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

Authors: Warr, Amanda and Affara, Nabeel and Aken, Bronwen and Beiki, Hamid and Bickhart, Derek M and Billis, Konstantinos and Chow, William and Eory, Lel and Finlayson, Heather A and Flicek, Paul and Girón, Carlos G and Griffin, Darren K and Hall, Richard and Hannum, Gregory and Hourlier, Thibaut and Howe, Kerstin and Hume, David A and Izuogu, Osagie and Kim, Kristi and Koren, Sergey and Liu, Haibo and Manchanda, Nancy and Martin, Fergal J and Nonneman, Dan J and OtextquoterightConnor, Rebecca E and Phillippy, Adam M and Rohrer, Gary A. and Rosen, Benjamin D. and Rund, Laurie A and Sargent, Carole A and Schook, Lawrence B and Schroeder, Steven G. and Schwartz, Ariel S and Skinner, Benjamin M and Talbot, Richard and Tseng, Elisabeth and Tuggle, Christopher K and Watson, Mick and Smith, Timothy P L and Archibald, Alan L

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) represented a purebred female pig from a commercial pork production breed (Duroc), and was established using older clone-based sequencing methods. The Sscrofa10.2 assembly was incomplete and unresolved redundancies, short range order and orientation errors and associated misassembled genes limited its utility. We present two 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 animal commonly used for commercial pork production (USMARCv1.0). Both assemblies are of substantially higher (>90-fold) continuity and accuracy compared to the earlier reference, and the availability of two independent assemblies provided an opportunity to identify large-scale variants and to error-check the accuracy of representation of the genome. We propose that the improved Duroc breed assembly (Sscrofa11.1) become the reference genome for genomic research in pigs.

Journal: BioRxiv
DOI: 10.1101/668921
Year: 2019

Read publication