Transcriptome analysis of the Nile tilapia (Oreochromis niloticus) reveals altered expression of immune genes by cadmium.

Nile tilapia (Oreochromis niloticus) is a worldwide farmed fish and has been widely used for the study on comparative immunology in teleosts. It is well known that cadmium (Cd) can cause a variety of adverse effects in fish. However, data on the effects of Cd in fish liver and the defensive mechanisms of these effects using transcriptome approach are relatively scarce to date. In this study, by using an RNA sequencing approach, the gene expression profiling was performed in livers of tilapia exposed to 0 (control), 50, 100, and 200 μg/L of Cd for 2 months. The results showed that exposure to 50 μg/L Cd altered the expressions of 911 genes, while exposure to 100 and 200 μg/L Cd resulted in 4318 and 3737 differentially expressed genes compared to the control. Weighted correlation network analysis (WGCNA) and gene ontology (GO) analysis identified a 14-gene network linked to the immune system development. Further, in a fuzzy analysis, the GO term immune system development was enriched in cluster 3, and gene expression decreased with increasing Cd levels in a concentration-dependent manner. The qPCR and RNA-seq results identified 4 genes, i.e., dnmt3bb.1, sf3b1, SMARCAL1, and zap70, as convenient potential biological indicators for detecting waterborne Cd. The present results help systematically understand the effects of Cd on the hepatic transcriptome in tilapia.