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De novo genome assembly depicts the immune genomic characteristics of cattle

Author

Listed:
  • Ting-Ting Li

    (National Center of Biomedical Analysis)

  • Tian Xia

    (National Center of Biomedical Analysis)

  • Jia-Qi Wu

    (National Center of Biomedical Analysis)

  • Hao Hong

    (National Center of Biomedical Analysis)

  • Zhao-Lin Sun

    (Beijing Institute of Pharmacology and Toxicology)

  • Ming Wang

    (China Agricultural University
    China Agricultural University)

  • Fang-Rong Ding

    (China Agricultural University)

  • Jing Wang

    (Beijing Institute of Pharmacology and Toxicology)

  • Shuai Jiang

    (National Center of Biomedical Analysis)

  • Jin Li

    (National Center of Biomedical Analysis)

  • Jie Pan

    (National Center of Biomedical Analysis)

  • Guang Yang

    (Beijing Institute of Pharmacology and Toxicology)

  • Jian-Nan Feng

    (Beijing Institute of Pharmacology and Toxicology)

  • Yun-Ping Dai

    (China Agricultural University)

  • Xue-Min Zhang

    (National Center of Biomedical Analysis
    Fudan University)

  • Tao Zhou

    (National Center of Biomedical Analysis)

  • Tao Li

    (National Center of Biomedical Analysis
    Fudan University)

Abstract

Immunogenomic loci remain poorly understood because of their genetic complexity and size. Here, we report the de novo assembly of a cattle genome and provide a detailed annotation of the immunogenomic loci. The assembled genome contains 143 contigs (N50 ~ 74.0 Mb). In contrast to the current reference genome (ARS-UCD1.2), 156 gaps are closed and 467 scaffolds are located in our assembly. Importantly, the immunogenomic regions, including three immunoglobulin (IG) loci, four T-cell receptor (TR) loci, and the major histocompatibility complex (MHC) locus, are seamlessly assembled and precisely annotated. With the characterization of 258 IG genes and 657 TR genes distributed across seven genomic loci, we present a detailed depiction of immune gene diversity in cattle. Moreover, the MHC gene structures are integrally revealed with properly phased haplotypes. Together, our work describes a more complete cattle genome, and provides a comprehensive view of its complex immune-genome.

Suggested Citation

  • Ting-Ting Li & Tian Xia & Jia-Qi Wu & Hao Hong & Zhao-Lin Sun & Ming Wang & Fang-Rong Ding & Jing Wang & Shuai Jiang & Jin Li & Jie Pan & Guang Yang & Jian-Nan Feng & Yun-Ping Dai & Xue-Min Zhang & Ta, 2023. "De novo genome assembly depicts the immune genomic characteristics of cattle," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-42161-1
    DOI: 10.1038/s41467-023-42161-1
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    References listed on IDEAS

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    1. Wai Yee Low & Rick Tearle & Derek M. Bickhart & Benjamin D. Rosen & Sarah B. Kingan & Thomas Swale & Françoise Thibaud-Nissen & Terence D. Murphy & Rachel Young & Lucas Lefevre & David A. Hume & Andre, 2019. "Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity," Nature Communications, Nature, vol. 10(1), pages 1-11, December.
    2. Glennis A. Logsdon & Mitchell R. Vollger & PingHsun Hsieh & Yafei Mao & Mikhail A. Liskovykh & Sergey Koren & Sergey Nurk & Ludovica Mercuri & Philip C. Dishuck & Arang Rhie & Leonardo G. Lima & Tatia, 2021. "The structure, function and evolution of a complete human chromosome 8," Nature, Nature, vol. 593(7857), pages 101-107, May.
    3. Devin Sok & Khoa M. Le & Melissa Vadnais & Karen L. Saye-Francisco & Joseph G. Jardine & Jonathan L. Torres & Zachary T. Berndsen & Leopold Kong & Robyn Stanfield & Jennifer Ruiz & Alejandra Ramos & C, 2017. "Rapid elicitation of broadly neutralizing antibodies to HIV by immunization in cows," Nature, Nature, vol. 548(7665), pages 108-111, August.
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