Transcriptomics analysis provides new insights into the fish antiviral mechanism and identification of interferon-stimulated genes in grass carp (Ctenopharyngodon idella)

Grass carp is an economically important freshwater fish in China, and haemorrhagic disease caused by GCRV has seriously restricted its farming scale. To understand the host molecular basis for antiviral defence and explore the effector molecules, a global transcriptional profiling of four major immune tissues (liver, spleen, head kidney, and trunk kidney) of GCRV-infected grass carp was established. A total of 192.65 Gb clean data was obtained with 6.11 Gb per sample and stored in the NCBI Sequence Read Archive (with accession number PRJNA759556). Based on the GO and KEEG analyses, 108 unique GO terms were enriched in the four tissues. Thirty-five enriched pathways were obtained, with 21 metabolism-related pathways mainly gained in the liver and trunk kidney, and 14 immune response pathways were enriched in the spleen and head kidney. Also demonstrated was that GCRV stimulates not only the expression of interferon-stimulated genes (ISGs) but also proinflammatory cytokines. 27 ISGs were screened from the candidate DEGs, and eight ISGs were identified for the first time in grass crap. These ISGs were classified into three categories by their function found in mammals: (i) positively regulates the IFN signalling pathway (RIG-I, MDA5, IRF7, IRF9, STAT2, and TRIM25); (ii) negatively regulates the IFN signalling pathway (usp18 and SOCS1); and (iii) exerts direct antiviral activity such as Mx1, ISG15, ISG56, ISG58, viperin, and PKR. Eight major ISGs and four typical differentially inflammatory cytokines were used for further expression analysis with prominent expression in the liver, spleen and kidney. The onset time of IFN-mediated antiviral response was trunk kidney (12–24 h) > liver (48 h) > spleen (96–120 h), and the intensity was liver > spleen > trunk kidney. Notably, the inflammatory reaction occurs early in the liver and trunk kidney. This result implies that ISGs may act synergistically and that the IFN response is closely related to the inflammatory response against GCRV infection. The transcriptomic profiles obtained and the function of ISGs predicted in this study provide new insights into fish antiviral mechanisms and developing effective therapeutic directions.