MicroRNA regulation during Nibea albiflora immuno-resistant against Cryptocaryon irritans challenge in fish skin

Nibea albiflora (Yellow drum) was discovered to be highly resistant to the infection of Cryptocaryon irritans a lethal ciliate protozoa parasite during disease outbreak. Investigation of miRNAs which post-transcriptionally regulate genes will deeper our understanding of regulation of immune response against infection. In this study, we challenged N. albiflora with C. irritans at median lethal concentration (2050 theronts/g fish). Skins from infected and controlled fish were sampled at 24 h and 72 h for miRNA sequencing. In total, we identified 180 known and 71 novel miRNAs, in which 30 miRNAs were significantly affected by infection, 19 were influenced by time and 16 significantly affected by the interaction between time and infection. Totally, 7396 genes were predicted as targeted regulated by infection differential expressed genes. The genes were significantly enriched in C-type lectin receptor pathway, MAPK signaling pathway and mTOR signaling pathway which closely related to antigen recognition, presentation and downstream signal transduction for immuno-activation. Overall, our data suggest that most of miRNAs were intensively regulating gene expression involved in C-type lectin receptor pathway, MAPK signaling pathway and mTOR signaling pathway rather than directly involve in immunological factor regulation during immune response against parasite infection.