An improved pig reference genome sequence to enable pig genetics and genomics research
Derek M. Bickhart,
Heather A Finlayson,
Carlos G Girón,
Darren K Griffin,
David A. Hume,
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,
Christopher K Tuggle,
Timothy P. L. Smith,
Alan L. Archibald
Posted 13 Jun 2019
bioRxiv DOI: 10.1101/668921 (published DOI: 10.1093/gigascience/giaa051)
Posted 13 Jun 2019
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.
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