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

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. Martin, Konstantinos Billis, Jay Ghurye, Alex R. Hastie, Joyce Lee, Andy W. C. Pang, Michael P. Heaton, Adam M. Phillippy, Stefan Hiendleder (), Timothy P. L. Smith () and John L. Williams ()
Additional contact information
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

Nature Communications, 2020, vol. 11, issue 1, 1-14

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41467-020-15848-y

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