Transcriptomic characterization of Atlantic salmon (Salmo salar) head kidney following administration of Aeromonas salmonicida subsp. masoucida vaccine

Atlantic salmon is one of the most famous and economically important fish species globally. However, bacterial diseases constantly constrain salmon aquaculture. Thereinto, Aeromonas salmonicida subsp. masoucida (ASM), classified as atypical A. salmonicida, caused huge losses to salmonid industry in China. In this regard, we conducted transcriptome analysis in Atlantic salmon head kidney following the administration of ASM vaccination to reveal genes, their expression patterns, and pathways involved in immune responses. A total of 448.71 million clean reads were obtained, and 397.69 million reads were mapped onto the Atlantic salmon reference genome. In addition, 117, 1891, 741, 207, and 377 genes were significantly up-regulated, and 183, 1920, 695, 83, and 539 genes were significantly down-regulated post ASM vaccination at 12 h, 24 h, 1 m, 2 m, and 3 m, respectively. Furthermore, KEGG pathway analysis revealed that many differentially expressed genes (DEGs) following ASM vaccination were involved in cell adhesion molecules (H2-Aa-l and CD28-l),cytokine-cytokine receptor interaction (IL10, CXCL9, CXCL11, CXCR3, and CCL19), herpes simplex infection (IL1B, SOCS3-l, and C3-l), HTLV-I infection (Il1r2 and BCL2L1), influenza A (CXCL8 and Il12b), and PI3K-Akt signaling pathway (PIK3R3-l and Ddit4-l). Finally, the results of qRT-PCR showed a significant correlation with RNA-Seq results, suggesting the reliability of RNA-Seq for gene expression analysis. This study sets the foundation for further study on the vaccine protective mechanism in Atlantic salmon as well as other teleost species. •RNA-seq was conducted to reveal the immune responses in Atlantic salmon head kidney following the administration of vaccine.•A total of 300, 3811, 1436, 290, and 916 genes were differentially expressed following vaccination at 12 h, 24 h, 1 m, 2 m, and 3 m, respectively.•Many DEGs were involved in immune-related pathways such as Cytokine-cytokine receptor interaction and PI3K-Akt signaling pathway.•The results of RT-qPCR showed a significant correlation with RNA-Seq results, suggesting the reliability of RNA-Seq.