Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation
Year: 2019
Type: preprint
Abstract: We present high quality, phased genome assemblies representative of taurine and indicine cattle, subspecies that differ markedly in productivity-related traits and environmental adaptation. We report a new haplotype-aware scaffolding and polishing pipeline using contigs generated by the trio binning method to produce haplotype-resolved, chromosome-level genome assemblies of Angus (taurine) and Brahman (indicine) cattle breeds. These assemblies were used to identify structural and copy number variants that differentiate the subspecies and we found variant detection was sensitive to the specific reference genome chosen. Six gene families with immune related functions are expanded in the indicine lineage. Assembly of the genomes of both subspecies from a single individual enabled transcripts to be phased to detect allele-specific expression, and to study genome-wide selective sweeps. An indicus-specific extra copy of fatty acid desaturase is under positive selection and may contribute to indicine adaptation to heat and drought.
DOI: 10.1101/720797
Authors: 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, John L. Williams
Institutions: The University of Adelaide, National Institutes of Health, National Human Genome Research Institute, U.S. Dairy Forage Research Center, Agricultural Research Service, Pacific Biosciences (United States), National Center for Biotechnology Information, European Bioinformatics Institute, University of Maryland, College Park, BioNano Genomics (United States), Roman L. Hruska U.S. Meat Animal Research Center
Language: English
Subfield: Genetics
Domain: Life Sciences
SDG: Zero hunger
Open Access status: green
OpenAlex ID: W2965490818