Viral nervous necrosis (VNN) is an acute and serious fish disease caused by nervous necrosis virus (NNV) which has been reported massive mortality in more than fifty teleost species worldwide. VNN causes damage of necrosis and vacuolation to central nervous system (CNS) cells in fish. It is difficult to identify the specific type of cell targeted by NNV, and to decipher the host immune response because of the functional diversity and highly complex anatomical and cellular composition of the CNS. In this study, we found that the red spotted grouper NNV (RGNNV) mainly attacked the midbrain of orange-spotted grouper (Epinephelus coioides). We conducted single-cell RNA-seq analysis of the midbrain of healthy and RGNNV-infected fish and identified 35 transcriptionally distinct cell subtypes, including 28 neuronal and 7 non-neuronal cell types. An evaluation of the subpopulations of immune cells revealed that macrophages were enriched in RGNNV-infected fish, and the transcriptional profiles of macrophages indicated an acute cytokine and inflammatory response. Unsupervised pseudotime analysis of immune cells showed that microglia transformed into M1-type activated macrophages to produce cytokines to reduce the damage to nerve tissue caused by the virus. We also found that RGNNV targeted neuronal cell types was GLU1 and GLU3, and we found that the key genes and pathways by which causes cell cytoplasmic vacuoles and autophagy significant enrichment, this may be the major route viruses cause cell death. These data provided a comprehensive transcriptional perspective of the grouper midbrain and the basis for further research on how viruses infect the teleost CNS.

The three croakers (Nibea coibor, Protonibea diacanthus and Argyrosomus amoyensis, Perciformes, Sciaenidae) are important commercial species inhabiting the Eastern Indian Ocean and Western Pacific. Molecular data employed in previous research on phylogenetic reconstruction have not been adequate and complete, and systematic and comprehensive phylogenetic relationships for these fish are unresolved. We sequenced the complete mitochondrial genomes of the three croakers using next-generation sequencing for the first time. We analyzed the composition and phylogenies between 19 species in the family Sciaenidae using the mitochondrial protein coding sequences of 204 species in the Series Eupercaria. We present the characterization of the complete mitochondrial genome sequences of the three croakers. Gene arrangement and distribution of the three croakers are canonically identical and consistent with other vertebrates. We found that the family Sciaenidae is an independent branch that is isolated from the order Perciformes and does not belong to any extant classification. Therefore, this family is expected to belong to a new classification at the order level and needs further analysis. The evolution of Sciaenidae has lagged far behind the Perciformes differentiation. This study presents a novel insight into the phylogenetics of the family Sciaenidae from the order Perciformes and facilitates additional studies on the evolution and phylogeny of Series Eupercaria.