Transcriptome analysis of Giant grouper (Epinephelus lanceolatus) kidney and spleen in response to spotted knifejaw iridovirus (SKIV) infection

Giant grouper (Epinephelus lanceolatus) is an important economical aquaculture species that suffers from severe outbreaks of infectious diseases caused by infectious viruses, such as iridovirus and nervous necrosis virus (NNV). To investigate the regulatory mechanisms of the antiviral immune response, we analysed the transcriptome profiling of the spleen and kidney of the giant grouper after spotted knifejaw iridovirus (SKIV) infection. We obtained a total of 3359 and 1294 differentially expressed genes (DEGs) in the spleen and kidney, respectively, among which 418 DEGs were shared between spleen and kidney. A total of 933 gene ontology (GO) terms and 27 significantly enriched GO terms (corrected p-value < 0.05) were obtained in the spleen based on DEGs, and the corresponding values in the kidney were 720 and 3 respectively. GO analysis indicated that 'metabolism', 'transmembrane transport' and 'binding' occupied the dominant functional categories involved in the SKIV infection response. KEGG analysis revealed that the enriched pathways associated with several innate immune pathways, such as the Toll-like receptor, RIG-I-like receptor and NOD-like receptor signalling pathways, as well as gene expression associated with these pathways, were significantly affected in response to the SKIV infection. In addition, changes in the profiles of immune-related gene expression from two highlighted pathways, namely the Toll-like receptor signalling pathway and RIG-I-like receptor signalling pathway, were validated by qRT-PCR.