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Non-coding RNAs (ncRNAs) play vital roles in regulating the expression levels of genes that control essential biological functions, including immune response to bacterial infections in teleost. To dissect the roles of ncRNAs in the Channa argus (snakehead), a systematic analysis of the expression profiles of circRNA, miRNA and mRNA, as well as competing endogenous RNAs (ceRNA) regulatory networks in the kidney of snakehead following Nocardia seriolae infection were performed in the present study. A total of 111 differentially expressed circRNAs, 706 differentially expressed miRNAs, and 2548 differentially expressed mRNAs were identified in the N. seriolae infected snakehead. Based on these differently expressed RNAs, we identified 55 circRNA-mRNA pairs, 124 miRNA-mRNA pairs, and 35 circRNA-miRNA-mRNA regulatory networks, including dre-miR-103-CD302, dre-miR-27e-IGSF3, novel_circ_0005462/novel_403-IGKC, novel_circ_0001750/novel_circ_0002162-novel_477-OCLN, and novel_circ_0003847-novel_4-KCNAB3. In addition, luciferase reporter assay was employed to detect the target relationships of several circRNA-miRNA-mRNA pairs. Taken together, this study demonstrates that the genes associated with immunity and structures in the kidney of snakehead can be regulated by circRNAs and miRNAs at post-transcription levels, and provided theoretical guidance for ncRNAs studies for other teleost. However, further studies are still in great need to validate the regulatory mechanisms of ncRNAs in snakehead. • 111 circRNAs, 706 miRNAs and 2548 mRNAs were identified at four infection time points in N. seriolae infected snakehead. • We identified 55 circRNA-mRNA pairs, 124 miRNA-mRNA pairs and 35 circRNA-miRNA-mRNA regulatory networks. • Luciferase reporter assay was used to detect their target relationships. [ABSTRACT FROM AUTHOR]