superfamily in the silkwormFinally, we estimated the insertion time for each copy of Tcl/Mariner in the silkworm and found that most of members were dramatically amplified during a period from 0 mya to 1 mya. This implied that Tcl/Mariner might have potential transposition activity. Moreover, the detailed functional data analysis showed that Bmmarl, Bmmar6 and Bmmar9 had EST evidence and intact transposases. In conclusion, this study provides some new insights into the landscape, origin and evolution of Tcl/Mariner in the insect genomes.