Transcriptome analysis of differentially expressed genes in the fore- and hind-intestine of ovate pompano Trachinotus ovatus

Abstract The fish intestine is a highly complex organ and plays an important role in fish immunity and nutrition. To characterize the molecular functions of the intestine of ovate pompano, we compared the gene expression differences and explored the molecular functions of the fore- and hind-intestine (FI and HI) using transcriptomic analysis. Our analysis yielded a total of approximately 21 Gb (gigabytes) of clean bases and 144 M of clean reads (mean of 24 M for each sample). Most of the 61,572 genes in the FI and HI were not differentially expressed, and only 105 genes were identified as the differentially expressed genes (DEGs). Among the 61,572 genes, the genes that exhibited the highest expression levels were mostly related to various digestive enzymes. Among the 105 DEGs, 86 were annotated as immune- and absorption-related genes in ovate pompano. Detailed analysis of these DEGs in FI and HI indicated that the FI required more abundant genes to handle the attacks and digestion, whereas the HI recruited more genes to deal with the absorption, suggesting that FI focused mainly on immunity and digestion, and the HI focused on absorption. Our results provided an insight on the molecular mechanisms of the function of intestine in ovate pompano.