RT Journal Article
SR Electronic
T1 An improved pig reference genome sequence to enable pig genetics and genomics research
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 668921
DO 10.1101/668921
A1 Warr, Amanda
A1 Affara, Nabeel
A1 Aken, Bronwen
A1 Beiki, Hamid
A1 Bickhart, Derek M
A1 Billis, Konstantinos
A1 Chow, William
A1 Eory, Lel
A1 Finlayson, Heather A
A1 Flicek, Paul
A1 Girón, Carlos G
A1 Griffin, Darren K
A1 Hall, Richard
A1 Hannum, Gregory
A1 Hourlier, Thibaut
A1 Howe, Kerstin
A1 Hume, David A
A1 Izuogu, Osagie
A1 Kim, Kristi
A1 Koren, Sergey
A1 Liu, Haibo
A1 Manchanda, Nancy
A1 Martin, Fergal J
A1 Nonneman, Dan J
A1 O’Connor, Rebecca E
A1 Phillippy, Adam M
A1 Rohrer, Gary A.
A1 Rosen, Benjamin D.
A1 Rund, Laurie A
A1 Sargent, Carole A
A1 Schook, Lawrence B
A1 Schroeder, Steven G.
A1 Schwartz, Ariel S
A1 Skinner, Benjamin M
A1 Talbot, Richard
A1 Tseng, Elisabeth
A1 Tuggle, Christopher K
A1 Watson, Mick
A1 Smith, Timothy P L
A1 Archibald, Alan L
YR 2019
UL http://biorxiv.org/content/early/2019/06/13/668921.abstract
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.