Expression pattern and regulatory network of gibel carp (Carassius gibelio) miRNAs and their putative target genes in response to CyHV-2 infection

Abstract

MicroRNAs (miRNAs) are endogenous small non-coding RNAs that are post-transcriptional regulators. They not only play vital roles in a variety of biological processes, but also regulate the process of viral infection. Cyprinid herpesvirus 2 (CyHV-2), a pathogen of Gibel carp (Carassius gibelio), can induce herpesviral hematopoietic necrosis disease, causing great economic losses to the aquaculture industry. To date, no effective antiviral measures to control CyHV-2 infection have been developed, and the pathogenesis of CyHV-2 is still vague. Here, the miRNA expression pattern was investigated in uninfected and CyHV-2-infected Carassius gibelio using small RNA sequencing. A total of 503 (209 novel) and 525 (219 novel) miRNAs were identified from the uninfected and infected groups, respectively. When compared with the uninfected group, 92 miRNAs were significantly differentially expressed, among which, 66 and 26 miRNAs were upregulated and downregulated, respectively, following viral infection. Analysis of target genes of these differentially expressed miRNAs found that the targeted mRNAs were involved in immunity, carbohydrate and amino acid metabolism, and were enriched in the MAPK, calcium, and GnRH signaling pathways. These results indicated that CyHV-2 infection not only affects the immunity pathways, but also causes imbalance of carbohydrate and amino acid basic metabolism. Taken together, the findings of this study provide novel information for deeply investigation of miRNA regulatory mechanism during host-virus interaction in Carassius gibelio.