Transcriptome Analysis of Epithelioma Papulosum Cyprini Cells Infected by Reovirus Isolated from Allogynogenetic Silver Crucian Carp

Cui-Yu Ba,Xiao-Yan Du,Ping Chen,Ya-Nan Cai,Yue-Hong Li,Pei-Jun Zhang

doi:10.3390/v10030135

Abstract

The present study aimed to identify differentially expressed genes (DEGs) and major signal transduction pathways that were related to the immune response of epithelioma papulosum cyprinid (EPC) cells to reoviruses isolated from allogynogenetic silver crucian carp. The study also lays a theoretical foundation for the pathogenesis and immunity of the reovirus, which is helpful to the breeding of cyprinids fish. Reovirus infected and uninfected EPC cells were analyzed by using a new-generation high-throughput sequencing technology. DEGs were identified, annotated, and classified, and the signal pathways involved in the response to reovirus infection were identified by using bioinformatics tool. The data were assembled into 92,101 contigs with an average length of 835.24 bp and an N50 value of 1432 nt. Differential expression analysis of all the genes identified 3316 DEGs at a false discovery rate (FDR) of <0.01 and a fold-change of ≥3, of which 1691 were upregulated genes, 1625 were downregulated, and about 305 were immune-related genes. Gene Ontology (GO) enrichment analysis resulted in the annotation of 3941 GO terms, including 2719 biological processes (37,810 unigenes), 376 cell components (7943 unigenes), and 846 molecular functions (11,750 unigenes). KEGG metabolic pathway analysis matched the DEGs from pre-and post-infection EPC cells to 193 pathways, of which 35 were immune-related, including the Toll-like receptor, cytokine-cytokine receptor interaction, and the JAK-STAT signaling pathways.

Highlights

Aquareoviruses are characterized to have a double capsid, icosahedral symmetry, and no capsule.The average diameter of aquareoviruses is 60–70 nm and its genome consists of 11 segments of double-stranded RNA [1,2]
The results showed that the concentration and total amount of the four samples were in accordance with the sequencing requirements
The second-generation transcriptome sequencing (RNA-Seq) technology is a high-throughput sequencing approach involving the cDNA from fragmentally processed mRNA, sequence splicing assembly, and statistical correlation of number of sequences to obtain different transcripts

Summary

Introduction

Aquareoviruses are characterized to have a double capsid, icosahedral symmetry, and no capsule. The average diameter of aquareoviruses is 60–70 nm and its genome consists of 11 segments of double-stranded RNA [1,2]. Aquatic reoviruses have infected various economically important economic aquaculture fishes such as grass carp, black carp, barley fish, Atlantic salmon, and rare crucian carp, thereby resulting in higher mortality rates. Reoviruses have been isolated from ostriches, bats, and ducks. Reports on the isolation of reoviruses that infect allogynogenetic crucian carp are limited. The transcriptome is the sum of all the transcripts of a given organism in a given state, including mRNAs and non-coding RNAs [3,4]. The transcriptome is an essential link between genetic information and biological function (proteome).

Methods

Results

Discussion

Conclusion