A Reference Genome Assembly of American Bison, Bison bison bison

Jonas Oppenheimer; Benjamin D. Rosen; Michael P. Heaton; Brian L. Vander Ley; Wade R. Shafer; Fred T. Schuetze; Brad Stroud; Larry A. Kuehn; Jennifer C. Mcclure; Jennifer P. Barfield; Harvey D. Blackburn; Theodore S. Kalbfleisch; Derek M. Bickhart; Kimberly M. Davenport; Kristen L. Kuhn; Richard E. Green; Beth Shapiro; Timothy P.L. Smith

doi:10.1093/jhered/esab003

A Reference Genome Assembly of American Bison, Bison bison bison

Jonas Oppenheimer, Benjamin D. Rosen, Michael P. Heaton, Brian L. Vander Ley, Wade R. Shafer, Fred T. Schuetze, Brad Stroud, Larry A. Kuehn, Jennifer C. Mcclure, Jennifer P. Barfield, Harvey D. Blackburn, Theodore S. Kalbfleisch, Derek M. Bickhart, Kimberly M. Davenport, Kristen L. Kuhn, Richard E. Green, Beth Shapiro, Timothy P.L. Smith

Research output: Contribution to journal › Article › peer-review

15 Scopus citations

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.

Original language	English
Pages (from-to)	174-183
Number of pages	10
Journal	Journal of Heredity
Volume	112
Issue number	2
DOIs	https://doi.org/10.1093/jhered/esab003
State	Published - Mar 1 2021

Bibliographical note

Publisher Copyright:
© 2021 The American Genetic Association.

Funding

J.O. was supported by the National Institutes of Health (T32 HG008345-01) and B.S. and J.O. were supported by the U.S. National Science Foundation (DEB-1754451). Funding for this research was provided by the USDA, ARS-appropriated projects 3040-31000-100-00D (T.P.L.S. and L.A.K.) and 5438-32000-034- 00D (M.P.H.), The University of Nebraska Great Plains Veterinary Educational Center project 2162390003 (B.L.V.L.) and the Nebraska Beef Industry Endowment 2662390323001 (B.L.V.L.). The reproductive and animal husbandry portions of the project were supported by the American Simmental Association. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Funders	Funder number
American Simmental Association
Nebraska Beef Industry Endowment	2662390323001
University of Nebraska Great Plains Veterinary Educational Center	2162390003
National Science Foundation Arctic Social Science Program	DEB-1754451
National Science Foundation Arctic Social Science Program
National Institutes of Health (NIH)
National Human Genome Research Institute	T32HG008345
National Human Genome Research Institute
U.S. Department of Agriculture	3040-31000-100-00D, 5438-32000-034- 00D
U.S. Department of Agriculture

Keywords

Genome resources
bovine
interspecies hybrid
nanopore sequencing
trio binning

ASJC Scopus subject areas

General Medicine

Access to Document

10.1093/jhered/esab003

Cite this

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

@article{75fe67d55fdb4d8b88291e402231b242,

title = "A Reference Genome Assembly of American Bison, Bison bison bison",

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.",

keywords = "Genome resources, bovine, interspecies hybrid, nanopore sequencing, trio binning",

author = "Jonas Oppenheimer and Rosen, {Benjamin D.} and Heaton, {Michael P.} and {Vander Ley}, {Brian L.} and Shafer, {Wade R.} and Schuetze, {Fred T.} and Brad Stroud and Kuehn, {Larry A.} and Mcclure, {Jennifer C.} and Barfield, {Jennifer P.} and Blackburn, {Harvey D.} and Kalbfleisch, {Theodore S.} and Bickhart, {Derek M.} and Davenport, {Kimberly M.} and Kuhn, {Kristen L.} and Green, {Richard E.} and Beth Shapiro and Smith, {Timothy P.L.}",

note = "Publisher Copyright: {\textcopyright} 2021 The American Genetic Association.",

year = "2021",

month = mar,

day = "1",

doi = "10.1093/jhered/esab003",

language = "English",

volume = "112",

pages = "174--183",

number = "2",

}

Oppenheimer, J, Rosen, BD, Heaton, MP, Vander Ley, BL, Shafer, WR, Schuetze, FT, Stroud, B, Kuehn, LA, Mcclure, JC, Barfield, JP, Blackburn, HD, Kalbfleisch, TS, Bickhart, DM, Davenport, KM, Kuhn, KL, Green, RE, Shapiro, B & Smith, TPL 2021, 'A Reference Genome Assembly of American Bison, Bison bison bison', Journal of Heredity, vol. 112, no. 2, pp. 174-183. https://doi.org/10.1093/jhered/esab003

TY - JOUR

T1 - A Reference Genome Assembly of American Bison, Bison bison bison

AU - Oppenheimer, Jonas

AU - Rosen, Benjamin D.

AU - Heaton, Michael P.

AU - Vander Ley, Brian L.

AU - Shafer, Wade R.

AU - Schuetze, Fred T.

AU - Stroud, Brad

AU - Kuehn, Larry A.

AU - Mcclure, Jennifer C.

AU - Barfield, Jennifer P.

AU - Blackburn, Harvey D.

AU - Kalbfleisch, Theodore S.

AU - Bickhart, Derek M.

AU - Davenport, Kimberly M.

AU - Kuhn, Kristen L.

AU - Green, Richard E.

AU - Shapiro, Beth

AU - Smith, Timothy P.L.

PY - 2021/3/1

Y1 - 2021/3/1

N2 - 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.

AB - 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.

KW - Genome resources

KW - bovine

KW - interspecies hybrid

KW - nanopore sequencing

KW - trio binning

UR - http://www.scopus.com/inward/record.url?scp=85103683107&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85103683107&partnerID=8YFLogxK

U2 - 10.1093/jhered/esab003

DO - 10.1093/jhered/esab003

M3 - Article

C2 - 33595645

AN - SCOPUS:85103683107

SN - 0022-1503

VL - 112

SP - 174

EP - 183

JO - Journal of Heredity

JF - Journal of Heredity

IS - 2

ER -

A Reference Genome Assembly of American Bison, Bison bison bison

Abstract

Bibliographical note

Funding

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this