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

Amanda Warr¹, Nabeel Affara², Bronwen Aken³, Hamid Beiki⁴, Derek M Bickhart⁵, Konstantinos Billis³, William Chow⁶, Lel Eory¹, Heather A Finlayson¹, Paul Flicek³, Carlos G Girón³, Darren K Griffin⁷, Richard Hall⁸, Greg Hannum⁹, Thibaut Hourlier³, Kerstin Howe⁶, David A Hume^{1

10}, Osagie Izuogu³, Kristi Kim⁸, Sergey Koren¹¹, Haibou Liu⁴, Nancy Manchanda¹², Fergal J Martin³, Dan J Nonneman¹³, Rebecca E O'Connor⁷, Adam M Phillippy¹¹, Gary A Rohrer¹³, Benjamin D Rosen¹⁴, Laurie A Rund¹⁵, Carole A Sargent², Lawrence B Schook¹⁵, Steven G Schroeder¹⁴, Ariel S Schwartz⁹, Ben M Skinner², Richard Talbot¹⁶, Elizabeth Tseng⁸, Christopher K Tuggle^{4

12}, Mick Watson¹, Timothy P L Smith¹³, Alan L Archibald¹

Affiliations

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.

PMID: 32543654
PMCID: PMC7448572
DOI: 10.1093/gigascience/giaa051

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

Amanda Warr et al. Gigascience. 2020.

. 2020 Jun 1;9(6):giaa051.

doi: 10.1093/gigascience/giaa051.

Authors

Affiliations

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.

PMID: 32543654
PMCID: PMC7448572
DOI: 10.1093/gigascience/giaa051

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.

Keywords: genome annotation; pig; pig genomes; reference assembly.

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Figures

**Figure 1:**
Assemblies and radiation hybrid (RH) map alignments. Plots illustrating co-linearity between RH map and (a) Sscrofa11.1 and (b) USMARCv1.0 assemblies (autosomes only).

**Figure 2:**
Visualization of improvements in assembly contiguity. Graphical visualization of contigs for Sscrofa11 (*top*) and Sscrofa10.2 (*bottom*) as alternating dark and light grey bars.

See this image and copyright information in PMC

References

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

Affiliations

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

Authors

Affiliations

Abstract

Figures

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources