A Reference Genome Assembly of Simmental Cattle, Bos taurus taurus

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

doi:10.1093/jhered/esab002

A Reference Genome Assembly of Simmental Cattle, Bos taurus taurus

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

Veterinary Science

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

12 Scopus citations

Abstract

Genomics research has relied principally on the establishment and curation of a reference genome for the species. However, it is increasingly recognized that a single reference genome cannot fully describe the extent of genetic variation within many widely distributed species. Pangenome representations are based on high-quality genome assemblies of multiple individuals and intended to represent the broadest possible diversity within a species. A Bovine Pangenome Consortium (BPC) has recently been established to begin assembling genomes from more than 600 recognized breeds of cattle, together with other related species to provide information on ancestral alleles and haplotypes. Previously reported de novo genome assemblies for Angus, Brahman, Hereford, and Highland breeds of cattle are part of the initial BPC effort. The present report describes a complete single haplotype assembly at chromosome-scale for a fullblood Simmental cow from an F1 bison-cattle hybrid fetus by trio binning. Simmental cattle, also known as Fleckvieh due to their red and white spots, originated in central Europe in the 1830s as a triple-purpose breed selected for draught, meat, and dairy production. There are over 50 million Simmental cattle in the world, known today for their fast growth and beef yields. This assembly (ARS-Simm1.0) is similar in length to the other bovine assemblies at 2.86 Gb, with a scaffold N50 of 102 Mb (max scaffold 156.8 Mb) and meets or exceeds the continuity of the best Bos taurus reference assemblies to date.

Original language	English
Pages (from-to)	184-191
Number of pages	8
Journal	Journal of Heredity
Volume	112
Issue number	2
DOIs	https://doi.org/10.1093/jhered/esab002
State	Published - Mar 1 2021

Bibliographical note

Funding Information:
U.S. Department of Agriculture, Agricultural Research Service appropriated projects (3040-31000-100-00D to T.P.L.S. and L.A.K., and 5438-32000-034-00D to M.P.H.); The University of Nebraska Great Plains Veterinary Educational Center project (2162390003 to B.L.V.L.); the Nebraska Beef Industry Endowment (2662390323001 to B.L.V.L.); USDA, ARS appropriated project (5090-31000-026- 00D to D.M.B. and J.C.M.); National Institutes of Health (T32 HG008345-01 to J.O.); U.S. National Science Foundation (DEB- 1754451 to B.S. and J.O.). The reproductive and animal husbandry portions of the project were supported by the American Simmental Association.

Publisher Copyright:
© 2021 Published by Oxford University Press.

Keywords

F1 hybrid
Fleckvieh
bison
nanopore
pangenome
trio binning

ASJC Scopus subject areas

Medicine (all)

Access to Document

10.1093/jhered/esab002

Cite this

Heaton, M. P., Smith, T. P. L., Bickhart, D. M., Vander Ley, B. L., Kuehn, L. A., Oppenheimer, J., Shafer, W. R., Schuetze, F. T., Stroud, B., Mcclure, J. C., Barfield, J. P., Blackburn, H. D., Kalbfleisch, T. S., Davenport, K. M., Kuhn, K. L., Green, R. E., Shapiro, B., & Rosen, B. D. (2021). A Reference Genome Assembly of Simmental Cattle, Bos taurus taurus. Journal of Heredity, 112(2), 184-191. https://doi.org/10.1093/jhered/esab002

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title = "A Reference Genome Assembly of Simmental Cattle, Bos taurus taurus",

abstract = "Genomics research has relied principally on the establishment and curation of a reference genome for the species. However, it is increasingly recognized that a single reference genome cannot fully describe the extent of genetic variation within many widely distributed species. Pangenome representations are based on high-quality genome assemblies of multiple individuals and intended to represent the broadest possible diversity within a species. A Bovine Pangenome Consortium (BPC) has recently been established to begin assembling genomes from more than 600 recognized breeds of cattle, together with other related species to provide information on ancestral alleles and haplotypes. Previously reported de novo genome assemblies for Angus, Brahman, Hereford, and Highland breeds of cattle are part of the initial BPC effort. The present report describes a complete single haplotype assembly at chromosome-scale for a fullblood Simmental cow from an F1 bison-cattle hybrid fetus by trio binning. Simmental cattle, also known as Fleckvieh due to their red and white spots, originated in central Europe in the 1830s as a triple-purpose breed selected for draught, meat, and dairy production. There are over 50 million Simmental cattle in the world, known today for their fast growth and beef yields. This assembly (ARS-Simm1.0) is similar in length to the other bovine assemblies at 2.86 Gb, with a scaffold N50 of 102 Mb (max scaffold 156.8 Mb) and meets or exceeds the continuity of the best Bos taurus reference assemblies to date.",

keywords = "F1 hybrid, Fleckvieh, bison, nanopore, pangenome, trio binning",

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

note = "Funding Information: U.S. Department of Agriculture, Agricultural Research Service appropriated projects (3040-31000-100-00D to T.P.L.S. and L.A.K., and 5438-32000-034-00D to M.P.H.); The University of Nebraska Great Plains Veterinary Educational Center project (2162390003 to B.L.V.L.); the Nebraska Beef Industry Endowment (2662390323001 to B.L.V.L.); USDA, ARS appropriated project (5090-31000-026- 00D to D.M.B. and J.C.M.); National Institutes of Health (T32 HG008345-01 to J.O.); U.S. National Science Foundation (DEB- 1754451 to B.S. and J.O.). The reproductive and animal husbandry portions of the project were supported by the American Simmental Association. Publisher Copyright: {\textcopyright} 2021 Published by Oxford University Press.",

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Heaton, MP, Smith, TPL, Bickhart, DM, Vander Ley, BL, Kuehn, LA, Oppenheimer, J, Shafer, WR, Schuetze, FT, Stroud, B, Mcclure, JC, Barfield, JP, Blackburn, HD, Kalbfleisch, TS, Davenport, KM, Kuhn, KL, Green, RE, Shapiro, B & Rosen, BD 2021, 'A Reference Genome Assembly of Simmental Cattle, Bos taurus taurus', Journal of Heredity, vol. 112, no. 2, pp. 184-191. https://doi.org/10.1093/jhered/esab002

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AU - Heaton, Michael P.

AU - Smith, Timothy P.L.

AU - Bickhart, Derek M.

AU - Vander Ley, Brian L.

AU - Kuehn, Larry A.

AU - Oppenheimer, Jonas

AU - Shafer, Wade R.

AU - Schuetze, Fred T.

AU - Stroud, Brad

AU - Mcclure, Jennifer C.

AU - Barfield, Jennifer P.

AU - Blackburn, Harvey D.

AU - Kalbfleisch, Theodore S.

AU - Davenport, Kimberly M.

AU - Kuhn, Kristen L.

AU - Green, Richard E.

AU - Shapiro, Beth

AU - Rosen, Benjamin D.

N1 - Funding Information: U.S. Department of Agriculture, Agricultural Research Service appropriated projects (3040-31000-100-00D to T.P.L.S. and L.A.K., and 5438-32000-034-00D to M.P.H.); The University of Nebraska Great Plains Veterinary Educational Center project (2162390003 to B.L.V.L.); the Nebraska Beef Industry Endowment (2662390323001 to B.L.V.L.); USDA, ARS appropriated project (5090-31000-026- 00D to D.M.B. and J.C.M.); National Institutes of Health (T32 HG008345-01 to J.O.); U.S. National Science Foundation (DEB- 1754451 to B.S. and J.O.). The reproductive and animal husbandry portions of the project were supported by the American Simmental Association. Publisher Copyright: © 2021 Published by Oxford University Press.

PY - 2021/3/1

Y1 - 2021/3/1

N2 - Genomics research has relied principally on the establishment and curation of a reference genome for the species. However, it is increasingly recognized that a single reference genome cannot fully describe the extent of genetic variation within many widely distributed species. Pangenome representations are based on high-quality genome assemblies of multiple individuals and intended to represent the broadest possible diversity within a species. A Bovine Pangenome Consortium (BPC) has recently been established to begin assembling genomes from more than 600 recognized breeds of cattle, together with other related species to provide information on ancestral alleles and haplotypes. Previously reported de novo genome assemblies for Angus, Brahman, Hereford, and Highland breeds of cattle are part of the initial BPC effort. The present report describes a complete single haplotype assembly at chromosome-scale for a fullblood Simmental cow from an F1 bison-cattle hybrid fetus by trio binning. Simmental cattle, also known as Fleckvieh due to their red and white spots, originated in central Europe in the 1830s as a triple-purpose breed selected for draught, meat, and dairy production. There are over 50 million Simmental cattle in the world, known today for their fast growth and beef yields. This assembly (ARS-Simm1.0) is similar in length to the other bovine assemblies at 2.86 Gb, with a scaffold N50 of 102 Mb (max scaffold 156.8 Mb) and meets or exceeds the continuity of the best Bos taurus reference assemblies to date.

AB - Genomics research has relied principally on the establishment and curation of a reference genome for the species. However, it is increasingly recognized that a single reference genome cannot fully describe the extent of genetic variation within many widely distributed species. Pangenome representations are based on high-quality genome assemblies of multiple individuals and intended to represent the broadest possible diversity within a species. A Bovine Pangenome Consortium (BPC) has recently been established to begin assembling genomes from more than 600 recognized breeds of cattle, together with other related species to provide information on ancestral alleles and haplotypes. Previously reported de novo genome assemblies for Angus, Brahman, Hereford, and Highland breeds of cattle are part of the initial BPC effort. The present report describes a complete single haplotype assembly at chromosome-scale for a fullblood Simmental cow from an F1 bison-cattle hybrid fetus by trio binning. Simmental cattle, also known as Fleckvieh due to their red and white spots, originated in central Europe in the 1830s as a triple-purpose breed selected for draught, meat, and dairy production. There are over 50 million Simmental cattle in the world, known today for their fast growth and beef yields. This assembly (ARS-Simm1.0) is similar in length to the other bovine assemblies at 2.86 Gb, with a scaffold N50 of 102 Mb (max scaffold 156.8 Mb) and meets or exceeds the continuity of the best Bos taurus reference assemblies to date.

KW - F1 hybrid

KW - Fleckvieh

KW - bison

KW - nanopore

KW - pangenome

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A Reference Genome Assembly of Simmental Cattle, Bos taurus taurus

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

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