International Journal of Molecular Sciences Article Megalocytivirus Induces Complicated Fish Immune Response at Multiple RNA Levels Involving mRNA, miRNA, and circRNA Qian Wu 1,2,3, Xianhui Ning 1 and Li Sun 1,2,3,* 1 CAS and Shandong Province Key Laboratory of Experimental Marine Biology, CAS Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China;
[email protected] (Q.W.);
[email protected] (X.N.) 2 Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao 266237, China 3 College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China * Correspondence:
[email protected]; Tel.: +86-532-82898829 Abstract: Megalocytivirus is an important viral pathogen to many farmed fishes, including Japanese flounder (Paralichthys olivaceus). In this study, we examined megalocytivirus-induced RNA responses in the spleen of flounder by high-throughput sequencing and integrative analysis of various RNA- seq data. A total of 1327 microRNAs (miRNAs), including 368 novel miRNAs, were identified, among which, 171 (named DEmiRs) exhibited significantly differential expressions during viral infection in a time-dependent manner. For these DEmiRs, 805 differentially expressed target mRNAs (DETmRs) were predicted, whose expressions not only significantly changed after megalocytivirus infection but were also negatively correlated with their paired DEmiRs. Integrative analysis of Citation: Wu, Q.; Ning, X.; Sun, L. Megalocytivirus Induces immune-related DETmRs and their target DEmiRs identified 12 hub DEmiRs, which, together with Complicated Fish Immune Response their corresponding DETmRs, formed an interaction network containing 84 pairs of DEmiR and at Multiple RNA Levels Involving DETmR.