Combined ATAC-seq, RNA-seq, and GWAS analysis reveals glycogen metabolism regulatory network in Jinjiang oyster (Crassostrea ariakensis)
文献类型： 外文期刊
作者： Wu, Biao 1 ; Chen, Xi 1 ; Hu, Jie 3 ; Wang, Zhen-Yuan 1 ; Wang, Yan 1 ; Xu, Da-You 3 ; Guo, Hao-Bing 3 ; Shao, Chang-Wei 1 ; Zhou, Li-Qing 1 ; Sun, Xiu-Jun 1 ; Yu, Tao 5 ; Wang, Xiao-Mei 5 ; Zheng, Yan-Xin 5 ; Fan, Guang-Yi 3 ; Liu, Zhi-Hong 1 ;
作者机构： 1.Chinese Acad Fishery Sci, Yellow Sea Fisheries Res Inst, State Key Lab Mariculture Biobreeding & Sustainabl, Qingdao 266071, Shandong, Peoples R China
2.Laoshan Lab, Lab Marine Fisheries Sci & Food Prod Proc, Qingdao 266071, Shandong, Peoples R China
3.BGI Qingdao, BGI Shenzhen, Qingdao 266426, Shandong, Peoples R China
4.Shanghai Ocean Univ, Natl Demonstrat Ctr Expt Fisheries Sci Educ, Shanghai 201306, Peoples R China
5.Chinese Acad Fishery Sci, Changdao Enhancement & Expt Stn, Yantai 265800, Shandong, Peoples R China
6.BGI Shenzhen, State Key Lab Agr Genom, Shenzhen 518083, Guangdong, Peoples R China
关键词： Crassostrea ariakensis; Glycogen; Transcriptome; ATAC; GWAS
期刊名称：ZOOLOGICAL RESEARCH （ 影响因子：4.0； 五年影响因子：4.5 ）
ISSN： 2095-8137
年卷期： 2024 年 45 卷 1 期
页码：
收录情况： SCI
摘要： Glycogen serves as the principal energy reserve for metabolic processes in aquatic shellfish and substantially contributes to the flavor and quality of oysters. The Jinjiang oyster (Crassostrea ariakensis) is an economically and ecologically important species in China. In the present study, RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin using sequencing (ATAC-seq) were performed to investigate gene expression and chromatin accessibility variations in oysters with different glycogen contents. Analysis identified 9 483 differentially expressed genes (DEGs) and 7 215 genes with significantly differential chromatin accessibility (DCAGs) were obtained, with an overlap of 2 600 genes between them. Notably, a significant proportion of these genes were enriched in pathways related to glycogen metabolism, including "Glycogen metabolic process" and "Starch and sucrose metabolism". In addition, genomewide association study (GWAS) identified 526 single nucleotide polymorphism (SNP) loci associated with glycogen content. These loci corresponded to 241 genes, 63 of which were categorized as both DEGs and DCAGs. This study enriches basic research data and provides insights into the molecular mechanisms underlying the regulation of glycogen metabolism in C. ariakensis.
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