Transcriptome analysis of head kidney and liver in grass carp (Ctenopharyngodon idella) symptomatically or asymptomatically infected with Flavobacterium columnare

Flavobacterium columnare is an important pathogen causing columnaris disease, which can result in high mortality in freshwater fish worldwide. Understanding the immune response in infection status of fish may be essential for developing effective prevention and treatment strategies. In this study, transcriptomes of liver and head kidney tissues in grass carp (Ctenopharyngodon idella) were compared under symptomatic and asymptomatic statuses following the immersion infection of F. columnare. Significant differences in expression of genes were observed between fish showing disease symptoms and those without symptoms. The number of differentially expressed genes (DEGs) between infected and control groups ranged from 4752 to 8,277, while the DEGs between exposed and control groups ranged from 272 to 1,751, suggesting a strong acute inflammatory response in infected groups. KEGG pathway enrichment analysis of infected groups revealed that among the top 30 enriched pathways, liver and head kidney shared 22 and 16 common pathways, respectively. These common enriched pathways are involved in various functions such as metabolism, diseases, cellular processes, biological systems, and information processing, indicating their roles in the immune response to F. columnare. Notably, we investigated in detail the gene expression profiles associated with complement molecules and three classes of cytokines (interleukin, tumor necrosis factor, and interferon) in different organs/tissues and disease states during the pathogenesis of columnaris disease. The findings highlight the importance of inflammatory responses and complement pathways in the pathogenesis of columnaris disease and suggest potential targets for future research and disease management strategies. The present study thus provides valuable insights into the transcriptomic changes and immune responses in grass carp infected with F. columnare, and sheds light on how highly virulent strains of F. columnare cause morbidity and mortality in the host.