Genome-wide analysis of common carp (Cyprinus carpio) mucin genes and their roles in mucosal immune response following the Aeromonas hydrophila infection

• A set of 11 mucin family genes were identified across the common carp genome. • The common carp mucin genes presented tissue-specific expression patterns. • The expression of mucin genes in mucosal tissues were regulated after bacterial infection. Common carp is a globally farmed and economically important freshwater fish species. Due to the intensive culture conditions, the farmed common carp are susceptible to various pathogens, causing high mortality and serious economic losses to the carp culture industry. The route of infection is usually through the main mucosal tissues. In order to generate an effective strategy to better manage the fish disease, it is important to understand mucosal immune related genes as well as their expressions during infection. In this study, the common carp mucin gene family were identified and characterized through bioinformatics analysis, and their expression patterns were examined in healthy tissues of common carp as well as the mucosal tissues after the infection of Aeromonas hydrophila . Our results showed that, there were a set of 11 mucin genes across the entire common carp genome. Functional domain prediction and phylogenetic analysis supported their annotation and orthologies. Examining gene copy number across several vertebrates showed that muc4 and muc6 genes were present in other vertebrate, but were lost in teleost fish, which appeared as a result of gene loss after the split of teleost fish from tetrapods during evolution. The mucin genes presented tissue-specific expression patterns in various healthy common carp tissues, with relatively high expression levels in mucosal tissues, indicating their important roles likely in mucosal immune response. Furthermore, the expression of all mucin genes except for muc2-1 were significantly regulated at one or more timepoints in minimum one mucosal tissue after bacterial infection, suggesting that the mucin gene family played critical roles in the mucosal immunity of common carp in response to pathogenic invasion. Collectively, our findings provided fundamental genomic resources for better understanding the vital roles of mucin genes in the defense against pathogen invasion in teleost.