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

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Abstract

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.

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Acknowledgements

This work is supported by the National Natural Science Foundation of China (31700318 and 31560308 to ZHH, 31471197 to ZZ).

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Authors and Affiliations

  1. College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China

    Li-Qin Xie, Ping-Lan Wang, Shen-Hua Jiang & Hua-Hao Zhang

  2. School of Life Sciences, Chongqing University, Chongqing, 400044, China

    Ze Zhang

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  1. Li-Qin Xie
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  2. Ping-Lan Wang
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  4. Ze Zhang
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Correspondence to Ze Zhang or Hua-Hao Zhang.

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Li-Qin Xie declares that she does not have conflict of interest. Ping-Lan Wang declares that e/she does not have conflict of interest. Shen-Hua Jiang declares that he does not have conflict of interest. Ze Zhang declares that he does not have conflict of interest. Hua-Hao Zhang declares that he does not have conflict of interest.

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Dataset S1

: Multiple alignments of catalytic domain sequences of each TC1/Mariner family used for phylogenetic analysis. (TXT 7 KB)

Fig. S1

: The outline of the procedure in this study. (PDF 14 KB)

Fig. S2

: Structure analysis. As shown that the DNA-binding domain of Bmmars in the silkworm contained six α-helix (black underline), between this two HTH motifs there was a conserved motif GRPR (bright red). DDxD/E domain of these transposases was shown using black letter. DD37D/E, DD40D, and DD41D/E were shown using light green box, deep yellow underline, blue letters, respectively. In this study, we did not consider Bmmar5, Bmmar18, Bmmar19, as transposases of these family that we did not find the DNA binding domain or the catalytic domain. The transposase sequences were aligned by means of MUSCLE program, and then the aligned sequences were modified using the software GeneDoc (http://www.nrbsc.org/gfx/genedoc/whygd.htm) and Illustrator (http://en.wikipedia.org/wiki/Illustrator). (PDF 105 KB)

Table S1

: The information about insertion sites of the TC1/Mariner members into scaffolds. (XLS 401 KB)

Table S2

: TIRs of each TC1/Mariner transposon family. (DOC 73 KB)

Table S3

: Sequence logo of TIRs of TC1/Mariner transposon families created by using WebLogo server. (DOC 1002 KB)

Table S4

: The Accession Number and the matching organisms of each lineage of TC1/Mariner elements. (DOC 67 KB)

Table S5

: The insertion time of each TC1/Mariner copy. (XLS 161 KB)

Table S6

: EST evidence of each TC1/Mariner transposon family. (XLS 21 KB)

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Xie, LQ., Wang, PL., Jiang, SH. et al. Genome-wide identification and evolution of TC1/Mariner in the silkworm (Bombyx mori) genome. Genes Genom 40, 485–495 (2018). https://doi.org/10.1007/s13258-018-0648-6

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