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

Amanda Warr, Nabeel Affara, Bronwen Aken, H. Beiki, Derek M. Bickhart, Konstantinos Billis, William Chow, Lel Eory, Heather A. Finlayson, Paul Flicek, Carlos G. Girón, Darren K. Griffin, Richard Hall, Greg Hannum, Thibaut Hourlier, Kerstin Howe, David A. Hume, Osagie Izuogu, Kristi Kim, Sergey Koren, Haibou Liu, Nancy Manchanda, Fergal J. Martin, Dan J. Nonneman, Rebecca E. O’Connor, Adam M. Phillippy, Gary A. Rohrer, Benjamin D. Rosen, Laurie A. Rund, Carole A. Sargent, Lawrence B. Schook, Steven G. Schroeder, Ariel S. Schwartz, Ben M. Skinner, Richard Talbot, Elizabeth Tseng, Christopher K. Tuggle, Mick Watson, Timothy P. L. Smith, View ORCID ProfileAlan L. Archibald
doi: https://doi.org/10.1101/668921
Amanda Warr
1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, U.K.
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Nabeel Affara
2Department of Pathology, University of Cambridge, Cambridge CB2 1QP, U.K.
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Bronwen Aken
3European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, U.K.
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H. Beiki
4Department of Animal Science, Iowa State University, Ames, Iowa, U.S.A.
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Derek M. Bickhart
5Dairy Forage Research Center, USDA-ARS, Madison, Wisconsin, U.S.A.
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Konstantinos Billis
3European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, U.K.
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William Chow
6Wellcome Sanger Institute, Cambridge, CB10 1SA, U.K.
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Lel Eory
1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, U.K.
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Heather A. Finlayson
1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, U.K.
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Paul Flicek
3European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, U.K.
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Carlos G. Girón
3European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, U.K.
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Darren K. Griffin
7School of Biosciences, University of Kent, Canterbury CT2 7AF, U.K.
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Richard Hall
8Pacific Biosciences, Menlo Park, California, U.S.A.
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Greg Hannum
9Denovium Inc., San Diego, California, U.S.A.
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Thibaut Hourlier
3European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, U.K.
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Kerstin Howe
6Wellcome Sanger Institute, Cambridge, CB10 1SA, U.K.
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David A. Hume
1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, U.K.
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Osagie Izuogu
3European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, U.K.
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Kristi Kim
8Pacific Biosciences, Menlo Park, California, U.S.A.
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Sergey Koren
10Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland, U.S.A.
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Haibou Liu
4Department of Animal Science, Iowa State University, Ames, Iowa, U.S.A.
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Nancy Manchanda
11Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, U.S.A.
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Fergal J. Martin
3European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, U.K.
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Dan J. Nonneman
12USDA-ARS U.S. Meat Animal Research Center, Clay Center, Nebraska 68933, U.S.A.
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Rebecca E. O’Connor
7School of Biosciences, University of Kent, Canterbury CT2 7AF, U.K.
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Adam M. Phillippy
10Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland, U.S.A.
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Gary A. Rohrer
12USDA-ARS U.S. Meat Animal Research Center, Clay Center, Nebraska 68933, U.S.A.
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Benjamin D. Rosen
13Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, Maryland, U.S.A
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Laurie A. Rund
14Department of Animal Sciences, University of Illinois, Urbana, Illinois, U.S.A.
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Carole A. Sargent
2Department of Pathology, University of Cambridge, Cambridge CB2 1QP, U.K.
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Lawrence B. Schook
14Department of Animal Sciences, University of Illinois, Urbana, Illinois, U.S.A.
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Steven G. Schroeder
13Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, Maryland, U.S.A
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Ariel S. Schwartz
9Denovium Inc., San Diego, California, U.S.A.
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Ben M. Skinner
2Department of Pathology, University of Cambridge, Cambridge CB2 1QP, U.K.
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Richard Talbot
15Edinburgh Genomics, University of Edinburgh, Edinburgh EH9 3FL, U.K.
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Elizabeth Tseng
8Pacific Biosciences, Menlo Park, California, U.S.A.
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Christopher K. Tuggle
4Department of Animal Science, Iowa State University, Ames, Iowa, U.S.A.
11Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, U.S.A.
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Mick Watson
1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, U.K.
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  • For correspondence: alan.archibald@roslin.ed.ac.uk tim.smith@ARS.USDA.GOV mick.watson@roslin.ed.ac.uk
Timothy P. L. Smith
12USDA-ARS U.S. Meat Animal Research Center, Clay Center, Nebraska 68933, U.S.A.
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  • For correspondence: alan.archibald@roslin.ed.ac.uk tim.smith@ARS.USDA.GOV mick.watson@roslin.ed.ac.uk
Alan L. Archibald
1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, U.K.
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  • ORCID record for Alan L. Archibald
  • For correspondence: alan.archibald@roslin.ed.ac.uk tim.smith@ARS.USDA.GOV mick.watson@roslin.ed.ac.uk
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Abstract

The domestic pig (Sus scrofa) is important both as a food source and as a biomedical model with high anatomical and immunological similarity 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. We present two annotated highly contiguous chromosome-level genome assemblies created with more recent long read technologies and a whole genome shotgun strategy, one for the same Duroc female (Sscrofa11.1) and one for an outbred, composite breed male (USMARCv1.0). Both assemblies are of substantially higher (>90-fold) continuity and accuracy than Sscrofa10.2. 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.

Footnotes

  • ↵† Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia

  • This version of the manuscript has been revised to include updated Ensembl annotation of Sscrofa11.1 and to report annotation of a further eleven short read pig genome assemblies (summarised in a new supplementary table). The description of the Ensembl annotation pipeline has been revised. Some supplementary tables have been removed.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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An improved pig reference genome sequence to enable pig genetics and genomics research
Amanda Warr, Nabeel Affara, Bronwen Aken, H. Beiki, Derek M. Bickhart, Konstantinos Billis, William Chow, Lel Eory, Heather A. Finlayson, Paul Flicek, Carlos G. Girón, Darren K. Griffin, Richard Hall, Greg Hannum, Thibaut Hourlier, Kerstin Howe, David A. Hume, Osagie Izuogu, Kristi Kim, Sergey Koren, Haibou Liu, Nancy Manchanda, Fergal J. Martin, Dan J. Nonneman, Rebecca E. O’Connor, Adam M. Phillippy, Gary A. Rohrer, Benjamin D. Rosen, Laurie A. Rund, Carole A. Sargent, Lawrence B. Schook, Steven G. Schroeder, Ariel S. Schwartz, Ben M. Skinner, Richard Talbot, Elizabeth Tseng, Christopher K. Tuggle, Mick Watson, Timothy P. L. Smith, Alan L. Archibald
bioRxiv 668921; doi: https://doi.org/10.1101/668921
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An improved pig reference genome sequence to enable pig genetics and genomics research
Amanda Warr, Nabeel Affara, Bronwen Aken, H. Beiki, Derek M. Bickhart, Konstantinos Billis, William Chow, Lel Eory, Heather A. Finlayson, Paul Flicek, Carlos G. Girón, Darren K. Griffin, Richard Hall, Greg Hannum, Thibaut Hourlier, Kerstin Howe, David A. Hume, Osagie Izuogu, Kristi Kim, Sergey Koren, Haibou Liu, Nancy Manchanda, Fergal J. Martin, Dan J. Nonneman, Rebecca E. O’Connor, Adam M. Phillippy, Gary A. Rohrer, Benjamin D. Rosen, Laurie A. Rund, Carole A. Sargent, Lawrence B. Schook, Steven G. Schroeder, Ariel S. Schwartz, Ben M. Skinner, Richard Talbot, Elizabeth Tseng, Christopher K. Tuggle, Mick Watson, Timothy P. L. Smith, Alan L. Archibald
bioRxiv 668921; doi: https://doi.org/10.1101/668921

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