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

  1. Amanda Warr
  2. Nabeel Affara
  3. Bronwen Aken
  4. Hamid Beiki
  5. Derek M Bickhart
  6. Konstantinos Billis
  7. William Chow
  8. Lel Eory
  9. Heather A Finlayson
  10. Paul Flicek
  11. Carlos G Girón
  12. Darren K Griffin
  13. Richard Hall
  14. Greg Hannum
  15. Thibaut Hourlier
  16. Kerstin Howe
  17. David A Hume
  18. Osagie Izuogu
  19. Kristi Kim
  20. Sergey Koren
  21. Haibou Liu
  22. Nancy Manchanda
  23. Fergal J Martin
  24. Dan J Nonneman
  25. Rebecca E O'Connor
  26. Adam M Phillippy
  27. Gary A Rohrer
  28. Benjamin D Rosen
  29. Laurie A Rund
  30. Carole A Sargent
  31. Lawrence B Schook
  32. Steven G Schroeder
  33. Ariel S Schwartz
  34. Ben M Skinner
  35. Richard Talbot
  36. Elizabeth Tseng
  37. Christopher K Tuggle
  38. Mick Watson
  39. Timothy P L Smith
  40. Alan L Archibald

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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.

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  1. GigaScience

    Now published in GigaScience doi: 10.1093/gigascience/giaa051

    Amanda Warr 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteNabeel Affara 2Department of Pathology, University of Cambridge, Cambridge CB2 1QP, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteBronwen Aken 3European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteH. Beiki 4Department of Animal Science, Iowa State University, Ames, Iowa, U.S.A.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteDerek M. Bickhart 5Dairy Forage Research Center, USDA-ARS, Madison, Wisconsin, U.S.A.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteKonstantinos Billis 3European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteWilliam Chow 6Wellcome Sanger Institute, Cambridge, CB10 1SA, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteLel Eory 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteHeather A. Finlayson 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this sitePaul Flicek 3European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteCarlos G. Girón 3European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteDarren K. Griffin 7School of Biosciences, University of Kent, Canterbury CT2 7AF, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteRichard Hall 8Pacific Biosciences, Menlo Park, California, U.S.A.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteGreg Hannum 9Denovium Inc., San Diego, California, U.S.A.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteThibaut Hourlier 3European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteKerstin Howe 6Wellcome Sanger Institute, Cambridge, CB10 1SA, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteDavid A. Hume 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteOsagie Izuogu 3European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteKristi Kim 8Pacific Biosciences, Menlo Park, California, U.S.A.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteSergey Koren 10Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland, U.S.A.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteHaibou Liu 4Department of Animal Science, Iowa State University, Ames, Iowa, U.S.A.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteNancy Manchanda 11Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, U.S.A.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteFergal J. Martin 3European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteDan J. Nonneman 12USDA-ARS U.S. Meat Animal Research Center, Clay Center, Nebraska 68933, U.S.A.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteRebecca E. O’Connor 7School of Biosciences, University of Kent, Canterbury CT2 7AF, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteAdam M. Phillippy 10Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland, U.S.A.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteGary A. Rohrer 12USDA-ARS U.S. Meat Animal Research Center, Clay Center, Nebraska 68933, U.S.A.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteBenjamin D. Rosen 13Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, Maryland, U.S.AFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLaurie A. Rund 14Department of Animal Sciences, University of Illinois, Urbana, Illinois, U.S.A.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteCarole A. Sargent 2Department of Pathology, University of Cambridge, Cambridge CB2 1QP, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteLawrence B. Schook 14Department of Animal Sciences, University of Illinois, Urbana, Illinois, U.S.A.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteSteven G. Schroeder 13Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, Maryland, U.S.AFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAriel S. Schwartz 9Denovium Inc., San Diego, California, U.S.A.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteBen M. Skinner 2Department of Pathology, University of Cambridge, Cambridge CB2 1QP, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteRichard Talbot 15Edinburgh Genomics, University of Edinburgh, Edinburgh EH9 3FL, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteElizabeth Tseng 8Pacific Biosciences, Menlo Park, California, U.S.A.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteChristopher 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.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteMick Watson 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: alan.archibald@roslin.ed.ac.uk tim.smith@ARS.USDA.GOV mick.watson@roslin.ed.ac.ukTimothy P. L. Smith 12USDA-ARS U.S. Meat Animal Research Center, Clay Center, Nebraska 68933, U.S.A.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: alan.archibald@roslin.ed.ac.uk tim.smith@ARS.USDA.GOV mick.watson@roslin.ed.ac.ukAlan L. Archibald 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Alan L. ArchibaldFor correspondence: alan.archibald@roslin.ed.ac.uk tim.smith@ARS.USDA.GOV mick.watson@roslin.ed.ac.uk

    A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa051 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.

    These peer reviews were as follows:

    Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102287 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102288

  2. Version published to 10.1093/gigascience/giaa051
  3. Version published to 10.1101/668921v3 on bioRxiv
  4. Version published to 10.1101/668921v2 on bioRxiv
  5. Version published to 10.1101/668921v1 on bioRxiv