@article{c023e732e5e043bf9358880f6887cba7,
title = "An improved pig reference genome sequence to enable pig genetics and genomics research",
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",
author = "Amanda Warr and Nabeel Affara and Bronwen Aken and Hamid Beiki and Bickhart, {Derek M.} and Konstantinos Billis and William Chow and Lel Eory and Finlayson, {Heather A.} and Paul Flicek and Gir{\'o}n, {Carlos G.} and Griffin, {Darren K.} and Richard Hall and Greg Hannum and Thibaut Hourlier and Kerstin Howe and Hume, {David A.} and Osagie Izuogu and Kristi Kim and Sergey Koren and Haibou Liu and Nancy Manchanda 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 Richard Talbot and Elizabeth Tseng and Tuggle, {Christopher K.} and Mick Watson and Smith, {Timothy P.L.} and Archibald, {Alan L.}",
note = "Funding Information: In addition to the funding acknowledged above we are grateful for support from the University of Cambridge, Department of Pathology, the European Molecular Biology Laboratory, and the Roslin Foundation. In addition H.L. and H.B. were supported by USDA NRSP-8 Swine Genome Coordination funding; S.K. and A.M.P. were supported by the Intramural Research Program of the National Human Genome Research Institute, US National Institutes of Health. This work used the computational resources of the NIH HPC Biowulf cluster (https://hpc.nih.gov)and theIowa State University Lightning3 and ResearchIT clusters. The Ceres cluster (part of the USDA SCInet Initiative) was used to analyse part of this dataset. Funding Information: This work was supported by the Biotechnology and Biological Sciences Research Council, Institute Strategic Programme Grant, BBS/E/D/20211550, A.L.A., M.W.; the Biotechnology and Biological Sciences Research Council, Institute Strategic Programme Grant, BBS/E/D/10002070, A.L.A., M.W.; the Biotechnology and Biological Sciences Research Council, Response Mode Grant, BB/F021372/1, N.A.; the Biotechnology and Biological Sciences Research Council, Response Mode Grant, BB/M011461/1, A.L.A.; the Biotechnology and Biological Sciences Research Council, Response Mode Grant, BB/M011615/1, P.F.; the Biotechnology and Biological Sciences Research Council, Response Mode Grant, BB/M01844X/1, A.L.A., M.W.; EU, FP7 Programme Quan-tomics, KBBE222664, A.L.A.;Wellcome Trust, WT108749/Z/15/Z, P.F.;USDA, CRIS Project, 8042-31000-001-00-D, D.M.B., B.D.R.; USDA, CRIS Project, 5090-31000-026-00-D, D.M.B.; USDA, CRIS Project, 3040-31000-100-00-D, T.P.L.S. Publisher Copyright: {\textcopyright} The Author(s) 2020. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.",
year = "2020",
doi = "10.1093/GIGASCIENCE/GIAA051",
language = "English (US)",
volume = "9",
journal = "GigaScience",
issn = "2047-217X",
publisher = "BioMed Central",
number = "6",
}