The DOI matches its Crossref record; 32 of the 35 references it cites were found in a registry or an index, and 1 are not checked yet.
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 These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies.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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Cites
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A cattle graph genome incorporating global breed diversity
Talenti, A., Powell, J., Hemmink, J. D., Cook, E. A. J., Wragg, D., Jayaraman, S., Paxton, E. A., Ezeasor, C., Obishakin, E., Agusi, E. R., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28605-0 · Cited by 109
Novel Functional Sequences Uncovered through a Bovine Multiassembly Graph
Crysnanto, D., Leonard, A. S., Fang, Z.-H., & Pausch, H. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2101056118 · Cited by 96
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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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