An improved pig reference genome sequence to enable pig genetics and genomics research - PubMed (original) (raw)

. 2020 Jun 1;9(6):giaa051.

doi: 10.1093/gigascience/giaa051.

Nabeel Affara 2, Bronwen Aken 3, Hamid Beiki 4, Derek M Bickhart 5, Konstantinos Billis 3, William Chow 6, Lel Eory 1, Heather A Finlayson 1, Paul Flicek 3, Carlos G Girón 3, Darren K Griffin 7, Richard Hall 8, Greg Hannum 9, Thibaut Hourlier 3, Kerstin Howe 6, David A Hume 1 10, Osagie Izuogu 3, Kristi Kim 8, Sergey Koren 11, Haibou Liu 4, Nancy Manchanda 12, Fergal J Martin 3, Dan J Nonneman 13, Rebecca E O'Connor 7, Adam M Phillippy 11, Gary A Rohrer 13, Benjamin D Rosen 14, Laurie A Rund 15, Carole A Sargent 2, Lawrence B Schook 15, Steven G Schroeder 14, Ariel S Schwartz 9, Ben M Skinner 2, Richard Talbot 16, Elizabeth Tseng 8, Christopher K Tuggle 4 12, Mick Watson 1, Timothy P L Smith 13, Alan L Archibald 1

Affiliations

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

Amanda Warr et al. Gigascience. 2020.

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.

Keywords: genome annotation; pig; pig genomes; reference assembly.

© The Author(s) 2020. Published by Oxford University Press.

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Figures

Figure 1:

Figure 1:

Assemblies and radiation hybrid (RH) map alignments. Plots illustrating co-linearity between RH map and (a) Sscrofa11.1 and (b) USMARCv1.0 assemblies (autosomes only).

Figure 2:

Figure 2:

Visualization of improvements in assembly contiguity. Graphical visualization of contigs for Sscrofa11 (top) and Sscrofa10.2 (bottom) as alternating dark and light grey bars.

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