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A cattle graph genome incorporating global breed diversity

Author

Listed:
  • A. Talenti

    (University of Edinburgh, Easter Bush Campus)

  • J. Powell

    (University of Edinburgh, Easter Bush Campus)

  • J. D. Hemmink

    (University of Edinburgh, Easter Bush Campus
    The International Livestock Research Institute
    Centre for Tropical Livestock Genetics and Health, Easter Bush
    Centre for Tropical Livestock Genetics and Health, ILRI Kenya)

  • E. A. J. Cook

    (The International Livestock Research Institute
    Centre for Tropical Livestock Genetics and Health, ILRI Kenya)

  • D. Wragg

    (University of Edinburgh, Easter Bush Campus
    Centre for Tropical Livestock Genetics and Health, Easter Bush)

  • S. Jayaraman

    (University of Edinburgh, Easter Bush Campus)

  • E. Paxton

    (University of Edinburgh, Easter Bush Campus)

  • C. Ezeasor

    (University of Nigeria)

  • E. T. Obishakin

    (National Veterinary Research Institute
    Biomedical Research Centre, Ghent University Global Campus, Songdo)

  • E. R. Agusi

    (National Veterinary Research Institute
    Biomedical Research Centre, Ghent University Global Campus, Songdo)

  • A. Tijjani

    (International Livestock Research Institute (ILRI) PO
    Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Ethiopia)

  • W. Amanyire

    (Makerere University)

  • D. Muhanguzi

    (Makerere University)

  • K. Marshall

    (The International Livestock Research Institute
    Centre for Tropical Livestock Genetics and Health, ILRI Kenya)

  • A. Fisch

    (University of Sao Paulo)

  • B. R. Ferreira

    (University of Sao Paulo)

  • A. Qasim

    (Gomal University)

  • U. Chaudhry

    (University of Edinburgh, Easter Bush Campus)

  • P. Wiener

    (University of Edinburgh, Easter Bush Campus)

  • P. Toye

    (The International Livestock Research Institute
    Centre for Tropical Livestock Genetics and Health, ILRI Kenya)

  • L. J. Morrison

    (University of Edinburgh, Easter Bush Campus
    Centre for Tropical Livestock Genetics and Health, Easter Bush)

  • T. Connelley

    (University of Edinburgh, Easter Bush Campus
    Centre for Tropical Livestock Genetics and Health, Easter Bush)

  • J. G. D. Prendergast

    (University of Edinburgh, Easter Bush Campus
    Centre for Tropical Livestock Genetics and Health, Easter Bush)

Abstract

Despite only 8% of cattle being found in Europe, European breeds dominate current genetic resources. This adversely impacts cattle research in other important global cattle breeds, especially those from Africa for which genomic resources are particularly limited, despite their disproportionate importance to the continent’s economies. To mitigate this issue, we have generated assemblies of African breeds, which have been integrated with genomic data for 294 diverse cattle into a graph genome that incorporates global cattle diversity. We illustrate how this more representative reference assembly contains an extra 116.1 Mb (4.2%) of sequence absent from the current Hereford sequence and consequently inaccessible to current studies. We further demonstrate how using this graph genome increases read mapping rates, reduces allelic biases and improves the agreement of structural variant calling with independent optical mapping data. Consequently, we present an improved, more representative, reference assembly that will improve global cattle research.

Suggested Citation

  • A. Talenti & J. Powell & J. D. Hemmink & E. A. J. Cook & D. Wragg & S. Jayaraman & E. Paxton & C. Ezeasor & E. T. Obishakin & E. R. Agusi & A. Tijjani & W. Amanyire & D. Muhanguzi & K. Marshall & A. F, 2022. "A cattle graph genome incorporating global breed diversity," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-28605-0
    DOI: 10.1038/s41467-022-28605-0
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    References listed on IDEAS

    as
    1. Francesco Vezzi & Giuseppe Narzisi & Bud Mishra, 2012. "Feature-by-Feature – Evaluating De Novo Sequence Assembly," PLOS ONE, Public Library of Science, vol. 7(2), pages 1-12, February.
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    4. Prasun Dutta & Andrea Talenti & Rachel Young & Siddharth Jayaraman & Rebecca Callaby & Santosh Kumar Jadhav & Velu Dhanikachalam & Mayakannan Manikandan & Bhim B. Biswa & Wai Y. Low & John L. Williams, 2020. "Whole genome analysis of water buffalo and global cattle breeds highlights convergent signatures of domestication," Nature Communications, Nature, vol. 11(1), pages 1-13, December.
    5. 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.
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    Cited by:

    1. Xinfeng Liu & Wenyu Liu & Johannes A. Lenstra & Zeyu Zheng & Xiaoyun Wu & Jiao Yang & Bowen Li & Yongzhi Yang & Qiang Qiu & Hongyu Liu & Kexin Li & Chunnian Liang & Xian Guo & Xiaoming Ma & Richard J., 2023. "Evolutionary origin of genomic structural variations in domestic yaks," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    2. Alexander S. Leonard & Danang Crysnanto & Zih-Hua Fang & Michael P. Heaton & Brian L. Vander Ley & Carolina Herrera & Heinrich Bollwein & Derek M. Bickhart & Kristen L. Kuhn & Timothy P. L. Smith & Be, 2022. "Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies," Nature Communications, Nature, vol. 13(1), pages 1-13, December.

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