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Biao Wu, Xi Chen, Jie Hu, Zhenyuan Wang, Yan Wang, Dayou Xu, Haobing Guo, Changwei Shao, Liqing Zhou, Xiujun Sun, Tao Yu, Xiaomei Wang, Yanxin Zheng, Guangyi Fan, Zhihong Liu. Combined analysis of ATAC-Seq, RNA-Seq and GWAS reveals glycogen metabolism regulatory network in Jinjiang oyster Crassostrea ariakensis. Zoological Research. doi: 10.24272/j.issn.2095-8137.2023.021
Citation: Biao Wu, Xi Chen, Jie Hu, Zhenyuan Wang, Yan Wang, Dayou Xu, Haobing Guo, Changwei Shao, Liqing Zhou, Xiujun Sun, Tao Yu, Xiaomei Wang, Yanxin Zheng, Guangyi Fan, Zhihong Liu. Combined analysis of ATAC-Seq, RNA-Seq and GWAS reveals glycogen metabolism regulatory network in Jinjiang oyster Crassostrea ariakensis. Zoological Research. doi: 10.24272/j.issn.2095-8137.2023.021

Combined analysis of ATAC-Seq, RNA-Seq and GWAS reveals glycogen metabolism regulatory network in Jinjiang oyster Crassostrea ariakensis

doi: 10.24272/j.issn.2095-8137.2023.021
Funds:  National Key R&D Program of China (2022YFD2400100, 2018YFD0900104), Central Public-interest Scientific Institution Basal Research Fund, CAFS (2021XT0102, 2020TD19), Marine S&T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology (Qingdao)(2021QNLM050103), Key Research and Development Project of Shandong Province (2021LZGC028), and National Marine Genetic Resource Center
  • Received Date: 2023-01-16
  • Accepted Date: 2023-05-19
  • Rev Recd Date: 2023-05-10
  • Published Online: 2023-09-08
  • Glycogen is the most effective energy reserve for metabolism in aquatic shellfish, and also contributes to the flavor and quality of oyster. Jinjiang oyster Crassostrea ariakensis is an economically and ecologically important species in China. In this study, RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin using sequencing (ATAC-seq) were performed respectively to explore the gene expression and dynamic changes of chromatin accessibility among the oysters with different glycogen contents. A total of 9483 differentially expressed genes (DEGs) and 7215 significantly differential chromatin accessibility genes (DCAGs) were obtained, with the intersection of DEGs and DCAGs reaching 2600. Many of those genes were enriched in the pathways related to glycogen metabolism such as "Glycogen metabolic process" and "Starch and sucrose metabolism". In addition, a total of 526 SNP loci associated with glycogen content obtained by the genome wide association study (GWAS) corresponded to 241 genes, 63 of which were also DEGs and DCAGs as revealed above. This study will enrich basic research data and provide insights into the molecular mechanisms underlying the regulation of glycogen metabolism in oyster.
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      沈阳化工大学材料科学与工程学院 沈阳 110142

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