Combined transcriptomic/proteomic analysis of crucian carp Carassius auratus gibelio in cyprinid herpesvirus 2 infection

Abstract Cyprinid herpesvirus 2 (CyHV-2) is a pathogen of herpesviral hematopoietic necrosis disease of crucian carp. Our study aimed to investigate the molecular mechanisms and immune response at the mRNA and protein levels in head kidney during CyHV-2 infection. Three days after infection with CyHV-2, 7085 differentially expressed genes were identified by transcriptome sequencing, of which 3090 were up-regulated and 3995 were down-regulated. And 338 differentially expressed proteins including 277 up-regulated and 61 down-regulated were identified using tandem mass tag labeling followed by liquid chromatography tandem mass spectrometry. Notably, 128 differentially co-expressed genes at mRNA and protein levels (cDEGs) were reliably quantified, including 86 co-up-regulated and 42 co-down-regulated. In addition, 10 cDGEs in the above pathways were selected for qRT-PCR to confirm the validity of the transcriptome and proteome changes by showing that RIG-I, MDA5, LGP2, FAS, PKR and PKZ up-regulated and Integrin α, Integrin β2, NCF2 and NCF4 down-regulated. This indicated that after CyHV-2 infection, the herpes simplex infection pathway, RIG-I like receptor signaling pathway, necroptosis pathway and p53 signaling pathway were activated and the phagosome pathway was suppressed. Our findings reveal the pathogenesis and the host immune mechanism of CyHV-2 infection of crucian carp.