Genome-wide identification of microRNAs and their target genes in Cynoglossus semilaevis using computational approach

Abstract MicroRNAs (miRNAs) are endogenous non-protein-coding RNAs of approximately 22 nucleotides which regulate gene expression at the posttranscriptional level in plants and animals. Until recently, only limited numbers of miRNAs were identified in Cynoglossus semilaevis , which is an important commercial mariculture fish species in China. The recently sequenced genome of C. semilaevis provides an opportunity to identify some novel miRNAs in this species by computational approach. A total of 217 miRNAs belonging to 87 families were identified in C. semilaevis , including 96 known miRNAs and 121 putative novel miRNAs. To verify the predicted miRNAs, a qRT-PCR-based assay was performed, the results showed that randomly selected 6 miRNAs have different expression patterns in the liver, spleen, kidney and muscles tissues of C. semilaevis, and suggest that these miRNAs might be involved in tissue-specific expression. Following this, 20,614 potential target genes were predicted by searching the mRNA database, and these targets are involved in several key pathways. Finally, the analysis on GO enrichment and KEGG pathway showed that the predicted targets genes for these identified miRNAs participate in diverse physiological and metabolic processes. Taken together, the present study expands the collection of miRNAs and provides a foundation for further understanding the role of these miRNAs in the C. semilaevis .