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 Amanda Warr
A1 Nabeel Affara
A1 Bronwen Aken
A1 Hamid Beiki
A1 Derek M Bickhart
A1 Konstantinos Billis
A1 William Chow
A1 Lel Eory
A1 Heather A Finlayson
A1 Paul Flicek
A1 Carlos G Girón
A1 Darren K Griffin
A1 Richard Hall
A1 Gregory Hannum
A1 Thibaut Hourlier
A1 Kerstin Howe
A1 David A Hume
A1 Osagie Izuogu
A1 Kristi Kim
A1 Sergey Koren
A1 Haibo Liu
A1 Nancy Manchanda
A1 Fergal J Martin
A1 Dan J Nonneman
A1 Rebecca E O’Connor
A1 Adam M Phillippy
A1 Gary A. Rohrer
A1 Benjamin D. Rosen
A1 Laurie A Rund
A1 Carole A Sargent
A1 Lawrence B Schook
A1 Steven G. Schroeder
A1 Ariel S Schwartz
A1 Benjamin M Skinner
A1 Richard Talbot
A1 Elisabeth Tseng
A1 Christopher K Tuggle
A1 Mick Watson
A1 Timothy P L Smith
A1 Alan L Archibald
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.