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Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle.
Low, Wai Yee; Tearle, Rick; Liu, Ruijie; Koren, Sergey; Rhie, Arang; Bickhart, Derek M; Rosen, Benjamin D; Kronenberg, Zev N; Kingan, Sarah B; Tseng, Elizabeth; Thibaud-Nissen, Françoise; Martin, Fergal J; Billis, Konstantinos; Ghurye, Jay; Hastie, Alex R; Lee, Joyce; Pang, Andy W C; Heaton, Michael P; Phillippy, Adam M; Hiendleder, Stefan; Smith, Timothy P L; Williams, John L.
Afiliação
  • Low WY; The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia.
  • Tearle R; The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia.
  • Liu R; The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia.
  • Koren S; Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA.
  • Rhie A; Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA.
  • Bickhart DM; Dairy Forage Research Center, ARS USDA, Madison, WI, USA.
  • Rosen BD; Animal Genomics and Improvement Laboratory, ARS USDA, Beltsville, MD, USA.
  • Kronenberg ZN; Phase Genomics, 4000 Mason Road, Suite 225, Seattle, WA, 98195, USA.
  • Kingan SB; Pacific Biosciences, Menlo Park, CA, 94025, USA.
  • Tseng E; Pacific Biosciences, Menlo Park, CA, 94025, USA.
  • Thibaud-Nissen F; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
  • Martin FJ; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
  • Billis K; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
  • Ghurye J; Center for Bioinformatics and Computational Biology, Lab 3104A, Biomolecular Science Building, University of Maryland, College Park, MD, 20742, USA.
  • Hastie AR; Bionano Genomics, San Diego, CA, USA.
  • Lee J; Bionano Genomics, San Diego, CA, USA.
  • Pang AWC; Bionano Genomics, San Diego, CA, USA.
  • Heaton MP; US Meat Animal Research Center, ARS USDA, Clay Center, NE, USA.
  • Phillippy AM; Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA.
  • Hiendleder S; The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia. stefan.hiendleder@adelaide.edu.au.
  • Smith TPL; US Meat Animal Research Center, ARS USDA, Clay Center, NE, USA. tim.smith2@usda.gov.
  • Williams JL; The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia. john.williams01@adelaide.edu.au.
Nat Commun ; 11(1): 2071, 2020 04 29.
Article em En | MEDLINE | ID: mdl-32350247
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.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Variação Genética / Haplótipos / Bovinos / Genoma Limite: Animals Idioma: En Revista: Nat Commun Assunto da revista: BIOLOGIA / CIENCIA Ano de publicação: 2020 Tipo de documento: Article País de afiliação: Austrália
Texto completo
Adicionar na Minha BVS
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Variação Genética / Haplótipos / Bovinos / Genoma Limite: Animals Idioma: En Revista: Nat Commun Assunto da revista: BIOLOGIA / CIENCIA Ano de publicação: 2020 Tipo de documento: Article País de afiliação: Austrália