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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.

SUBMITTER: Warr A

PROVIDER: S-EPMC7448572 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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

Warr Amanda A Affara Nabeel N Aken Bronwen B Beiki Hamid H Bickhart Derek M DM Billis Konstantinos K Chow William W Eory Lel L Finlayson Heather A HA Flicek Paul P Girón Carlos G CG Griffin Darren K DK Hall Richard R Hannum Greg G Hourlier Thibaut T Howe Kerstin K Hume David A DA Izuogu Osagie O Kim Kristi K Koren Sergey S Liu Haibou H Manchanda Nancy N Martin Fergal J FJ Nonneman Dan J DJ O'Connor Rebecca E RE Phillippy Adam M AM Rohrer Gary A GA Rosen Benjamin D BD Rund Laurie A LA Sargent Carole A CA Schook Lawrence B LB Schroeder Steven G SG Schwartz Ariel S AS Skinner Ben M BM Talbot Richard R Tseng Elizabeth E Tuggle Christopher K CK Watson Mick M Smith Timothy P L TPL Archibald Alan L AL

GigaScience 20200601 6

<h4>Background</h4>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.<h4>Results</h4>We p ...[more]

PMID: 32543654

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Project description:BackgroundGenerally, there is unanimity about the value of community engagement in health-related research. There is also a growing tendency to view genetics and genomics research (GGR) as a special category of research, the conduct of which including community engagement (CE) as needing additional caution. One of the motivations of this study was to establish how differently if at all, we should think about CE in GGR.AimTo assess the perspectives of genetics and genomics researchers in Uganda on CE in GGR.MethodA cross-sectional qualitative study was conducted at Makerere University and Uganda Virus Research Institute. Twenty-five individuals participated, the majority being male (sixteen). Participants included nineteen genetics and genomics researchers (researchers and research coordinators), two CE officers, three nurses and one nursing counsellor. Data were collected using in-depth interviews and analyzed in a thematic manner using NVivo version 12 Plus.Study findingsThirteen of the respondents had conducted CE in their GGR in either a geographical and disease-specific community. Some respondents said CE principles are the same and there is no need for special consideration for CE in GGR. Others gave ethical issues in GGR that require special consideration for CE in such research and these were categorized into six themes: GGR is new to communities, Difficulty in communicating GGR by the researchers, Genes are shared in communities, Cultural sensitivities against GGR, Community attitude toward GGR, Some GGR studies take long to end, and Negotiation of research benefits. Special considerations for CE when conducting GGR were suggested and categorized into seven themes: creating awareness of GGR in communities, obtaining both community acceptance and individual consent, CE team composition, involve communities in solving GGR challenges, prolong CE in some GGR, develop guidelines for CE in GGR, and legal considerations on GGR.ConclusionGGR was characterized by special issues that require special CE considerations for such research.

Dataset Information

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

Publications

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

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