A Reference Genome Assembly of American Bison, Bison bison bison

Authors

Jonas Oppenheimer, University of California, Santa CruzFollow
Benjamin D. Rosen, USDA ARS Beltsville Agricultural Research CenterFollow
Michael P. Heaton, USDA ARS Roman L. Hruska U.S. Meat Animal Research CenterFollow
Brian L. Vander Ley, University of Nebraska–Lincoln
Wade R. Shafer, American Simmental Association
Fred T. Schuetze, Simmentals of Texas
Brad Stroud, Stroud Veterinary Embryo Services
Larry A. Kuehn, USDA ARS Roman L. Hruska U.S. Meat Animal Research Center
Jennifer C. Mcclure, USDA ARS U.S. Dairy Forage Research Center
Jennifer P. Barfield, Colorado State University
Harvey D. Blackburn, USDA Agricultural Research Service
Theodore S. Kalbfleisch, University of Kentucky
Derek M. Bickhart, USDA ARS U.S. Dairy Forage Research Center
Kimberly M. Davenport, University of Idaho
Kristen L. Kuhn, USDA ARS Roman L. Hruska U.S. Meat Animal Research Center
Richard E. Green, University of California, Santa Cruz
Beth Shapiro, University of California, Santa Cruz
Timothy P.L. Smith, USDA ARS Roman L. Hruska U.S. Meat Animal Research Center

Date of this Version

3-1-2021

Document Type

Article

Citation

Journal of Heredity, 2021, 174–183

doi:10.1093/jhered/esab003

Comments

This is an Open Access article distributed under the terms of the Creative Commons Attribution License

Abstract

Bison are an icon of the American West and an ecologically, commercially, and culturally important species. Despite numbering in the hundreds of thousands today, conservation concerns remain for the species, including the impact on genetic diversity of a severe bottleneck around the turn of the 20th century and genetic introgression from domestic cattle. Genetic diversity and admixture are best evaluated at genome-wide scale, for which a high-quality reference is necessary. Here, we use trio binning of long reads from a bison-Simmental cattle (Bos taurus taurus) male F1 hybrid to sequence and assemble the genome of the American plains bison (Bison bison bison). The male haplotype genome is chromosome-scale, with a total length of 2.65 Gb across 775 scaffolds (839 contigs) and a scaffold N50 of 87.8 Mb. Our bison genome is ∼13× more contiguous overall and ∼3400× more contiguous at the contig level than the current bison reference genome. The bison genome sequence presented here (ARS-UCSC-bison1.0) will enable new research into the evolutionary history of this iconic megafauna species and provide a new tool for the management of bison populations in federal and commercial herds.