Discovery And Analysis Of Small Ncrnas In Silkworm (Bombyx Mori) By SOLiD Sequencing Technology

Small non-coding RNAs are a class of endogenously-initiated gene expression regulators that play key roles in the development of eukaryotes. Silkworm(Bombyx mori),as an important economic insect and bioreactor, has become a model for small non-coding RNAs identification and mechanism studies based on the publishment of their genome sequences.This research focuses on identifying silkworm small non-coding RNAs as well as their regulatory roles by the next-generation SOLiD sequencing technology combined with bioinformatic analysis.After sequencing the library constructed from a mixture of14silkworm RNA samples from different developmental stages, we identified54known silkworm miRNAs which include50miRNA molecules (stored in miRBase13.0) with both miRNA and miRNA*strand sequenced. We predicted287candidate novel miRNAs by RNAfold,of which20percent have miRNA*strands. Some miRNA*strand exhibit a higher expression level than their counterpart miRNAs that implied their functional importance. We predicted13miRNA clusters, which is a typical feature of miRNAs,that members of the same cluster might be co-transcripted and share functional similarity. Besides,the SNPs of mature miRNAs identified in this study lead to the deduction of miRNA functional diversity controlled in post-transcriptional level. Use stem-loop RT PCR method,we validated the existence and expression level of a subset of the novel miRNAs. Based on the fact that most of the validated miRNAs tend to be upregulated in ecdysis and prepupa.it is possible that miRNAs participate in the regulation of ecdysis.In the light of target prediction results.we studied the potential functions of silkworm miRNAs and the relevance with ecdysis. As a result,we find that the targets of silkworm specific miRNAs are usually compose of hormone metabolism-related enzymes as well as transcription factors and receptors involved in hormone regulation.We also found18451piRNA,1346mRNA originated siRNA and2401TE originated siRNA in our library according to their biogenesis and sequence features.piRNA and TE-siRNAs were predicted to target LINE,SINE and LTR. While mRNA-siRNAs were predicted to aim at transcription factors,enzymes and hormone receptors,which implied their possible functions in ecdysis-related regulations.We identified and characterized small non-coding RNAs in the silkworm genome by SOLiD sequencing technology.Hence,this study will not only elucidate the small non-coding RNAs and their possible functions in silkworm genome,but also facilitate our understanding of the developmental mechanisms of B.mori in gene expression levels controlled by small non-coding RNAs.