A reference genome assembly of American bison, Bison bison bison

Authors: OPPENHEIMER, JONAS - University Of California Santa Cruz; Rosen, Benjamin - Ben; Heaton, Michael - Mike; VANDER LEY, BRIAN - University Of Nebraska; SHAFER, WADE - American Simmental Association; SCHUETZE, FRED - Simmentals Of Texas; STROUD, BRAD - Stroud Veterinary Embryo Services; Kuehn, Larry; McClure, Jennifer; BARFIELD, JENNIFER - Colorado State University; Blackburn, Harvey; KALBFLEISCH, THEODORE - University Of Kentucky; Bickhart, Derek; DAVENPORT, KIMBERLY - University Of Idaho; Kuhn, Kristen; GREEN, RICHARD - University Of California Santa Cruz; SHAPIRO, BETH - University Of California Santa Cruz; Smith, Timothy - Tim

Submitted to: Journal of Heredity
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/2/2021
Publication Date: 3/1/2021
Citation: Oppenheimer, J., Rosen, B.D., Heaton, M.P., Vander Ley, B.L., Shafer, W.R., Schuetze, F.T., Stroud, B., Kuehn, L.A., McClure, J.C., Barfield, J.P., Blackburn, H.D., Kalbfleisch, T.S., Bickhart, D.M., Davenport, K.M., Kuhn, K.L., Green, R.E., Shapiro, B., Smith, T.P.L. 2021. A reference genome assembly of American bison, Bison bison bison. Journal of Heredity. 112(2):174-183. https://doi.org/10.1093/jhered/esab003.
DOI: https://doi.org/10.1093/jhered/esab003

Interpretive Summary: The plains bison of the American West are of important cultural, economic, and ecological interest. Bison and bison-cattle hybrids are also used for meat in the U.S. with different flavor, leanness, and production characteristics. Despite numbering in the hundreds of thousands today, conservation concerns remain for bison, including their genetic diversity. This was caused by severe species bottleneck that occurred at the turn of the 20th century in combination with beef cattle interbreeding. A high-quality reference genome for bison would advance the study of bison evolutionary history, as well as provide new genetic tools and information for effectively managing bison populations for conservation and commercial production. Furthermore, comparative studies of the bison and cattle genomes are expected to provide insights into the genes involved in domestication and potentially behavior in cattle breeds, as well as providing a basis for interpreting historical selection effects in cattle breeds. The present report describes the genome assembly of a Yellowstone bison bull from an F1 bison-cattle hybrid fetus in a process called “trio binning”, that results in an improved product compared to sequencing a purebred bison individual. The quality of this genome meets or exceeds that of the best vertebrate assemblies to date. This approach allows reference assemblies to be readily produced for related bovid species and would pave the way for understanding functional genetic differences between modern and ancient bison species.

Technical 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 ~13x more contiguous overall and ~3400x 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.