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

Animals Breeding / methods Cattle / genetics Genome Genomics / methods Polymorphism, Genetic RNA-Seq / methods Reference Standards Sequence Analysis, DNA / methods
Hereford bovine genome cattle reference assembly

Journal

GigaScience
ISSN: 2047-217X
Titre abrégé: Gigascience
Pays: United States
ID NLM: 101596872

Informations de publication

Date de publication:
01 03 2020
Historique:
received: 24 09 2019
revised: 31 01 2020
accepted: 14 02 2020
entrez: 20 3 2020
pubmed: 20 3 2020
medline: 28 1 2021
Statut: ppublish

Résumé

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 These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies. 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. 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.

Sections du résumé

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 These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies.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.

Identifiants

DOI: 10.1093/gigascience/giaa021 PMID: 32191811 PMC: PMC7081964
pubmed: 32191811
pii: 5810242
doi: 10.1093/gigascience/giaa021
pmc: PMC7081964
pii:
doi:

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, N.I.H., Intramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Langues

eng

Sous-ensembles de citation

IM

Subventions

Organisme : NICHD NIH HHS
ID : R01 HD084353
Pays : United States
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/M027155/1
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BBS/E/I/00007039
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BBS/E/I/00007035
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BBS/E/I/00007038
Pays : United Kingdom

Informations de copyright

© The Author(s) 2020. Published by Oxford University Press.

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Auteurs

Benjamin D Rosen (BD)

USDA-ARS, Beltsville, MD, 20705-2350 , Animal Genomics and Improvement Laboratory, USDA-ARS, 10300 Baltimore Ave, Beltsville, MD 20705-2350, USA.

Derek M Bickhart (DM)

Dairy Forage Research Center, USDA-ARS, 1925 Linden Drive, Madison, WI, 53706, USA.

Robert D Schnabel (RD)

Division of Animal Sciences, University of Missouri, 162 Animal Science Research Center, Columbia, MO 65211, USA.

Sergey Koren (S)

Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA.

Christine G Elsik (CG)

Division of Animal Sciences, University of Missouri, 162 Animal Science Research Center, Columbia, MO 65211, USA.

Elizabeth Tseng (E)

Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA.

Troy N Rowan (TN)

Division of Animal Sciences, University of Missouri, 162 Animal Science Research Center, Columbia, MO 65211, USA.

Wai Y Low (WY)

The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia.

Aleksey Zimin (A)

Johns Hopkins University, Welch Library of Medicine, Ste 105, 1900 E. Monument St., Baltimore, MD 21205, USA.

Christine Couldrey (C)

Livestock Improvement Corporation, Private Bag 3016, Hamilton 3240, New Zealand.

Richard Hall (R)

Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA.

Wenli Li (W)

Dairy Forage Research Center, USDA-ARS, 1925 Linden Drive, Madison, WI, 53706, USA.

Arang Rhie (A)

Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA.

Jay Ghurye (J)

Department of Computer Science, University of Maryland, 8125 Paint Branch Drive, College Park, MD 20742 USA.

Stephanie D McKay (SD)

Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT 05405, USA.

Françoise Thibaud-Nissen (F)

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.

Jinna Hoffman (J)

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.

Brenda M Murdoch (BM)

Department of Animal and Veterinary Science, University of Idaho, 875 Perimeter Drive MS 2330, Moscow, ID 83844-2330, USA.

Warren M Snelling (WM)

U.S. Meat Animal Research Center, USDA-ARS, 844 Road 313, Clay Center, NE 68933, USA.

Tara G McDaneld (TG)

U.S. Meat Animal Research Center, USDA-ARS, 844 Road 313, Clay Center, NE 68933, USA.

John A Hammond (JA)

The Pirbright Institute, Pirbright, Woking, Surrey, UK.

John C Schwartz (JC)

The Pirbright Institute, Pirbright, Woking, Surrey, UK.

Wilson Nandolo (W)

Division of Livestock Sciences, University of Natural Resources and Life Sciences, Gregor Mendel str. 33, A-1180, Vienna, Austria.
Animal Science Department, Lilongwe University of Agriculture and Natural Resources, P.O. Box 219, Lilongwe, Malawi.

Darren E Hagen (DE)

Department of Animal and Food Sciences, Oklahoma State University, 101 Animal Science Building, Stillwater, OK 74078, USA.

Christian Dreischer (C)

Computomics GmbH, Christophstr. 32, 72072 Tübingen, Germany.

Sebastian J Schultheiss (SJ)

Computomics GmbH, Christophstr. 32, 72072 Tübingen, Germany.

Steven G Schroeder (SG)

USDA-ARS, Beltsville, MD, 20705-2350 , Animal Genomics and Improvement Laboratory, USDA-ARS, 10300 Baltimore Ave, Beltsville, MD 20705-2350, USA.

Adam M Phillippy (AM)

Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA.

John B Cole (JB)

USDA-ARS, Beltsville, MD, 20705-2350 , Animal Genomics and Improvement Laboratory, USDA-ARS, 10300 Baltimore Ave, Beltsville, MD 20705-2350, USA.

Curtis P Van Tassell (CP)

USDA-ARS, Beltsville, MD, 20705-2350 , Animal Genomics and Improvement Laboratory, USDA-ARS, 10300 Baltimore Ave, Beltsville, MD 20705-2350, USA.

George Liu (G)

USDA-ARS, Beltsville, MD, 20705-2350 , Animal Genomics and Improvement Laboratory, USDA-ARS, 10300 Baltimore Ave, Beltsville, MD 20705-2350, USA.

Timothy P L Smith (TPL)

U.S. Meat Animal Research Center, USDA-ARS, 844 Road 313, Clay Center, NE 68933, USA.

Juan F Medrano (JF)

Department of Animal Science, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA.

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › De novo assembly of the cattle reference...
questionsmedicales.fr › Phénomènes génétiques › Sélection › De novo assembly of the cattle reference...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Artiodactyla › Ruminants › Bovins › De novo assembly of the cattle reference...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › De novo assembly of the cattle reference...
questionsmedicales.fr › Disciplines des sciences naturelles › Disciplines des sciences biologiques › Biologie › Génétique › Génomique › De novo assembly of the cattle reference...
questionsmedicales.fr › Phénomènes génétiques › Variation génétique › Polymorphisme génétique › De novo assembly of the cattle reference...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ARN › RNA-Seq › De novo assembly of the cattle reference...
questionsmedicales.fr › Techniques d'investigation › Poids et mesures › Normes de référence › De novo assembly of the cattle reference...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ADN › De novo assembly of the cattle reference...