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

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

doi:10.1093/gigascience/giaa051

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

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

Research output: Contribution to journal › Article › peer-review

Abstract / Description of output

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.

Original language	English
Pages (from-to)	1-14
Number of pages	14
Journal	GigaScience
Volume	9
Issue number	6
Early online date	16 Jun 2020
DOIs	https://doi.org/10.1093/gigascience/giaa051
Publication status	E-pub ahead of print - 16 Jun 2020

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10.1093/gigascience/giaa051

giaa051Final published version, 2.43 MBLicence: Creative Commons: Attribution (CC-BY)

Alan Archibald
- alan.archibaldroslin.ed.acuk
- Royal (Dick) School of Veterinary Studies - Personal Chair of Mammalian Molecular Genetics
Person: Academic: Research Active

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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., Girón, C. G., Griffin, D. K., Hall, R., Hannum, G., Hourlier, T., Howe, K., Hume, D. A., Izuogu, O., Kim, K., ... Archibald, A. L. (2020). An improved pig reference genome sequence to enable pig genetics and genomics research. GigaScience, 9(6), 1-14. Advance online publication. https://doi.org/10.1093/gigascience/giaa051

@article{ac0d3def8e534f6dbce68ffcb54243cc,

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.",

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 = "{\textcopyright} The Author(s) 2020. Published by Oxford University Press.",

year = "2020",

month = jun,

day = "16",

doi = "10.1093/gigascience/giaa051",

language = "English",

volume = "9",

pages = "1--14",

journal = "GigaScience",

issn = "2047-217X",

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Warr, A, Affara, N, Aken, B, Beiki, H, Bickhart, DM, Billis, K, Chow, W, Eory, L, Finlayson, HA, Flicek, P, Girón, CG, Griffin, DK, Hall, R, Hannum, G, Hourlier, T, Howe, K, Hume, DA, Izuogu, O, Kim, K, Koren, S, Liu, H, Manchanda, N, Martin, FJ, Nonneman, DJ, O'Connor, RE, Phillippy, AM, Rohrer, GA, Rosen, BD, Rund, LA, Sargent, CA, Schook, LB, Schroeder, SG, Schwartz, AS, Skinner, BM, Talbot, R, Tseng, E, Tuggle, CK, Watson, M, Smith, TPL & Archibald, AL 2020, 'An improved pig reference genome sequence to enable pig genetics and genomics research', GigaScience, vol. 9, no. 6, pp. 1-14. https://doi.org/10.1093/gigascience/giaa051

TY - JOUR

T1 - An improved pig reference genome sequence to enable pig genetics and genomics research

AU - Warr, Amanda

AU - Affara, Nabeel

AU - Aken, Bronwen

AU - Beiki, Hamid

AU - Bickhart, Derek M

AU - Billis, Konstantinos

AU - Chow, William

AU - Eory, Lel

AU - Finlayson, Heather A

AU - Flicek, Paul

AU - Girón, Carlos G

AU - Griffin, Darren K

AU - Hall, Richard

AU - Hannum, Greg

AU - Hourlier, Thibaut

AU - Howe, Kerstin

AU - Hume, David A

AU - Izuogu, Osagie

AU - Kim, Kristi

AU - Koren, Sergey

AU - Liu, Haibou

AU - Manchanda, Nancy

AU - Martin, Fergal J

AU - Nonneman, Dan J

AU - O'Connor, Rebecca E

AU - Phillippy, Adam M

AU - Rohrer, Gary A

AU - Rosen, Benjamin D

AU - Rund, Laurie A

AU - Sargent, Carole A

AU - Schook, Lawrence B

AU - Schroeder, Steven G

AU - Schwartz, Ariel S

AU - Skinner, Ben M

AU - Talbot, Richard

AU - Tseng, Elizabeth

AU - Tuggle, Christopher K

AU - Watson, Mick

AU - Smith, Timothy P L

AU - Archibald, Alan L

PY - 2020/6/16

Y1 - 2020/6/16

N2 - 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.

AB - 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.

U2 - 10.1093/gigascience/giaa051

DO - 10.1093/gigascience/giaa051

M3 - Article

C2 - 32543654

SN - 2047-217X

VL - 9

SP - 1

EP - 14

JO - GigaScience

JF - GigaScience

IS - 6

ER -

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

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