RNA-seq analysis of a zebrafish caudal fin cell line in response to infection with spring viraemia of carp virus

Abstract

A cell line, termed ZFIN, was established from the caudal fin of zebrafish and was shown to be susceptible to spring viremia of carp virus (SVCV). The ZFIN cells are epithelial like cells and have a moderate plasmid transfection efficiency of 13.9%. Using an RNA-seq approach, differentially expressed genes (DEGs) regulated by SVCV were identified. Infection of SVCV gave rise to 3931 DEGs and up-regulated DEGs were mostly enriched into the biological regulation and cellular processes, among which pathways for the type I interferon signaling and the response to exogenous dsRNA were the top two GO terms. Several KEGG signaling pathways including TLR signaling pathway, RLR receptor signaling pathway, cytosolic DNA-sensing pathway, NLR signaling pathway, cytokine-cytokine receptor interaction and ferroptosis were significantly enriched. Antiviral genes including ifnφ1, isg15 and mx were significantly up-regulated. In addition, key DEGs involved in autophagy were identified. The results indicate that the ZFIN cell line provides a useful in vitro tool for study on the gene functions and cellular responses to viral infection in fish.