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Open Access Highly Accessed Research article

MicroRNAs of Bombyx mori identified by Solexa sequencing

Shiping Liu1, Dong Li1, Qibin Li2, Ping Zhao1, Zhonghuai Xiang1 and Qingyou Xia13*

Author Affiliations

1 The Key Sericultural Laboratory of Agricultural Ministry, College of Biotechnology, Southwest University, Tiansheng Road, Beibei, Chongqing 400715, PR China

2 Beijing Genomics Institute, Beishan Road, Yantian District, Shenzhen 518083, PR China

3 Institute of Agricultural and Life Sciences, Chongqing University, Shazhengjie, Shapingba, Chongqing 400030, PR China

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BMC Genomics 2010, 11:148  doi:10.1186/1471-2164-11-148

Published: 3 March 2010

Abstract

Background

MicroRNA (miRNA) and other small regulatory RNAs contribute to the modulation of a large number of cellular processes. We sequenced three small RNA libraries prepared from the whole body, and the anterior-middle and posterior silk glands of Bombyx mori, with a view to expanding the repertoire of silkworm miRNAs and exploring transcriptional differences in miRNAs between segments of the silk gland.

Results

With the aid of large-scale Solexa sequencing technology, we validated 257 unique miRNA genes, including 202 novel and 55 previously reported genes, corresponding to 324 loci in the silkworm genome. Over 30 known silkworm miRNAs were further corrected in their sequence constitutes and length. A number of reads originated from the loop regions of the precursors of two previously reported miRNAs (bmo-miR-1920 and miR-1921). Interestingly, the majority of the newly identified miRNAs were silkworm-specific, 23 unique miRNAs were widely conserved from invertebrates to vertebrates, 13 unique miRNAs were limited to invertebrates, and 32 were confined to insects. We identified 24 closely positioned clusters and 45 paralogs of miRNAs in the silkworm genome. However, sequence tags showed that paralogs or clusters were not prerequisites for coordinated transcription and accumulation. The majority of silkworm-specific miRNAs were located in transposable elements, and displayed significant differences in abundance between the anterior-middle and posterior silk gland.

Conclusions

Conservative analysis revealed that miRNAs can serve as phylogenetic markers and function in evolutionary signaling. The newly identified miRNAs greatly enrich the repertoire of insect miRNAs, and provide insights into miRNA evolution, biogenesis, and expression in insects. The differential expression of miRNAs in the anterior-middle and posterior silk glands supports their involvement as new levels in the regulation of the silkworm silk gland.