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

Authors: WARR, AMANDA - Roslin Institute; AFFARA, NABEEL - University Of Cambridge; AKEN, BRONWEN - Embl-Ebi; BEIKI, HAMID - Iowa State University; Bickhart, Derek; BILLIS, KONSTANTINOS - Embl-Ebi; CHOW, WILLIAM - Wellcome Trust Sanger Institute; EORY, LEL - Roslin Institute; FINLAYSON, HEATHER - Roslin Institute; FLICEK, PAUL - Embl-Ebi; GIRON, CARLOS - Embl-Ebi; GRIFFIN, DARREN - University Of Kent; HALL, RICHARD - Pacific Biosciences Inc; HANNUM, GREGORY - Denovium; HOURLIER, THIBAUT - Embl-Ebi; HOWE, KERSTIN - Wellcome Trust Sanger Institute; HUME, DAVID - Roslin Institute; IZUOGU, OSAGIE - Embl-Ebi; KIM, KRISTI - Pacific Biosciences Inc; KOREN, SERGEY - National Institutes Of Health (NIH); LIU, HAIBO - Iowa State University; MANCHANDA, NANCY - Iowa State University; MARTIN, FERGAL - Embl-Ebi; Nonneman, Danny - Dan; O'CONNOR, REBECCA - University Of Kent; PHILLIPPY, ADAM - National Instiute Of Allergy And Infectious Diseases (NIAID, NIH); Rohrer, Gary; Rosen, Benjamin - Ben; RUND, LAURIE - University Of Illinois; SARGENT, CAROLE - University Of Cambridge; SCHOOK, LAWRENCE - University Of Illinois; Schroeder, Steven - Steve; SHWARTZ, ARIEL - Denovium; SKINNER, BENJAMIN - University Of Cambridge; TALBOT, RICHARD - University Of Edinburgh; TSENG, ELIZABETH - Pacific Biosciences Inc; TUGGLE, CHRISTOPHER - Iowa State University; WATSON, MICK - Roslin Institute; Smith, Timothy - Tim; ARCHIBALD, ALAN - Roslin Institute

Submitted to: Gigascience
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/22/2020
Publication Date: 6/16/2020
Citation: Warr, A., Affara, N., Aken, B., Beiki, H., Bickhart, D.M., Billis, K., Chow, W., Eory, L., Finlayson, H.A., Flicek, P., Giron, C.G., Griffin, D.K., Hall, R., Hannum, G., Hourlier, T., Howe, K., Hume, D.A., Izuogu, O., Kim, K., Koren, S., Liu, H., Manchanda, N., Martin, F.J., Nonneman, D.J., O'Connor, R.E., Phillippy, A.M., Rohrer, G.A., Rosen, B.D., Rund, L.A., Sargent, C.A., Schook, L.B., Schroeder, S.G., Shwartz, A.S., Skinner, B.M., Talbot, R., Tseng, E., Tuggle, C.K., Watson, M., Smith, T.P., Archibald, A.L. 2020. An improved pig reference genome sequence to enable pig genetics and genomics research. GigaScience. 9(6):giaa051. https://doi.org/10.1093/gigascience/giaa051.
DOI: https://doi.org/10.1093/gigascience/giaa051

Interpretive Summary: The domestic pig is an important species in US agriculture and medical research. We present a new reference genome for the pig that places it on par in quality with the human reference genome. This will enable better selective breeding for new pig lines. It will also allow more insight into shared genes that pigs have with human for future medical research. This result is due to an extensive collaboration between US and UK scientists.

Technical Abstract: The domestic pig is important both as a food source and as a biomedical model with high anatomical and immunological similarity to humans. The draft reference genome (Sscrofa10.2) represents a purebred female pig from a commercial pork production breed (Duroc), and was established using older clone-based sequencing methods. The Sscrofa10.2 assembly was incomplete and unresolved redundancies, short range order and orientation errors and associated misassembled genes limited its utility. We present two genome assemblies created with more recent long read technologies and a whole genome shotgun strategy, one for the same Duroc female (Sscrofa11.1) and one for an outbred, composite breed male animal commonly used for commercial pork production (USMARCv1.0). Both assemblies are of substantially higher (>90-fold) continuity and accuracy compared to the earlier reference, and the availability of two independent assemblies provided an opportunity to identify large-scale variants and to error-check the accuracy of representation of the genome. We propose that the improved Duroc breed assembly (Sscrofa11.1) become the reference genome for genomic research in pigs