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Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle

Author

Listed:
  • Wai Yee Low

    (University of Adelaide)

  • Rick Tearle

    (University of Adelaide)

  • Ruijie Liu

    (University of Adelaide)

  • Sergey Koren

    (National Human Genome Research Institute)

  • Arang Rhie

    (National Human Genome Research Institute)

  • Derek M. Bickhart

    (ARS USDA)

  • Benjamin D. Rosen

    (ARS USDA)

  • Zev N. Kronenberg

    (Phase Genomics)

  • Sarah B. Kingan

    (Pacific Biosciences)

  • Elizabeth Tseng

    (Pacific Biosciences)

  • Françoise Thibaud-Nissen

    (National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health)

  • Fergal J. Martin

    (European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus)

  • Konstantinos Billis

    (European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus)

  • Jay Ghurye

    (University of Maryland)

  • Alex R. Hastie

    (Bionano Genomics)

  • Joyce Lee

    (Bionano Genomics)

  • Andy W. C. Pang

    (Bionano Genomics)

  • Michael P. Heaton

    (ARS USDA)

  • Adam M. Phillippy

    (National Human Genome Research Institute)

  • Stefan Hiendleder

    (University of Adelaide)

  • Timothy P. L. Smith

    (ARS USDA)

  • John L. Williams

    (University of Adelaide)

Abstract

Inbred animals were historically chosen for genome analysis to circumvent assembly issues caused by haplotype variation but this resulted in a composite of the two genomes. Here we report a haplotype-aware scaffolding and polishing pipeline which was used to create haplotype-resolved, chromosome-level genome assemblies of Angus (taurine) and Brahman (indicine) cattle subspecies from contigs generated by the trio binning method. These assemblies reveal structural and copy number variants that differentiate the subspecies and that variant detection is sensitive to the specific reference genome chosen. Six genes with immune related functions have additional copies in the indicine compared with taurine lineage and an indicus-specific extra copy of fatty acid desaturase is under positive selection. The haplotyped genomes also enable transcripts to be phased to detect allele-specific expression. This work exemplifies the value of haplotype-resolved genomes to better explore evolutionary and functional variations.

Suggested Citation

  • Wai Yee Low & Rick Tearle & Ruijie Liu & Sergey Koren & Arang Rhie & Derek M. Bickhart & Benjamin D. Rosen & Zev N. Kronenberg & Sarah B. Kingan & Elizabeth Tseng & Françoise Thibaud-Nissen & Fergal J, 2020. "Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-15848-y
    DOI: 10.1038/s41467-020-15848-y
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    Cited by:

    1. 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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