MicroRNA expression and analysis of immune-related putative target genes in ISKNV-infected spleen of mandarin fish (Siniperca chuatsi)

Infectious spleen and kidney necrosis virus (ISKNV), a highly infectious and lethal pathogen of mandarin fish (Siniperca chuatsi), has resulted in major aquaculture losses over the past few decades. A lack of understanding of the regulatory mechanism of viral infection has impeded the development of effective measures to control ISKNV infection. MicroRNAs (miRNAs) are a class of non-coding RNAs that regulate the processes of viral infection and are involved in various physiological processes in vivo. In this study, miRNAs involved in the response of mandarin fish to ISKNV infection were identified at several time points following infection through Illumina high-throughput sequencing. A total of 434 (27 known and 407 novel) miRNAs were identified in mandarin fish; 26 (26 up-regulated), 38 (30 up-regulated, 8 down-regulated), and 18 (14 up-regulated and 4 down-regulated) differentially expressed miRNAs (DEMs) were identified at 12, 24, and 48 h post-infection (hpi), respectively. The putative target genes of DEMs were all significantly enriched in host immune response or signaling pathways, such as autophagy, endocytosis, phosphatidylinositol signaling system, Salmonella infection, cell cycle, protein export, and protein processing in endoplasmic reticulum pathway at 12 and 24 hpi and in vascular endothelial growth factor, phosphatidylinositol signaling system and lysosome at 48 hpi. Further analysis indicated that the targeted mRNAs of miRNAs were involved in innate immunity; autophagy and endocytosis might play an important role in immune regulation within 24 hpi with ISKNV. Although the number of DEMs was lowest at 48 hpi, they might still be involved in immunity through the above pathway. We also constructed a miRNA–mRNA targeting network. Generally, the findings of this study provide novel information that advance our understanding of the regulatory mechanisms of miRNA during ISKNV infection in mandarin fish as well as the development of new approaches for preventing ISKNV infection.