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 journalArticlepeer-review

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
Pages (from-to)1-14
Number of pages14
JournalGigaScience
Volume9
Issue number6
Early online date16 Jun 2020
DOIs
Publication statusE-pub ahead of print - 16 Jun 2020

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