Multi-Omics Data Reveal Amino Acids Related Genes in the Common Carp <i>Cyprinus carpio</i>
Hanyuan Zhang,
Youxiu Zhu,
Peng Xu,
Zixia Zhao,
Jianxin Feng,
Biyin Wu,
Yanliang Jiang,
Chuanju Dong,
Jian Xu
Affiliations
Hanyuan Zhang
Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China
Youxiu Zhu
Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China
Peng Xu
State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
Zixia Zhao
Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China
Jianxin Feng
Henan Academy of Fishery Sciences, Zhengzhou 450044, China
Biyin Wu
Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China
Yanliang Jiang
Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China
Chuanju Dong
College of Life Sciences, Henan Normal University, Xinxiang 453007, China
Jian Xu
Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China
Amino acids have important physiological effects on fish growth and development and are essential nutrition for humans. Flavor-related amino acids, such as glutamic acid and glycine, could have a significant effect on the taste of fish flesh. However, studies on the genetic mechanisms of amino acid metabolism in common carp (Cyprinus carpio) are still limited. This study identified divergent patterns on the genomic, transcriptomic and epigenomic levels in two groups of common carp with different amino acid contents. After genome-wide association analysis, a total of 62 genes was found to be associated with glycine, proline and tyrosine content. Transcriptome analysis of essential amino acids, branched-chain amino acids and flavor-related amino acids were performed using brain, liver and muscle tissues, resulting in 1643 differentially expressed genes (DEGs). Whole-genome bisulfite sequencing identified 3108 genes with differentially methylated promoters (DMPs). After the enrichment analysis, a series of pathways associated with amino acid metabolism, including growth regulation, lipid metabolism and the citrate cycle, was revealed. Integrated studies showed a strong correlation between DEGs and DMPs for amino acid contents in brain and muscle tissues. These multi-omics data revealed candidate genes and pathways related to amino acid metabolism in C. carpio.
