DeNovo assembly and annotation of the North American Bison (bison bison)reference genome and subsequent variant identification

Authors: DOBSON, LAUREN - Texas A&M University; DERR, JAMES - Texas A&M University; REECY, JAMES - Iowa State University; ZIMIN, ALEKSEY - University Of Maryland; BALNCHONG, JULIE - Iowa State University; Olsen, Steven; Alt, David; Bayles, Darrell; Smith, Timothy - Tim; FRITZ-WATERS, ERIC - Iowa State University; KONGANTI, KRANTI - Texas A&M University

Submitted to: Animal Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/4/2021
Publication Date: 3/29/2022
Citation: Dobson, L., Derr, J., Reecy, J., Zimin, A., Balnchong, J., Olsen, S.C., Alt, D.P., Bayles, D.O., Smith, T.P., Fritz-Waters, E., Konganti, K. 2022. DeNovo assembly and annotation of the North American Bison (bison bison)reference genome and subsequent variant identification. Animal Genetics. Animal Genetics Vol.52, Issue 3, pgs. 263-274. https://doi.org/10.1111/age.13060.
DOI: https://doi.org/10.1111/age.13060

Interpretive Summary: Brucellosis is an intracellular pathogen that causes zoonotic infections in people and is present in bison in Yellowstone National Park. Regulatory programs for brucellosis have been present for domestic livestock for almost 80 years. Differences in disease pathogenesis between bison and cattle has impacted development of intervention strategies to control brucellosis in bison. In this paper, we report the characteristics of the bison genome, including annotation, and compare it to other published species. This data allows understanding of how the genome is organized, helps identify targets for studying the unique physiology of bison, and provides a valuable tool to understand gene regulation in bison during infection. This data will be of interest to scientists interested in bison physiology and immunology, personnel with interests of genetic differences between species,regulatory personnel,people with responsibilities for management of brucellosis in bison,private owners of bison, and other parties with interests regarding bison management.

Technical Abstract: Genomic tools have improved the ability to manage bison populations and enhanced efforts to conserve this iconic species. While these tools have been very useful for detecting introgression of cattle genome withing bison herds, they are limited by the need to use the cattle genome as a surrogate for mapping reads. This complicates efforts to distinguish the species of origin of chromosomal segments in individual bison at the genomic level. As assembly based on a total of 75X genome coverage was generated using the MaSuRCA assembler to generate a 2.81 Gigabases de novo reference genome from American bison. Comparison of the bison and domestic cattle reference assemblies identified 28,443,364 single nucleotide variants and 2,627,645 insertions/deletions distinguishing the species. Sequence alignment of an additional twelve modern bison samples and two historic bison samples to the domestic cattle and bison reference genomes provide a dataset of genomic variants defining the different species, and within species variation. The annotated draft assembly represents a resource for management and conservation of bison, as well as a means to study the effects on the genome of inter-species hybridization. The assembly and population data represent a resource for management and conservation of bison based on the genomic variation data set. The comparisons of historical bison sequences to this new bison reference identified genomic differences between modern and pre-population bottleneck bison. The results support application of genomics to enhance future research on disease, establishment of satellite conservation herds, and insight into the bison and cattle speciation.