Transcriptome analysis of feed efficiency of Macrobrachium nipponense

In this study, the transcriptome and metabolome of hepatopancreas and muscle of Macrobrachium nipponense with different RFI (high RFI and low RFI) groups were characterized using combined transcriptomic and metabolomic analysis. A total of 4540 differentially expressed genes (DEGs) in hepatopancreas and 3894 DEGs in muscle were identified, respectively. These identified DEGs were mainly enriched in 47 metabolic pathways in the hepatopancreas and 106 metabolic pathways in the muscle. Those pathways included the pentose and glucuronate interconversions, metabolism of xenobiotics by cytochrome P450, carbohydrate digestion and absorption, etc. The transcriptomic analysis illustrated that those changes in foreign body metabolism, protein metabolism, energy production, and other related biological pathways may lead to changes in the RFI values of M. nipponense. 445 and 247 differently expressed metabolites (DEMs) were identified in the hepatopancreas and muscle. In addition, 11 KEGG pathways, which mainly include lysine biosynthesis, lysine degradation, aminoacyl-tRNA biosynthesis, and purine metabolism, were significantly enriched in hepatopancreas. Also, 14 KEGG pathways, which mainly include pyrimidine metabolism, glutathione metabolism, nitrogen metabolism, and mTOR signaling pathway, were significantly enriched in muscle.