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

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  • Nabeel Affara
  • Bronwen Aken
  • Hamid Beiki
  • Derek M Bickhart
  • Konstantinos Billis
  • William Chow
  • Paul Flicek
  • Carlos G Girón
  • Darren K Griffin
  • Richard Hall
  • Greg Hannum
  • Thibaut Hourlier
  • Kerstin Howe
  • 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
  • Elizabeth Tseng
  • Christopher K Tuggle
  • Timothy P L Smith

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Original languageEnglish
JournalGigaScience
Volume9
Issue number6
Early online date16 Jun 2020
DOIs
Publication statusE-pub ahead of print - 16 Jun 2020

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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