Transcriptome data analysis of grass carp (Ctenopharyngodon idella) infected by reovirus provides insights into two immune-related genes

• Published in: Fish & shellfish immunology 2017-05, Vol.64, p.68-77
• Main Authors: Dai, Zao, Li, Jicheng, Hu, Chengyu, Wang, Fang, Wang, Binhua, Shi, Xiao, Hou, Qunhao, Huang, Waigen, Lin, Gang
• Format: Article
• Language: English
• Subjects: Animals; Carps - classification; Carps - genetics; Carps - immunology; Co-expression network analysis; Fish Diseases - genetics; Fish Diseases - virology; Function analysis; Gene Expression Profiling - veterinary; Grass carp; Immune response; Pathway analysis; Phylogeny; qPCR; Reoviridae - physiology; Reoviridae Infections - genetics; Reoviridae Infections - veterinary; Reoviridae Infections - virology; Reovirus; Transcriptome
• ISSN: 1050-4648; 1095-9947
• DOI: 10.1016/j.fsi.2017.03.008

Grass carp (Ctenopharyngodon idella) was one of the economically important freshwater fish in China. However, hemorrhagic disease caused by grass carp reovirus (GCRV) results in a tremendous loss in the process of grass carp cultivation. Transcriptome analysis could provide a comprehensive understanding of the molecular mechanisms involved in specific biological processes and diseases for the resistance to reovirus infection of grass carp. In this study, the raw data from NCBI (accession number: SRA099702) were analyzed, in which, 50 significant differentially expressed genes by routine transcriptome analysis and 84 notably differentially expressed genes by co-expression network method. KEGG analysis revealed that the pathway in hemorrhagic diseases in grass carp was similar to the influenza A induced pathway. The interferon-stimulated gene ISG15 and sacsin-like gene, which were up-regulated in data (SRA099702), were also up-regulated in data (SRP049081) from a similar assay. QPCR experiment was performed to validate these up-regulated genes. The ISG15 gene was shown to be the core gene in the co-expression network. The results would enhance our understanding of the antivirus system of grass carp infected by reovirus. •Same function and pathway were detected while different expression genes calculated by two ways.•The signaling pathway of grass carp infected by reovirus was similar to Influenza A.•ISG15, which performed important function in immunoreaction when grass carp infected by reovirus, was the core gene.