Integrated transcriptomic and proteomic analysis of the physiological changes of the liver in domesticated Eurasian perch, Perca fluviatilis

Artificial domestication during aquaculture practice has strongly shaped the physiological characteristics of Perca fluviatilis. Thus, revealing the genetic changes in domesticated P. fluviatilis will improve aquaculture and selective breeding. In this study, comparative analysis of the liver transcriptome, proteome, and physiological and biochemical indices of domesticated and wild P. fluviatilis was conducted. Our results indicated that the activity of lipase and the content of glucose were higher; however, the total antioxidant capacity and superoxide dismutase were lower in domesticated P. fluviatilis. Integrated analysis of "omics" data identified 174 and 127 genes and proteins that showed consistent upregulation and downregulation in domesticated P. fluviatilis, respectively. GO and KEGG enrichment of differentially expressed genes and proteins and the protein-protein interaction network indicated that energy metabolism (lipid and carbohydrate metabolism) was enhanced, and that signal transduction and the stress response were reduced in domesticated P. fluviatilis. This study revealed that artificial domestication may significantly shape the physiological changes in energy metabolism and stress resistance in domesticated P. fluviatilis, which makes them more adaptable to the artificial aquaculture environment, thereby promoting growth and development.