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

• DOI: 10.1101/668921
• Publication Date: 2019-06-13T14:39:02Z
• Authors: Amanda Warr; Nabeel Affara; Bronwen Aken; H. Beiki; Derek M. Bickhart; Konstantinos Billis; William Chow; Lel Eory; Heather A. Finlayson; Paul Flicek; Carlos G. Girón; Darren K. Griffin; Richard Hall; Greg Hannum; Thibaut Hourlier; Kerstin Howe; David A. Hume; Osagie Izuogu; Kristi Kim; Sergey Koren; Haibou Liu; Nancy Manchanda; Fergal J. Martin; 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; Richard Talbot; Elizabeth Tseng; Christopher K. Tu...; Mick Watson; Timothy P. L. Smith; Alan L. Archibald
• Keywords: Sequence assembly

Abstract The domestic pig ( Sus scrofa ) is important both as a food source and biomedical model with high anatomical immunological similarity to humans. draft reference genome (Sscrofa10.2) of purebred Duroc female established using older clone-based sequencing methods was incomplete unresolved redundancies, short range order orientation errors associated misassembled genes limited its utility. We present two annotated highly contiguous chromosome-level assemblies created more recent long read technologies whole shotgun strategy, one for the same (Sscrofa11.1) an outbred, composite breed male (USMARCv1.0). Both are substantially higher (>90-fold) continuity accuracy than Sscrofa10.2. These plus annotation further 11 provide unprecedented view genetic make-up this agricultural species. propose that improved assembly become genomic research in pigs.