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

Amanda Warr, Nabeel Affara, Bronwen Aken, Hamid 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 KorenHaibou 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

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
JournalGigaScience
Volume9
Issue number6
DOIs
StatePublished - Jun 1 2020

Keywords

  • genome annotation
  • pig
  • pig genomes
  • reference assembly

ASJC Scopus subject areas

  • Computer Science Applications
  • Health Informatics

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    Warr, A., Affara, N., Aken, B., Beiki, H., Bickhart, D. M., Billis, K., Chow, W., Eory, L., Finlayson, H. A., Flicek, P., Girón, C. G., Griffin, D. K., Hall, R., Hannum, G., Hourlier, T., Howe, K., Hume, D. A., Izuogu, O., Kim, K., ... Archibald, A. L. (2020). An improved pig reference genome sequence to enable pig genetics and genomics research. GigaScience, 9(6). https://doi.org/10.1093/gigascience/giaa051