Genome-wide integrated analysis reveals functions of lncRNA-miRNA-mRNA interactions in Atlantic salmon challenged by Aeromonas salmonicida

Aeromonas salmonicida (A. salmonicida) is a pathogenic bacterium that causes serious problems in the global Atlantic salmon aquaculture industry. In this study, we comprehensively analyzed the profiles of lncRNAs, miRNAs and mRNAs in gills of Atlantic salmon at high-dose A. salmonicida infection (3.06 x 10(8) CFU/mL), low-dose A. salmonicida infection (3.06 x 10(5) CFU/mL), and a PBS (100 mu L) control. We identified 65 differentially expressed lncRNAs, 41 miRNAs, and 512 mRNAs between the control group and infection groups. Functional analysis showed that these genes were significantly enriched in the p53 signaling pathway, Wnt signaling pathway, mTOR signaling pathway, JAK-STAT signaling pathway, and Toll-like receptor signaling pathway. In addition, we predicted key genes in immune-related pathways and constructed a lncRNA-miRNA-mRNA network based on whole transcriptomic analysis. We further predicted three lncRNA-miRNA-mRNA axes as potential novel biomarkers in regulating the immune response of Atlantic salmon against A. salmonicida infection.

Automated summary

This study comprehensively analyzed the profiles of lncRNAs, miRNAs, and mRNAs in gills of Atlantic salmon under high and low-dose A. salmonicida infection as well as a control group. Key genes in immune-related pathways were predicted and a lncRNA-miRNA-mRNA network was constructed to identify potential novel biomarkers in regulating the immune response of Atlantic salmon against A. salmonicida infection.