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Telomere-to-telomere genome assembly of a male goat reveals variants associated with cashmere traits

Author

Listed:
  • Hui Wu

    (China Agricultural University
    Chinese Academy of Agricultural Sciences)

  • Ling-Yun Luo

    (China Agricultural University)

  • Ya-Hui Zhang

    (China Agricultural University)

  • Chong-Yan Zhang

    (Inner Mongolia Agricultural University)

  • Jia-Hui Huang

    (China Agricultural University)

  • Dong-Xin Mo

    (China Agricultural University)

  • Li-Ming Zhao

    (Lanzhou University)

  • Zhi-Xin Wang

    (Inner Mongolia Agricultural University)

  • Yi-Chuan Wang

    (Inner Mongolia Agricultural University)

  • EEr He-Hua

    (NingXia Academy of Agriculture and Forestry Sciences)

  • Wen-Lin Bai

    (Shenyang Agricultural University)

  • Di Han

    (Modern Agricultural Production Base Construction Engineering Center of Liaoning Province)

  • Xing-Tang Dou

    (Ltd.)

  • Yan-Ling Ren

    (Shandong Binzhou Academy of Animal Science and Veterinary Medicine)

  • Renqing Dingkao

    (Gannan Institute of Animal Husbandry Science)

  • Hai-Liang Chen

    (Ltd.)

  • Yong Ye

    (Zhongwei Goat Breeding Center of Ningxia Province)

  • Hai-Dong Du

    (Zhongwei Goat Breeding Center of Ningxia Province)

  • Zhan-Qiang Zhao

    (Zhongwei Goat Breeding Center of Ningxia Province)

  • Xi-Jun Wang

    (Jiaxiang Animal Husbandry and Veterinary Development Center)

  • Shan-Gang Jia

    (China Agricultural University)

  • Zhi-Hong Liu

    (Inner Mongolia Agricultural University)

  • Meng-Hua Li

    (China Agricultural University)

Abstract

A complete goat (Capra hircus) reference genome enhances analyses of genetic variation, thus providing insights into domestication and selection in goats and related species. Here, we assemble a telomere-to-telomere (T2T) gap-free genome (2.86 Gb) from a cashmere goat (T2T-goat1.0), including a Y chromosome of 20.96 Mb. With a base accuracy of >99.999%, T2T-goat1.0 corrects numerous genome-wide structural and base errors in previous assemblies and adds 288.5 Mb of previously unresolved regions and 446 newly assembled genes to the reference genome. We sequence the genomes of five representative goat breeds for PacBio reads, and use T2T-goat1.0 as a reference to identify a total of 63,417 structural variations (SVs) with up to 4711 (7.42%) in the previously unresolved regions. T2T-goat1.0 was applied in population analyses of global wild and domestic goats, which revealed 32,419 SVs and 25,397,794 SNPs, including 870 SVs and 545,026 SNPs in the previously unresolved regions. Also, our analyses reveal a set of selective variants and genes associated with domestication (e.g., NKG2D and ABCC4) and cashmere traits (e.g., ABCC4 and ASIP).

Suggested Citation

  • Hui Wu & Ling-Yun Luo & Ya-Hui Zhang & Chong-Yan Zhang & Jia-Hui Huang & Dong-Xin Mo & Li-Ming Zhao & Zhi-Xin Wang & Yi-Chuan Wang & EEr He-Hua & Wen-Lin Bai & Di Han & Xing-Tang Dou & Yan-Ling Ren & , 2024. "Telomere-to-telomere genome assembly of a male goat reveals variants associated with cashmere traits," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-54188-z
    DOI: 10.1038/s41467-024-54188-z
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    References listed on IDEAS

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    1. Nick Patterson & Alkes L Price & David Reich, 2006. "Population Structure and Eigenanalysis," PLOS Genetics, Public Library of Science, vol. 2(12), pages 1-20, December.
    2. Arang Rhie & Sergey Nurk & Monika Cechova & Savannah J. Hoyt & Dylan J. Taylor & Nicolas Altemose & Paul W. Hook & Sergey Koren & Mikko Rautiainen & Ivan A. Alexandrov & Jamie Allen & Mobin Asri & And, 2023. "The complete sequence of a human Y chromosome," Nature, Nature, vol. 621(7978), pages 344-354, September.
    3. Kateryna D. Makova & Brandon D. Pickett & Robert S. Harris & Gabrielle A. Hartley & Monika Cechova & Karol Pal & Sergey Nurk & DongAhn Yoo & Qiuhui Li & Prajna Hebbar & Barbara C. McGrath & Francesca , 2024. "The complete sequence and comparative analysis of ape sex chromosomes," Nature, Nature, vol. 630(8016), pages 401-411, June.
    4. Christine Grossen & Frédéric Guillaume & Lukas F. Keller & Daniel Croll, 2020. "Purging of highly deleterious mutations through severe bottlenecks in Alpine ibex," Nature Communications, Nature, vol. 11(1), pages 1-12, December.
    5. Kanako Watanabe & Tomoichiro Oka & Hirotaka Takagi & Sergei Anisimov & Shun-ichi Yamashita & Yoshinori Katsuragi & Masahiko Takahashi & Masaya Higuchi & Tomotake Kanki & Akihiko Saitoh & Masahiro Fuji, 2023. "Myeloid-associated differentiation marker is an essential host factor for human parechovirus PeV-A3 entry," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    6. Andrea Guarracino & Silvia Buonaiuto & Leonardo Gomes Lima & Tamara Potapova & Arang Rhie & Sergey Koren & Boris Rubinstein & Christian Fischer & Jennifer L. Gerton & Adam M. Phillippy & Vincenza Colo, 2023. "Recombination between heterologous human acrocentric chromosomes," Nature, Nature, vol. 617(7960), pages 335-343, May.
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