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

Warr, Amanda and Affara, Nabeel and Aken, Bronwen and Beiki, Hamid and Bickhart, Derek M and Billis, Konstantinos and Chow, William and Eory, Lel and Finlayson, Heather A and Flicek, Paul and Girón, Carlos G and Griffin, Darren K and Hall, Richard and Hannum, Greg and Hourlier, Thibaut and Howe, Kerstin and Hume, David A and Izuogu, Osagie and Kim, Kristi and Koren, Sergey and Liu, Haibou and Manchanda, Nancy and Martin, Fergal J and Nonneman, Dan J and O'Connor, Rebecca E and Phillippy, Adam M and Rohrer, Gary A and Rosen, Benjamin D and Rund, Laurie A and Sargent, Carole A and Schook, Lawrence B and Schroeder, Steven G and Schwartz, Ariel S and Skinner, Ben M and Talbot, Richard and Tseng, Elizabeth and Tuggle, Christopher K and Watson, Mick and Smith, Timothy PL and Archibald, Alan L (2020) 'An improved pig reference genome sequence to enable pig genetics and genomics research.' GigaScience, 9 (6). ISSN 2047-217X

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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.

Item Type: Article
Divisions: Faculty of Science and Health > Life Sciences, School of
Depositing User: Elements
Date Deposited: 18 Aug 2020 13:35
Last Modified: 18 Aug 2020 13:35
URI: http://repository.essex.ac.uk/id/eprint/28033

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