PT  - JOURNAL ARTICLE
AU  - Warr, Amanda
AU  - Affara, Nabeel
AU  - Aken, Bronwen
AU  - Beiki, Hamid
AU  - Bickhart, Derek M
AU  - Billis, Konstantinos
AU  - Chow, William
AU  - Eory, Lel
AU  - Finlayson, Heather A
AU  - Flicek, Paul
AU  - Girón, Carlos G
AU  - Griffin, Darren K
AU  - Hall, Richard
AU  - Hannum, Gregory
AU  - Hourlier, Thibaut
AU  - Howe, Kerstin
AU  - Hume, David A
AU  - Izuogu, Osagie
AU  - Kim, Kristi
AU  - Koren, Sergey
AU  - Liu, Haibo
AU  - Manchanda, Nancy
AU  - Martin, Fergal J
AU  - Nonneman, Dan J
AU  - O’Connor, Rebecca E
AU  - Phillippy, Adam M
AU  - Rohrer, Gary A.
AU  - Rosen, Benjamin D.
AU  - Rund, Laurie A
AU  - Sargent, Carole A
AU  - Schook, Lawrence B
AU  - Schroeder, Steven G.
AU  - Schwartz, Ariel S
AU  - Skinner, Benjamin M
AU  - Talbot, Richard
AU  - Tseng, Elisabeth
AU  - Tuggle, Christopher K
AU  - Watson, Mick
AU  - Smith, Timothy P L
AU  - Archibald, Alan L
TI  - An improved pig reference genome sequence to enable pig genetics and genomics research
AID  - 10.1101/668921
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 668921
4099  - http://biorxiv.org/content/early/2019/06/13/668921.short
4100  - http://biorxiv.org/content/early/2019/06/13/668921.full
AB  - 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) represents 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 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.