An improved pig reference genome sequence to enable pig genetics and genomics research

Author:

Warr Amanda1ORCID,Affara Nabeel2,Aken Bronwen3ORCID,Beiki Hamid4ORCID,Bickhart Derek M5ORCID,Billis Konstantinos3ORCID,Chow William6ORCID,Eory Lel1ORCID,Finlayson Heather A1,Flicek Paul3ORCID,Girón Carlos G3ORCID,Griffin Darren K7ORCID,Hall Richard8ORCID,Hannum Greg9,Hourlier Thibaut3ORCID,Howe Kerstin6ORCID,Hume David A110ORCID,Izuogu Osagie3ORCID,Kim Kristi8,Koren Sergey11ORCID,Liu Haibou4,Manchanda Nancy12,Martin Fergal J3ORCID,Nonneman Dan J13ORCID,O'Connor Rebecca E7ORCID,Phillippy Adam M11ORCID,Rohrer Gary A13ORCID,Rosen Benjamin D14ORCID,Rund Laurie A15ORCID,Sargent Carole A2,Schook Lawrence B15ORCID,Schroeder Steven G14ORCID,Schwartz Ariel S9,Skinner Ben M2ORCID,Talbot Richard16,Tseng Elizabeth8ORCID,Tuggle Christopher K412ORCID,Watson Mick1ORCID,Smith Timothy P L13ORCID,Archibald Alan L1ORCID

Affiliation:

1. The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK

2. Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK

3. European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK

4. Department of Animal Science, 2255 Kildee Hall, Iowa State University, Ames, IA 50011-3150, USA

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

6. Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK

7. School of Biosciences, University of Kent, Giles Lane, Canterbury CT2 7NJ, UK

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

9. Denovium Inc., San Diego, CA, USA

10. Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane QLD 4104, Australia

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

12. Bioinformatics and Computational Biology Program, Iowa State University, 2014 Molecular Biology Building, Ames, IA 50011, USA

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

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

15. Department of Animal Sciences, University of Illinois, 1201 West Gregory Drive, Urbana, IL 61801, USA

16. Edinburgh Genomics, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK

Abstract

Abstract Background The domestic pig (Sus scrofa) is important both as a food source and as a biomedical model given its similarity in size, anatomy, physiology, metabolism, pathology, and pharmacology to humans. The draft reference genome (Sscrofa10.2) of a purebred Duroc female pig established using older clone-based sequencing methods was incomplete, and unresolved redundancies, short-range order and orientation errors, and associated misassembled genes limited its utility. Results We present 2 annotated highly contiguous chromosome-level genome assemblies created with more recent long-read technologies and a whole-genome shotgun strategy, 1 for the same Duroc female (Sscrofa11.1) and 1 for an outbred, composite-breed male (USMARCv1.0). Both assemblies are of substantially higher (>90-fold) continuity and accuracy than Sscrofa10.2. Conclusions These highly contiguous assemblies plus annotation of a further 11 short-read assemblies provide an unprecedented view of the genetic make-up of this important agricultural and biomedical model species. We propose that the improved Duroc assembly (Sscrofa11.1) become the reference genome for genomic research in pigs.

Funder

Biotechnology and Biological Sciences Research Council

Wellcome Trust

U.S. Department of Agriculture

Publisher

Oxford University Press (OUP)

Subject

Computer Science Applications,Health Informatics

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