Interaction analysis of miRNA and mRNA in the head kidney of black seabass (Centropristis striata) after Vibrio harveyi infection

Abstract The black seabass (Centropristis striata) is a marine teleost that is highly valued in commercial and recreational fisheries worldwide, but the industry suffers heavy economic losses each year due to disease outbreaks. To better understand the immune reaction to bacterial infection, we challenged black seabass with 1 × 108 CFU/mL of Vibrio harveyi, sampled the head kidney from control and infected fish after 24 h, and conducted mRNA and microRNA (miRNA) sequencing. We identified 14,619 differentially expressed mRNAs, including 151 immune-related genes. We also identified 391 known miRNAs and 145 novel miRNAs, of which 84 were significantly affected by V. harveyi. Additionally, 534 miRNAs targeting 13,075 target genes were predicted to be present, and they were separated into pathways such as carbon metabolism, insulin signaling, protein processing in the endoplasmic reticulum, mTOR signaling, and FoxO signaling. Quantitative PCR analysis revealed that immune-related genes (tumor necrosis factor receptor, interleukin-1 receptor, interferon regulatory factor, lipopolysaccharide-binding protein) were negatively regulated by miRNAs. These results were consistent with those of high-throughput sequencing data. We identified numerous mRNA-miRNA interactions, which provide insight into the immune reactions that occur during the antimicrobial process of black seabass.