Identification of the conserved and novel microRNAs by deep sequencing and prediction of their targets in Topmouth culter

Abstract

MicroRNAs (miRNAs) are endogenous non-coding small RNAs that play important roles in regulation of almost all biological processes in organisms. Topmouth culter is an economically important fish species in the Chinese freshwater polyculture system for its delicacy and high economic value. However, to date, no miRNAs have been reported in Topmouth culter species. In this study, the liver, muscle, spleen and kidney of Topmouth culter are sampled and used for construction of a small RNA library for deep sequencing. A total of 273 conserved miRNAs/miRNAs-star and 8 novel miRNAs/miRNAs-star were discovered, these miRNAs belong to 86 different miRNA families. There is a strong base bias on miRNA nucleotide compositions at certain positions. U is the dominant nucleotide, particularly at the beginning, middle, and end of conserved miRNAs. The expression of all 8 novel identified miRNAs in Topmouth culter was validated by using stem-loop qRT-PCR. Furthermore, the potential targets were predicted for these miRNAs, which were found to be involved in diverse biological processes. Our study is the first significantly enriches the Topmouth culter miRNA repertoire and provides a reference for further elucidation of complex miRNA-mediated regulatory networks for gene expression in the growth and developmental progression of Topmouth culter.