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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. • 503 (209 novel) and 525 (219 novel) miRNAs were found from the uninfected and infected groups. • 92 differentially expressed miRNAs were found from CyHV-2 uninfected and infected groups. • The targeted mRNAs were involved in immunity, carbohydrate and amino acid metabolism. • The targeted mRNAs were enriched in the MAPK, calcium, and GnRH signaling pathways. [ABSTRACT FROM AUTHOR]

Carassius auratus gibelio , in the family Cyprinidae, is one of the most popular freshwater aquaculture species in China. The infection of domestic cyprinid species by Cyprinid herpesvirus 2 (CyHV-2) causes herpesvirus hematopoietic necrosis (HVHN). Until now, the pathogenic mechanism of CyHV-2 has been unclear. In this study, we used RNA sequencing to investigate the gene expression patterns in C. auratus gibelio after CyHV-2 infection. We identified 163,365 unigenes with de novo transcriptome sequencing using the Trinity and TGICL software. In total, 8011 differentially expressed genes (DEGs) were identified in the CyHV-2-infected fish vs healthy fish, 4170 of which were upregulated and 3841 downregulated. A Gene Ontology (GO) analysis showed that most of the DEGs functioned in the cellular hyperosmotic response, inflammatory response, creatine: sodium symporter activity, voltage-gated potassium channel complex, complement activation, and oxygen binding categories. A Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the top five KEGG pathways enriched in upregulated genes were neuroactive ligand-receptor interaction, pyrimidine metabolism, IL-17 signaling pathway, glutathione metabolism, and arginine biosynthesis. The top five KEGG pathways enriched in downregulated unigenes were cytokine–cytokine receptor interaction, complement and coagulation cascades, Staphylococcus aureus infection, drug metabolism, and glycine, serine, and threonine metabolism. The expression of five key immunity-related genes was confirmed with real-time PCR. Specifically, the genes encoding interleukin-11 and interleukin-13 receptor, which are involved in immunity, were significantly upregulated and downregulated in CyHV-2-infected fish, respectively. Our findings not only extend our understanding of the host's response to CyHV-2, but also clarify the molecular pathogenicity mechanisms involved. • We identified 163,365 unigenes from Carassius auratus gibelio with de novo transcriptome sequencing. • 8011 differentially expressed genes (DEGs) were identified in the CyHV-2-infected fish vs healthy fish. • Most of the DEGs functioned in the cellular hyperosmotic response, inflammatory response. • KEGG analysis showed that the top five KEGG pathways enriched in DEGs were related with immunity pathways. [ABSTRACT FROM AUTHOR]