Cited by 857Genomics and Phylogenetic StudiesGenetic and phenotypic traits in livestockGenomic variations and chromosomal abnormalities

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De novo assembly of the cattle reference genome with single-molecule sequencing

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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, Thibaud-Nissen, Françoise, Hoffman, Jinna, Murdoch, Brenda M, Snelling, Warren M, McDaneld, Tara G, Hammond, John A, Schwartz, John C, Nandolo, Wilson, Hagen, Darren E, Dreischer, Christian, 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·2020·GigaScience

DOI 10.1093/gigascience/giaa021PMC PMC7081964

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Abstract

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 These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies.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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Figure 1: L1 Dominette 0 1449. The line-bred Hereford cow was selected as the original cattle reference animal for her high level of inbreeding.CC BY · PubMed Central

Figure 2: Dominette de novo assembly. A: Assembly pipeline. N50 is the minimum scaffold/contig length needed to cover 50% of the genome; L50 is the number of contigs required to reach N50. B: Cattle chromosomes painted with assembled contigs. A color shift indicates the switch from one contig to the next or the end of an alignment block. The left half of each chromosome shows UMD3.1.1 contigs while the right shows ARS-UCD1.2. To be conservative, contigs were ordered by UMD3.1.1 assembly positions; where there are conflicts in order between ARS-UCD1.2 and UMD3.1.1, the plot displays a color switch in ARS-UCD1.2. Asterisk indicates within scaffolds assigned to chromosomes.CC BY · PubMed Central

Figure 3: Assembly assessments computed for ARS-UCD1.2 and UMD3.1.1. A, Feature response curves computed for ARS-UCD1.2 and UMD3.1.1. B, Calculated contig NGx (minimum contig length needed to cover x% of the genome calculated on a fixed genome size of 2.8 Gb) showing a 280-fold increase of ARS-UCD1.2 in comparison with UMD3.1.1. C, The percentage of gaps in gene-flanking regions is reduced from 33% to 0.3% in ARS-UCD1.2 in comparison with UMD3.1.1.CC BY · PubMed Central

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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)
DOI: 10.1093/gigascience/giaa021
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: cc-by
creativecommons.org/licenses/by/4.0/ (vor, 18 d)
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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De novo assembly of the cattle reference genome with single-molecule sequencing

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