Integrative Transcriptomic Analysis Reveals the Immune Mechanism for A CyHV-3-Resistant Common Carp Strain

Anti-disease breeding is becoming the most promising solution to cyprinid herpesvirus-3 (CyHV-3) infection, the major threat to common carp aquaculture. Mortality studies suggested that a breeding strain of common carp is resistant to this disease. This study illustrates the immune mechanisms involved in anti-CyHV-3 ability. An integrative analysis of the protein-coding genes and long non-coding RNAs (lncRNAs) using transcriptomic data was also performed. Tissues from the head kidney of common carp were extracted at day 0 (the healthy control) and day 7 after CyHV-3 infection (the survivors), and used to analyze the transcriptome through both Illumina and Pac-bio sequencing. Following analysis of the Kyoto Encyclopedia of Genes and Genomes pathways and Gene Ontology terms involved, the immune-related genes were merged. These genes were filtered using the current common carp immune gene library, and information on the immune process was detailed. Immune gene categories and their corresponding genes in different comparison groups were revealed. Also, the immunological Gene Ontology terms for lncRNA modulation were retained. The weighted gene co-expression network analysis was used for the regulation of immune genes lncRNA. The results demonstrated that the breeding carp strain develops marked resistance to CyHV-3 through a specific innate immune mechanism. The featured biological processes were autophagy, phagocytosis, cytotoxicity, and virus blockage by lectins and mucin 3 (MUC3). Moreover, the immune suppressive signals, such as suppression of interleukin 21 receptor (IL21R) on STAT3, PI3K mediated the inhibition of inflammation by dopamine upon infection, as well as the inhibition of NLR family CARD domain containing 3 (NLRC3) on STING during a steady state. Possible susceptible factors for CyHV-3, such as integrin beta 1 (ITGB1), toll-like receptor 18 (TLR18), and C-C motif chemokine ligand 4 (CCL4), were also revealed from the common strain. The results of this study suggested that the regulation of galectin 3 (LGALS3) and T cell leukemia homeobox 3 (TLX3) by lncRNA may play a role in the resistance mechanism. Therefore, immune factors that are immunogenetically insensitive or susceptible to CyHV-3 infection have been revealed.