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De novo assembly of the cattle reference genome with single-molecule sequencing.
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.
Afiliación
  • Rosen BD; USDA-ARS, Beltsville, MD, 20705-2350 , Animal Genomics and Improvement Laboratory, USDA-ARS, 10300 Baltimore Ave, Beltsville, MD 20705-2350, USA.
  • Bickhart DM; Dairy Forage Research Center, USDA-ARS, 1925 Linden Drive, Madison, WI, 53706, USA.
  • Schnabel RD; Division of Animal Sciences, University of Missouri, 162 Animal Science Research Center, Columbia, MO 65211, USA.
  • 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.
  • Elsik CG; Division of Animal Sciences, University of Missouri, 162 Animal Science Research Center, Columbia, MO 65211, USA.
  • Tseng E; Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA.
  • Rowan TN; Division of Animal Sciences, University of Missouri, 162 Animal Science Research Center, Columbia, MO 65211, USA.
  • Low WY; The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia.
  • Zimin A; Johns Hopkins University, Welch Library of Medicine, Ste 105, 1900 E. Monument St., Baltimore, MD 21205, USA.
  • Couldrey C; Livestock Improvement Corporation, Private Bag 3016, Hamilton 3240, New Zealand.
  • Hall R; Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA.
  • Li W; Dairy Forage Research Center, USDA-ARS, 1925 Linden Drive, Madison, WI, 53706, USA.
  • 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.
  • Ghurye J; Department of Computer Science, University of Maryland, 8125 Paint Branch Drive, College Park, MD 20742 USA.
  • McKay SD; Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT 05405, USA.
  • Thibaud-Nissen F; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
  • Hoffman J; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
  • Murdoch BM; Department of Animal and Veterinary Science, University of Idaho, 875 Perimeter Drive MS 2330, Moscow, ID 83844-2330, USA.
  • Snelling WM; U.S. Meat Animal Research Center, USDA-ARS, 844 Road 313, Clay Center, NE 68933, USA.
  • McDaneld TG; U.S. Meat Animal Research Center, USDA-ARS, 844 Road 313, Clay Center, NE 68933, USA.
  • Hammond JA; The Pirbright Institute, Pirbright, Woking, Surrey, UK.
  • Schwartz JC; The Pirbright Institute, Pirbright, Woking, Surrey, UK.
  • Nandolo W; Division of Livestock Sciences, University of Natural Resources and Life Sciences, Gregor Mendel str. 33, A-1180, Vienna, Austria.
  • Hagen DE; Animal Science Department, Lilongwe University of Agriculture and Natural Resources, P.O. Box 219, Lilongwe, Malawi.
  • Dreischer C; Department of Animal and Food Sciences, Oklahoma State University, 101 Animal Science Building, Stillwater, OK 74078, USA.
  • Schultheiss SJ; Computomics GmbH, Christophstr. 32, 72072 Tübingen, Germany.
  • Schroeder SG; Computomics GmbH, Christophstr. 32, 72072 Tübingen, Germany.
  • Phillippy AM; USDA-ARS, Beltsville, MD, 20705-2350 , Animal Genomics and Improvement Laboratory, USDA-ARS, 10300 Baltimore Ave, Beltsville, MD 20705-2350, USA.
  • Cole JB; Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA.
  • Van Tassell CP; USDA-ARS, Beltsville, MD, 20705-2350 , Animal Genomics and Improvement Laboratory, USDA-ARS, 10300 Baltimore Ave, Beltsville, MD 20705-2350, USA.
  • Liu G; USDA-ARS, Beltsville, MD, 20705-2350 , Animal Genomics and Improvement Laboratory, USDA-ARS, 10300 Baltimore Ave, Beltsville, MD 20705-2350, USA.
  • Smith TPL; USDA-ARS, Beltsville, MD, 20705-2350 , Animal Genomics and Improvement Laboratory, USDA-ARS, 10300 Baltimore Ave, Beltsville, MD 20705-2350, USA.
  • Medrano JF; U.S. Meat Animal Research Center, USDA-ARS, 844 Road 313, Clay Center, NE 68933, USA.
Gigascience ; 9(3)2020 03 01.
Article en En | MEDLINE | ID: mdl-32191811
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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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Polimorfismo Genético / Cruzamiento / Bovinos / Genoma / Genómica Tipo de estudio: Prognostic_studies Límite: Animals Idioma: En Revista: Gigascience Año: 2020 Tipo del documento: Article País de afiliación: Estados Unidos
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Polimorfismo Genético / Cruzamiento / Bovinos / Genoma / Genómica Tipo de estudio: Prognostic_studies Límite: Animals Idioma: En Revista: Gigascience Año: 2020 Tipo del documento: Article País de afiliación: Estados Unidos