Novel microRNAs in silkworm (Bombyx mori)

Yimei Cai, Xiaomin Yu, Qing Zhou, Caixia Yu, Haiyan Hu, Jiucheng Liu, Hongbin Lin, Jin Yang, Bing Zhang, Peng Cui, Songnian Hu*, Jun Yu

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

35 Scopus citations

Abstract

We acquired more than 4 million useful sequences using a high-throughput method from a library for miRNA identification, which is constructed from a mixture of 14 RNA samples from different developmental stages. We mapped 247,410 reads to known silkworm miRNAs in miRBase (13.0), 701,913 reads to other RNA molecules based on sequence homology, and 3,219,395 reads to the silkworm genome. Our analysis identified 54 silkworm known miRNAs. A striking strand bias between miRNAs and their corresponding miRNA*s was found, and was speculated to reflect that transcripts from the passenger strand of pre-miRNAs may have important biological roles. Using an elaborate screening protocol, we predicted 287 candidate novel miRNAs (represent 116,494 short reads), and 59 of them have both miRNA and miRNA*sequences. Most of the previously identified silkworm miRNAs are cross-species conserved with a high abundance, while those predicted candidates tend to be species-specific miRNAs. Our discovery of SNPs among miRNAs implied within-species functional diversity. Target prediction uncovers that considerable silkworm miRNAs may aim at modulating more than one hormone signaling pathway components and/or hormone biosynthesis-related proteins implying their important roles in silkworm development.

Original languageEnglish (US)
Pages (from-to)405-415
Number of pages11
JournalFunctional and Integrative Genomics
Volume10
Issue number3
DOIs
StatePublished - Aug 1 2010

Keywords

  • High-throughput
  • SOLiD
  • Silkworm
  • microRNA

ASJC Scopus subject areas

  • Genetics

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