title: Transcriptome data analysis of grass carp (Ctenopharyngodon idella) infected by reovirus provides insights into two immune-related genes.
abstract: 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.
authors.affiliation: Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China.
authors.forename: Zao
authors.initials: Z
authors.lastname: Dai
authors.affiliation: Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China.
authors.forename: Jicheng
authors.initials: J
authors.lastname: Li
authors.affiliation: Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China.
authors.forename: Chengyu
authors.initials: C
authors.lastname: Hu
authors.affiliation: Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China.
authors.forename: Fang
authors.initials: F
authors.lastname: Wang
authors.affiliation: Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China.
authors.forename: Binhua
authors.initials: B
authors.lastname: Wang
authors.affiliation: Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Shi
authors.affiliation: Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China.
authors.forename: Qunhao
authors.initials: Q
authors.lastname: Hou
authors.affiliation: Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China.
authors.forename: Waigen
authors.initials: W
authors.lastname: Huang
authors.affiliation: Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China. Electronic address: lgang@ncu.edu.cn.
authors.forename: Gang
authors.initials: G
authors.lastname: Lin
mesh_terms: D000818:Animals; D002347:Carps / Q000145:classification / Q000235:genetics / Q000276:immunology; D005393:Fish Diseases / Q000235:genetics* / Q000821:virology; D020869:Gene Expression Profiling / Q000662:veterinary; D010802:Phylogeny; D012087:Reoviridae / Q000502:physiology*; D012088:Reoviridae Infections / Q000235:genetics / Q000662:veterinary* / Q000821:virology; D059467:Transcriptome
keywords: Co-expression network analysis; Function analysis; Grass carp; Immune response; Pathway analysis; Reovirus; Transcriptome; qPCR