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De novo assembly of the cattle reference genome with single-molecule sequencing
Open accessAbstract
BACKGROUND: Major advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10-12 years. These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies. RESULTS: We present the new reference genome for cattle, ARS-UCD1.2, based on the same animal as the original to facilitate transfer and interpretation of results obtained from the earlier version, but applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly includes 2.7 Gb and is >250× more continuous than the original assembly, with contig N50 >25 Mb and L50 of 32. We also greatly expanded supporting RNA-based data for annotation that identifies 30,396 total genes (21,039 protein coding). The new reference assembly is accessible in annotated form for public use. CONCLUSIONS: We demonstrate that improved continuity of assembled sequence warrants the adoption of ARS-UCD1.2 as the new cattle reference genome and that increased assembly accuracy will benefit future research on this species.
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“Traditional genomic studies have heavily relied on a single linear reference genome [180], such as ARS-UCD1.2, which is derived from an individual of a specific taurine breed, Hereford [181] (Table 3).”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [181]
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Metadata
- Authors
- Rosen, B. D., Bickhart, D. M., Schnabel, R. D., Koren, S., Elsik, C. G., Tseng, E., Rowan, T. N., Low, W. Y., Zimin, A., Couldrey, C., Hall, R., Li, W., Rhie, A., Ghurye, J., McKay, S. D., Thibaud-Nissen, F., Hoffman, J., Murdoch, B. M., Snelling, W. M., McDaneld, T. G., Hammond, J. A., Schwartz, J. C., Nandolo, W., Hagen, D. E., Dreischer, C., Schultheiss, S. J., Schroeder, S. G., Phillippy, A. M., Cole, J. B., Van Tassell, C. P., Liu, G., Smith, T. P. L., & Medrano, J. F.
- Affiliations
- Agricultural Research Service (US)
- University of Missouri (US)
- National Institutes of Health (US)
- Pacific Biosciences (United States) (US)
- The University of Adelaide (AU)
- Johns Hopkins University (US)
- Livestock Improvement Corporation (NZ)
- University of Maryland, College Park (US)
- University of Vermont (US)
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health , Bethesda, MD 20894,
- University of Idaho (US)
- The Pirbright Institute (GB)
- Lilongwe University of Agriculture and Natural Resources (MW)
- Oklahoma State University (US)
- Computomics GmbH , Christophstr. 32, 72072 Tübingen,
- USDA-ARS, Beltsville, MD, 20705-2350 , Animal Genomics and Improvement Laboratory , USDA-ARS, 10300 Baltimore Ave, Beltsville, MD 20705-2350,
- University of California, Davis (US)
- Corresponding author
- Rosen, Benjamin D
- Smith, Timothy P L
- ORCID
- Rosen, Benjamin D
- Bickhart, Derek M
- Schnabel, Robert D
- Koren, Sergey
- Elsik, Christine G
- Tseng, Elizabeth
- Rowan, Troy N
- Low, Wai Y
- Zimin, Aleksey
- Couldrey, Christine
- Hall, Richard
- Li, Wenli
- Rhie, Arang
- Ghurye, Jay
- McKay, Stephanie D
- Murdoch, Brenda M
- Snelling, Warren M
- McDaneld, Tara G
- Hammond, John A
- Schwartz, John C
- Nandolo, Wilson
- Hagen, Darren E
- Schultheiss, Sebastian J
- Schroeder, Steven G
- Phillippy, Adam M
- Cole, John B
- Van Tassell, Curtis P
- Liu, George
- Smith, Timothy P L
- Medrano, Juan F
- Venue
- GigaScience
- Publisher
- Oxford University Press (OUP)
- Published
- 2020-03-01
- Volume
- 9
- Issue
- 3
- ISSN
- 2047-217X (ISSN-L)
- PMC
- PMC7081964
- OpenAlex
- W3011183076
- Cited by
- 802
- References
- 35
- Citations by year
- 2026: 84 · 2025: 102 · 2024: 165 · 2023: 145 · 2022: 125 · 2021: 120 · 2020: 59
- FWCI
- 37.47
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- GigaScience (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Funders
- U.S. Department of Agriculture (8042-31000-001-00-D, 8042-31000-002-00-D, 5090-31000-026-00-D, 3040-31000-100-00-D)
- National Institute of Food and Agriculture (5090-31000-026-06-I, 2016-68004-24827, 2013-67015-21202, MO-HAAS0001, 2015-67015-23183)
- U.S. National Library of Medicine
- National Institutes of Health
- Biotechnology and Biological Sciences Research Council (BB/M027155/1, BBS/E/I/00007035, BBS/E/I/00007038, BBS/E/I/00007039)
- National Human Genome Research Institute
- Korea Health Industry Development Institute
- Ministry of Health (HI17C2098)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- cattle, de novo genome assembly, single-molecule sequencing, genome annotation, cattle genomics
- MeSH terms
- RNA-Seq, Animals, Breeding, Cattle, Polymorphism, Genetic, Reference Standards, Genome, Sequence Analysis, DNA, Genomics
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