An improved pig reference genome sequence to enable pig genetics and genomics research. Issue 6 (16th June 2020)

• Record Type: Journal Article
• Authors: Warr, Amanda; Affara, Nabeel; Aken, Bronwen; Beiki, Hamid; Bickhart, Derek M; Billis, Konstantinos; Chow, William; Eory, Lel; Finlayson, Heather A; Flicek, Paul; Girón, Carlos G; Griffin, Darren K; Hall, Richard; Hannum, Greg; Hourlier, Thibaut; Howe, Kerstin; Hume, David A; Izuogu, Osagie; Kim, Kristi; Koren, Sergey; Liu, Haibou; Manchanda, Nancy; Martin, Fergal J; Nonneman, Dan J; O'Connor, Rebecca E; Phillippy, Adam M; Rohrer, Gary A; Rosen, Benjamin D; Rund, Laurie A; Sargent, Carole A; Schook, Lawrence B; Schroeder, Steven G; Schwartz, Ariel S; Skinner, Ben M; Talbot, Richard; Tseng, Elizabeth; Tuggle, Christopher K; Watson, Mick; Smith, Timothy P L; Archibald, Alan L;
• Is Part Of: GigaScience. Volume 9:Issue 6(2020)
• Publication Date: 2020-06-16
• Subjects: pig genomes -- reference assembly -- pig -- genome annotation; Information storage and retrieval systems -- Research -- Periodicals; Biology -- Research -- Periodicals; Medical sciences -- Research -- Periodicals; Database management -- Periodicals; 570.285
• DOI: 10.1093/gigascience/giaa051
• Languages: English
• ISSNs: 2047-217X

Abstract

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