Genome-wide identification and characterization of microRNAs and target prediction by computational approaches in common carp

Abstract MicroRNAs (miRNAs) are a type of small non-coding RNAs, approximately 22 nt in length, are considered as key indispensable players in the regulation of a broad range of biological processes. In this study, we used a homology search based computational approach for identifying miRNAs in common carp genome. A total of 271 miRNAs were predicted and were found to belong to 95 families. Among them, 169 were novel miRNAs and 102 were previously known miRNAs. These identified common carp miRNAs possess a difference of 0–2 nucleotides from their homologous counterparts. Furthermore, nine identified miRNAs were randomly selected for expression confirmation by qRT-PCR and the results showed that the differential expression of miRNAs in four common carp tissues. By target prediction, these miRNAs potentially target 7684 mRNAs. To understand the miRNA mediated gene regulatory control, functional enrichment analysis (GO and KEGG) were carried out. Results indicated that the targets of common carp miRNA were involved in wide range of regulatory functions. Overall, findings from this study will accelerate the way for further research of miRNAs, their functions in common carp and laid the foundation for the prediction and analysis of miRNAs to those species whose genomes are available.