Hepatic Transcriptome Profiling under Shear Stress in Sciaenops ocellatus

Water flow is basic in the environment of fish. To date, most studies investigating the influence of water flow on fish behavior have focused on swimming speed and associated mechanisms, but few studies have addressed the molecular basis. This study used liver transcriptome profiling of Sciaenops ocellatus exposed to shear stress from the aquatic environment. De novo assembly yielded 70,148 genes with 12,465 unigenes > 1 kb. We identified 10,214 simple sequence repeat markers as well as 38,020 and 29,627 homozygous and 57,835 and 66,088 heterozygous single nucleotide polymorphisms in the experimental and control groups, respectively. After screening, there were 1773 differentially expressed genes, of which 204 were upregulated and 969 were downregulated. Gene Ontology analysis revealed 424 genes that were enriched in biological processes (90 in cellular component and 310 in molecular function). A total of 423 genes were annotated to a Kyoto Encyclopedia of Genes and Genome pathways (136 to metabolic pathways; 69 to environmental information processing; 67 to cellular process). There were four significantly enriched pathways, including glycine, serine, and threonine metabolism; tryptophan metabolism; retinol metabolism; and steroid biosynthesis. Some genes were known to be related to flow stress; those in the Hedgehog signaling pathway were upregulated, whereas others related to RNA degradation were downregulated. There was strong correlation between up- and downregulated genes identified by quantitative PCR and RNA sequencing. Thus, shear stress from aquatic environments greatly influences liver function in S. ocellatus. The results provide a reference that can be useful for selecting appropriate breeding sites for S. ocellatus aquaculture.