De novo RNA-seq assembly and differential transcriptome analysis of Carassius auratus gibelio after Cyprinid herpesvirus 2 infection

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.