Volume 45 Issue 1
Jan.  2024
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Article Contents
Biao Wu, Xi Chen, Jie Hu, Zhen-Yuan Wang, Yan Wang, Da-You Xu, Hao-Bing Guo, Chang-Wei Shao, Li-Qing Zhou, Xiu-Jun Sun, Tao Yu, Xiao-Mei Wang, Yan-Xin Zheng, Guang-Yi Fan, Zhi-Hong Liu. Combined ATAC-seq, RNA-seq, and GWAS analysis reveals glycogen metabolism regulatory network in Jinjiang oyster (Crassostrea ariakensis). Zoological Research, 2024, 45(1): 201-214. doi: 10.24272/j.issn.2095-8137.2023.021
Citation: Biao Wu, Xi Chen, Jie Hu, Zhen-Yuan Wang, Yan Wang, Da-You Xu, Hao-Bing Guo, Chang-Wei Shao, Li-Qing Zhou, Xiu-Jun Sun, Tao Yu, Xiao-Mei Wang, Yan-Xin Zheng, Guang-Yi Fan, Zhi-Hong Liu. Combined ATAC-seq, RNA-seq, and GWAS analysis reveals glycogen metabolism regulatory network in Jinjiang oyster (Crassostrea ariakensis). Zoological Research, 2024, 45(1): 201-214. doi: 10.24272/j.issn.2095-8137.2023.021

Combined ATAC-seq, RNA-seq, and GWAS analysis reveals glycogen metabolism regulatory network in Jinjiang oyster (Crassostrea ariakensis)

doi: 10.24272/j.issn.2095-8137.2023.021
The C. ariakensis RNA-seq data and ATAC-seq data generated in this study were submitted to the China National GeneBank Database (CNGBdb; https://db.cngb.org/; accession number CNP0003045), National Center for Biotechnology Information (NCBI SRA; https://www.ncbi.nlm.nih.gov/sra; accession number PRJNA999955), Genome Sequence Archive (GSA; https://ngdc.cncb.ac.cn/gsa; accession number PRJCA018671), and Science Data Bank (SDB; https://www.scidb.cn/en; Data DOI: 10.57760/sciencedb.09809). The C. ariakensis assembled genome and whole-genome resequencing datasets that support the findings of this study are available at CNGBdb (doi.org/10.1111/1755-0998.13556, accession number CNP0001149).
Supplementary data to this article can be found online.
The authors declare that they have no competing interests.
B.W., X.C., and G.Y.F. designed the research. X.C., J.H., D.Y.X., and H.B.G. analyzed the data. B.W. and X.C. wrote the manuscript. Y.W. and Z.Y.W. performed histological sectioning and validation experiments. C.W.S., L.Q.Z., X.J.S., T.Y., X.M.W., and Y.X.Z. revised the manuscript. Z.H.L. guided revision of the manuscript. All authors read and approved the final version of the manuscript.
#Authors contributed equally to this work
Funds:  This work was supported by the National Key R&D Program of China (2022YFD2400105, 2018YFD0900104), Central Public-interest Scientific Institution Basal Research Fund, CAFS (2021XT0102, 2023TD30), 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
More Information
  • 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, genome-wide 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.
  • The C. ariakensis RNA-seq data and ATAC-seq data generated in this study were submitted to the China National GeneBank Database (CNGBdb; https://db.cngb.org/; accession number CNP0003045), National Center for Biotechnology Information (NCBI SRA; https://www.ncbi.nlm.nih.gov/sra; accession number PRJNA999955), Genome Sequence Archive (GSA; https://ngdc.cncb.ac.cn/gsa; accession number PRJCA018671), and Science Data Bank (SDB; https://www.scidb.cn/en; Data DOI: 10.57760/sciencedb.09809). The C. ariakensis assembled genome and whole-genome resequencing datasets that support the findings of this study are available at CNGBdb (doi.org/10.1111/1755-0998.13556, accession number CNP0001149).
    Supplementary data to this article can be found online.
    The authors declare that they have no competing interests.
    B.W., X.C., and G.Y.F. designed the research. X.C., J.H., D.Y.X., and H.B.G. analyzed the data. B.W. and X.C. wrote the manuscript. Y.W. and Z.Y.W. performed histological sectioning and validation experiments. C.W.S., L.Q.Z., X.J.S., T.Y., X.M.W., and Y.X.Z. revised the manuscript. Z.H.L. guided revision of the manuscript. All authors read and approved the final version of the manuscript.
    #Authors contributed equally to this work
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