Comprehensive analysis of circRNA expression pattern and circRNA–mRNA–miRNA network in Ctenopharyngodon idellus kidney (CIK) cells after grass carp reovirus (GCRV) infection

Grass carp reovirus (GCRV) causes grass carp hemorrhage disease and is one of the most damaging factors in the culture of grass carp (Ctenopharyngodon idellus). Until now, the mechanisms underlying GCRV infection have been largely unknown. To explore the molecular responses to GCRV infection in C. idellus kidney (CIK) cells, we used high-throughput sequencing to investigate the circRNA, mRNA, and miRNA expression patterns and the circRNA–miRNA–mRNA network. A total of 76 circRNAs, 798 mRNAs, and 186 miRNAs were identified as differentially expressed (DE) RNAs in GCRV-infected cells compared with uninfected cells, of which 40 circRNAs, 658 mRNAs, and 146 miRNAs were upregulated, and 36 circRNAs, 140 mRNAs, and 40 miRNAs were downregulated (fold change >2, p