Burst expansion, distribution and diversification of MITEs in the silkworm genome.
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.
Han
Min-Jin
MJ
The Key Sericultural Laboratory of Agricultural Ministry, Southwest University, Chongqing 400715, China. mzkcly@yahoo.com.cn.
Shen
Yi-Hong
YH
Gao
Ying-Hui
YH
Chen
Li-Yong
LY
Xiang
Zhong-Huai
ZH
Zhang
Ze
Z
D000818:Animals; D001483:Base Sequence; D012831:Bombyx / Q000235:genetics*; D059006:Chromosomes, Insect / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics*; D057225:Data Mining; D020869:Gene Expression Profiling; D017344:Genes, Insect / Q000235:genetics; D014644:Genetic Variation; D049750:Genome, Insect / Q000235:genetics*; D055029:Inverted Repeat Sequences / Q000235:genetics*; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional / Q000235:genetics; D009690:Nucleic Acid Conformation; D012313:RNA / Q000235:genetics; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D012984:Software
D004251:DNA Transposable Elements; D012313:RNA