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

Benjamin D Rosen; Derek M Bickhart; Robert D Schnabel; Sergey Koren; Christine G Elsik; Elizabeth Tseng; Troy N Rowan; Wai Y Low; Aleksey Zimin; Christine Couldrey; Richard Hall; Wenli Li; Arang Rhie; Jay Ghurye; Stephanie D McKay; Françoise Thibaud-Nissen; Jinna Hoffman; Brenda M Murdoch; Warren M Snelling; Tara G McDaneld; John A Hammond; John C Schwartz; Wilson Nandolo; Darren E Hagen; Christian Dreischer; Sebastian J Schultheiss; Steven G Schroeder; Adam M Phillippy; John B Cole; Curtis P Van Tassell; George Liu; Timothy P L Smith; Juan F Medrano

doi:10.1093/gigascience/giaa021

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

Gigascience. 2020 Mar 1;9(3):giaa021. doi: 10.1093/gigascience/giaa021.

Authors

Benjamin D Rosen¹, Derek M Bickhart², Robert D Schnabel³, Sergey Koren⁴, Christine G Elsik³, Elizabeth Tseng⁵, Troy N Rowan³, Wai Y Low⁶, Aleksey Zimin⁷, Christine Couldrey⁸, Richard Hall⁵, Wenli Li², Arang Rhie⁴, Jay Ghurye⁹, Stephanie D McKay¹⁰, Françoise Thibaud-Nissen¹¹, Jinna Hoffman¹¹, Brenda M Murdoch¹², Warren M Snelling¹³, Tara G McDaneld¹³, John A Hammond¹⁴, John C Schwartz¹⁴, Wilson Nandolo^{15

16}, Darren E Hagen¹⁷, Christian Dreischer¹⁸, Sebastian J Schultheiss¹⁸, Steven G Schroeder¹, Adam M Phillippy⁴, John B Cole¹, Curtis P Van Tassell¹, George Liu¹, Timothy P L Smith¹³, Juan F Medrano¹⁹

Affiliations

¹ USDA-ARS, Beltsville, MD, 20705-2350 , Animal Genomics and Improvement Laboratory, USDA-ARS, 10300 Baltimore Ave, Beltsville, MD 20705-2350, USA.
² Dairy Forage Research Center, USDA-ARS, 1925 Linden Drive, Madison, WI, 53706, USA.
³ Division of Animal Sciences, University of Missouri, 162 Animal Science Research Center, Columbia, MO 65211, USA.
⁴ Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA.
⁵ Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA.
⁶ The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia.
⁷ Johns Hopkins University, Welch Library of Medicine, Ste 105, 1900 E. Monument St., Baltimore, MD 21205, USA.
⁸ Livestock Improvement Corporation, Private Bag 3016, Hamilton 3240, New Zealand.
⁹ Department of Computer Science, University of Maryland, 8125 Paint Branch Drive, College Park, MD 20742 USA.
¹⁰ Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT 05405, USA.
¹¹ National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
¹² Department of Animal and Veterinary Science, University of Idaho, 875 Perimeter Drive MS 2330, Moscow, ID 83844-2330, USA.
¹³ U.S. Meat Animal Research Center, USDA-ARS, 844 Road 313, Clay Center, NE 68933, USA.
¹⁴ The Pirbright Institute, Pirbright, Woking, Surrey, UK.
¹⁵ Division of Livestock Sciences, University of Natural Resources and Life Sciences, Gregor Mendel str. 33, A-1180, Vienna, Austria.
¹⁶ Animal Science Department, Lilongwe University of Agriculture and Natural Resources, P.O. Box 219, Lilongwe, Malawi.
¹⁷ Department of Animal and Food Sciences, Oklahoma State University, 101 Animal Science Building, Stillwater, OK 74078, USA.
¹⁸ Computomics GmbH, Christophstr. 32, 72072 Tübingen, Germany.
¹⁹ Department of Animal Science, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA.

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.

Keywords: Hereford; bovine genome; cattle; reference assembly.

Publication types

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.

MeSH terms

Animals
Breeding / methods
Breeding / standards*
Cattle / genetics*
Genome*
Genomics / methods
Genomics / standards*
Polymorphism, Genetic*
RNA-Seq / methods
RNA-Seq / standards
Reference Standards
Sequence Analysis, DNA / methods
Sequence Analysis, DNA / standards

Abstract

Publication types

MeSH terms

Grants and funding