Dynamic immune response in the spleens of rainbow trout (Oncorhynchus mykiss) to infectious hematopoietic necrosis virus revealed by transcriptome and immune-related genes expression analysis

Rainbow trout (Oncorhynchus mykiss) is, economically, one of the most important cultured fish in the world. Infectious hematopoietic necrosis virus (IHNV) is a serious pathogen causing high morbidity and mortality in rainbow trout. To gain more insight into the immune response of rainbow trout to the virus, RNA sequencing technology was used to examine the transcriptome profiles in spleens of trout infected and uninfected with IHNV. A total of 9144 differentially expressed genes (DEGs) were identified, of which 3274 were upregulated and 5870 were downregulated. The expression levels of 13 DEGs were validated by quantitative real-time PCR. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis showed that most DEGs were significantly enriched in major immune terms such as immune system process, immune effector process, response to stimulus and key immune signaling pathways. Moreover, we detected the expression levels of six key immune-related genes based on transcriptomic data and protein–protein interaction analysis in four important immune signaling pathways at 0, 6, 12, 24, 48, 72, 96, 120, and 144 h post-infection, including Toll-like receptor signaling pathway (TLR2 and TLR5M), RIG-I-like receptor signaling pathway (TRIM25), NOD-like receptor signaling pathway (RIPK2 and A20) and JAK-STAT signaling pathway (SOCS2). Results revealed that the immune-related genes in these pathways were involved in the antiviral immune response. Altogether, this study provides a better understanding of the dynamic immune response of rainbow trout infected with IHNV, which will lay a foundation for further study of molecular mechanisms of anti-IHNV innate immunity.