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Open Access Research article

Burst expansion, distribution and diversification of MITEs in the silkworm genome

Min-Jin Han1, Yi-Hong Shen1, Ying-Hui Gao1, Li-Yong Chen2*, Zhong-Huai Xiang1 and Ze Zhang13*

Author Affiliations

1 The Key Sericultural Laboratory of Agricultural Ministry, Southwest University, Chongqing 400715, China

2 Department of Anesthesiology, Research Institute of Surgery and Daping Hospital, Third Medical University, Chongqing, 400042, China

3 The Institute of Agricultural and Life Sciences, Chongqing University, Chongqing 400044, China

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BMC Genomics 2010, 11:520  doi:10.1186/1471-2164-11-520

Published: 27 September 2010

Abstract

Background

Miniature inverted-repeat transposable elements (MITEs) are widespread in plants and animals. Although silkworm (Bombyx mori) has a large amount of and a variety of transposable elements, the genome-wide information of the silkworm MITEs is unknown.

Results

We used structure-based and homology approaches to search for MITEs in the silkworm genome. We identified 17 MITE families with a total of 5785 members, accounting for ~0.4% of the genome. 7 of 17 MITE families are completely novel based on the nucleotide composition of target site duplication (TSD) and/or terminal inverted repeats (TIR). Silkworm MITEs were widely and nonrandom distributed in the genome. One family named BmMITE-2 might experience a recent burst expansion. Network and diversity analyses for each family revealed different diversification patterns of the silkworm MITEs, reflecting the signatures of genome-shocks that silkworm experienced. Most silkworm MITEs preferentially inserted into or near genes and BmMITE-11 that encodes a germline-restricted small RNA might silence its the closest genes in silkworm ovary through a small RNA pathway.

Conclusions

Silkworm harbors 17 MITE families. The silkworm MITEs preferred to reside in or near genes and one MITE might be involved in gene silence. Our results emphasize the exceptional role of MITEs in transcriptional regulation of genes and have general implications to understand interaction between MITEs and their host genome.