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

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.; Schwartz, A. S.; Skinner, B. M.; Talbot, R.; Tseng, E.; Tuggle, C. K.; Watson, M.; Smith, T. P.; Archibald, A. L.

doi:10.1101/668921

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bioRxiv · 10.1101/668921

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

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Abstract

The domestic pig (Sus scrofa) 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) 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. We present two annotated highly contiguous chromosome-level 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 (USMARCv1.0). Both assemblies are of substantially higher (>90-fold) continuity and accuracy than Sscrofa10.2. 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.

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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., Schwartz, A. S., Skinner, B. M., Talbot, R., Tseng, E., Tuggle, C. K., Watson, M., Smith, T. P., Archibald, A. L.. 2019-06-13. An improved pig reference genome sequence to enable pig genetics and genomics research. https://doi.org/10.1101/668921

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