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

Archibald, Alan L, Smith, Timothy P L, Watson, Mick, Tuggle, Christopher K, Tseng, Elizabeth, Talbot, Richard, Skinner, Ben M, Schwartz, Ariel S, Schroeder, Steven G, Schook, Lawrence B, and others. (2020) An improved pig reference genome sequence to enable pig genetics and genomics research. GigaScience, 9 (6). ISSN 2047-217X. (doi:10.1093/gigascience/giaa051) (KAR id:81763)

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https://doi.org/10.1093/gigascience%2Fgiaa051

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
DOI/Identification number: 10.1093/gigascience/giaa051
Uncontrolled keywords: pig genomes; reference assembly; pig; genome annotation
Subjects: Q Science
Divisions: Divisions > Division of Natural Sciences > School of Biosciences
Depositing User: Susan Davies
Date Deposited: 18 Jun 2020 10:44 UTC
Last Modified: 19 Jun 2020 09:44 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/81763 (The current URI for this page, for reference purposes)
O'Connor, Rebecca: https://orcid.org/0000-0002-4270-970X
Griffin, Darren K.: https://orcid.org/0000-0001-7595-3226
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