Genome sequence and analysis of the tuber crop potato

Xun Xu; Shengkai Pan; Shifeng Cheng; Bo Zhang; Desheng Mu; Peixiang Ni; Gengyun Zhang; Shuang Yang; Ruiqiang Li; Jun Wang; Gisella Orjeda; Frank Guzman; Michael Torres; Roberto Lozano; Olga Ponce; Diana Martinez; Germán De La Cruz; S. K. Chakrabarti; Virupaksh U. Patil; G. Skryabin; Boris B. Kuznetsov; Nikolai V. Ravin; Tatjana V. Kolganova; Alexey V. Beletsky; Andrei V. Mardanov; Alex Di Genova; Daniel M. Bolser; David M.A. Martin; Guangcun Li; Yu Yang; Hanhui Kuang; Qun Hu; Xingyao Xiong; Gerard J. Bishop; Boris Sagredo; Nilo Mejía; Wlodzimierz Zagorski; Robert Gromadka; Jan Gawor; Pawel Szczesny; Sanwen Huang; Zhonghua Zhang; Chunbo Liang; Jun He; Ying Li; Ying He; Jianfei Xu; Youjun Zhang; Binyan Xie; Yongchen Du; Dongyu Qu; Merideth Bonierbale; Marc Ghislain; Maria Del Rosario Herrera; Giovanni Giuliano; Marco Pietrella; Gaetano Perrotta; Paolo Facella; Kimberly O'Brien; Sergio E. Feingold; Leandro E. Barreiro; Gabriela A. Massa; Luis Diambra; Brett R. Whitty; Brieanne Vaillancourt; Haining Lin; Alicia N. Massa; Michael Geoffroy; Steven Lundback; Dean DellaPenna; C. Robin Buell; Sanjeev Kumar Sharma; David F. Marshall; Robbie Waugh; Glenn J. Bryan; Marialaura Destefanis; Istvan Nagy; Dan Milbourne; Susan J. Thomson; Mark Fiers; Jeanne M.E. Jacobs; Kare L. Nielsen; Mads Sønderkær; Marina Iovene; Giovana A. Torres; Jiming Jiang; Richard E. Veilleux; Christian W.B. Bachem; Jan De Boer; Theo Borm; Bjorn Kloosterman; Herman Van Eck; Erwin Datema; Baste Lintel Hekkert; Aska Goverse; Roeland C.H.J. Van Ham; Richard G.F. Visser

doi:10.1038/nature10158

Genome sequence and analysis of the tuber crop potato

Xun Xu, Shengkai Pan, Shifeng Cheng, Bo Zhang, Desheng Mu, Peixiang Ni, Gengyun Zhang, Shuang Yang, Ruiqiang Li, Jun Wang, Gisella Orjeda, Frank Guzman, Michael Torres, Roberto Lozano, Olga Ponce, Diana Martinez, Germán De La Cruz, S. K. Chakrabarti, Virupaksh U. Patil, G. SkryabinBoris B. Kuznetsov, Nikolai V. Ravin, Tatjana V. Kolganova, Alexey V. Beletsky, Andrei V. Mardanov, Alex Di Genova, Daniel M. Bolser, David M.A. Martin, Guangcun Li, Yu Yang, Hanhui Kuang, Qun Hu, Xingyao Xiong, Gerard J. Bishop, Boris Sagredo, Nilo Mejía, Wlodzimierz Zagorski, Robert Gromadka, Jan Gawor, Pawel Szczesny, Sanwen Huang, Zhonghua Zhang, Chunbo Liang, Jun He, Ying Li, Ying He, Jianfei Xu, Youjun Zhang, Binyan Xie, Yongchen Du, Dongyu Qu, Merideth Bonierbale, Marc Ghislain, Maria Del Rosario Herrera, Giovanni Giuliano, Marco Pietrella, Gaetano Perrotta, Paolo Facella, Kimberly O'Brien, Sergio E. Feingold, Leandro E. Barreiro, Gabriela A. Massa, Luis Diambra, Brett R. Whitty, Brieanne Vaillancourt, Haining Lin, Alicia N. Massa, Michael Geoffroy, Steven Lundback, Dean DellaPenna, C. Robin Buell, Sanjeev Kumar Sharma, David F. Marshall, Robbie Waugh, Glenn J. Bryan, Marialaura Destefanis, Istvan Nagy, Dan Milbourne, Susan J. Thomson, Mark Fiers, Jeanne M.E. Jacobs, Kare L. Nielsen, Mads Sønderkær, Marina Iovene, Giovana A. Torres, Jiming Jiang, Richard E. Veilleux, Christian W.B. Bachem, Jan De Boer, Theo Borm, Bjorn Kloosterman, Herman Van Eck, Erwin Datema, Baste Lintel Hekkert, Aska Goverse, Roeland C.H.J. Van Ham, Richard G.F. Visser

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

1673 Scopus citations

Abstract

Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop.

Original language	English
Pages (from-to)	189-195
Number of pages	7
Journal	Nature
Volume	475
Issue number	7355
DOIs	https://doi.org/10.1038/nature10158
State	Published - 14 Jul 2011
Externally published	Yes

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10.1038/nature10158

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@article{0d3f83082b3641e8b41d281637144517,

title = "Genome sequence and analysis of the tuber crop potato",

abstract = "Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop.",

author = "Xun Xu and Shengkai Pan and Shifeng Cheng and Bo Zhang and Desheng Mu and Peixiang Ni and Gengyun Zhang and Shuang Yang and Ruiqiang Li and Jun Wang and Gisella Orjeda and Frank Guzman and Michael Torres and Roberto Lozano and Olga Ponce and Diana Martinez and {De La Cruz}, Germ{\'a}n and Chakrabarti, {S. K.} and Patil, {Virupaksh U.} and G. Skryabin and Kuznetsov, {Boris B.} and Ravin, {Nikolai V.} and Kolganova, {Tatjana V.} and Beletsky, {Alexey V.} and Mardanov, {Andrei V.} and {Di Genova}, Alex and Bolser, {Daniel M.} and Martin, {David M.A.} and Guangcun Li and Yu Yang and Hanhui Kuang and Qun Hu and Xingyao Xiong and Bishop, {Gerard J.} and Boris Sagredo and Nilo Mej{\'i}a and Wlodzimierz Zagorski and Robert Gromadka and Jan Gawor and Pawel Szczesny and Sanwen Huang and Zhonghua Zhang and Chunbo Liang and Jun He and Ying Li and Ying He and Jianfei Xu and Youjun Zhang and Binyan Xie and Yongchen Du and Dongyu Qu and Merideth Bonierbale and Marc Ghislain and Herrera, {Maria Del Rosario} and Giovanni Giuliano and Marco Pietrella and Gaetano Perrotta and Paolo Facella and Kimberly O'Brien and Feingold, {Sergio E.} and Barreiro, {Leandro E.} and Massa, {Gabriela A.} and Luis Diambra and Whitty, {Brett R.} and Brieanne Vaillancourt and Haining Lin and Massa, {Alicia N.} and Michael Geoffroy and Steven Lundback and Dean DellaPenna and Buell, {C. Robin} and Sharma, {Sanjeev Kumar} and Marshall, {David F.} and Robbie Waugh and Bryan, {Glenn J.} and Marialaura Destefanis and Istvan Nagy and Dan Milbourne and Thomson, {Susan J.} and Mark Fiers and Jacobs, {Jeanne M.E.} and Nielsen, {Kare L.} and Mads S{\o}nderk{\ae}r and Marina Iovene and Torres, {Giovana A.} and Jiming Jiang and Veilleux, {Richard E.} and Bachem, {Christian W.B.} and {De Boer}, Jan and Theo Borm and Bjorn Kloosterman and {Van Eck}, Herman and Erwin Datema and Hekkert, {Baste Lintel} and Aska Goverse and {Van Ham}, {Roeland C.H.J.} and Visser, {Richard G.F.}",

year = "2011",

month = jul,

day = "14",

doi = "10.1038/nature10158",

language = "Ingl{\'e}s",

volume = "475",

pages = "189--195",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Research",

number = "7355",

}

Xu, X, Pan, S, Cheng, S, Zhang, B, Mu, D, Ni, P, Zhang, G, Yang, S, Li, R, Wang, J, Orjeda, G, Guzman, F, Torres, M, Lozano, R, Ponce, O, Martinez, D, De La Cruz, G, Chakrabarti, SK, Patil, VU, Skryabin, G, Kuznetsov, BB, Ravin, NV, Kolganova, TV, Beletsky, AV, Mardanov, AV, Di Genova, A, Bolser, DM, Martin, DMA, Li, G, Yang, Y, Kuang, H, Hu, Q, Xiong, X, Bishop, GJ, Sagredo, B, Mejía, N, Zagorski, W, Gromadka, R, Gawor, J, Szczesny, P, Huang, S, Zhang, Z, Liang, C, He, J, Li, Y, He, Y, Xu, J, Zhang, Y, Xie, B, Du, Y, Qu, D, Bonierbale, M, Ghislain, M, Herrera, MDR, Giuliano, G, Pietrella, M, Perrotta, G, Facella, P, O'Brien, K, Feingold, SE, Barreiro, LE, Massa, GA, Diambra, L, Whitty, BR, Vaillancourt, B, Lin, H, Massa, AN, Geoffroy, M, Lundback, S, DellaPenna, D, Buell, CR, Sharma, SK, Marshall, DF, Waugh, R, Bryan, GJ, Destefanis, M, Nagy, I, Milbourne, D, Thomson, SJ, Fiers, M, Jacobs, JME, Nielsen, KL, Sønderkær, M, Iovene, M, Torres, GA, Jiang, J, Veilleux, RE, Bachem, CWB, De Boer, J, Borm, T, Kloosterman, B, Van Eck, H, Datema, E, Hekkert, BL, Goverse, A, Van Ham, RCHJ & Visser, RGF 2011, 'Genome sequence and analysis of the tuber crop potato', Nature, vol. 475, no. 7355, pp. 189-195. https://doi.org/10.1038/nature10158

TY - JOUR

T1 - Genome sequence and analysis of the tuber crop potato

AU - Xu, Xun

AU - Pan, Shengkai

AU - Cheng, Shifeng

AU - Zhang, Bo

AU - Mu, Desheng

AU - Ni, Peixiang

AU - Zhang, Gengyun

AU - Yang, Shuang

AU - Li, Ruiqiang

AU - Wang, Jun

AU - Orjeda, Gisella

AU - Guzman, Frank

AU - Torres, Michael

AU - Lozano, Roberto

AU - Ponce, Olga

AU - Martinez, Diana

AU - De La Cruz, Germán

AU - Chakrabarti, S. K.

AU - Patil, Virupaksh U.

AU - Skryabin, G.

AU - Kuznetsov, Boris B.

AU - Ravin, Nikolai V.

AU - Kolganova, Tatjana V.

AU - Beletsky, Alexey V.

AU - Mardanov, Andrei V.

AU - Di Genova, Alex

AU - Bolser, Daniel M.

AU - Martin, David M.A.

AU - Li, Guangcun

AU - Yang, Yu

AU - Kuang, Hanhui

AU - Hu, Qun

AU - Xiong, Xingyao

AU - Bishop, Gerard J.

AU - Sagredo, Boris

AU - Mejía, Nilo

AU - Zagorski, Wlodzimierz

AU - Gromadka, Robert

AU - Gawor, Jan

AU - Szczesny, Pawel

AU - Huang, Sanwen

AU - Zhang, Zhonghua

AU - Liang, Chunbo

AU - He, Jun

AU - Li, Ying

AU - He, Ying

AU - Xu, Jianfei

AU - Zhang, Youjun

AU - Xie, Binyan

AU - Du, Yongchen

AU - Qu, Dongyu

AU - Bonierbale, Merideth

AU - Ghislain, Marc

AU - Herrera, Maria Del Rosario

AU - Giuliano, Giovanni

AU - Pietrella, Marco

AU - Perrotta, Gaetano

AU - Facella, Paolo

AU - O'Brien, Kimberly

AU - Feingold, Sergio E.

AU - Barreiro, Leandro E.

AU - Massa, Gabriela A.

AU - Diambra, Luis

AU - Whitty, Brett R.

AU - Vaillancourt, Brieanne

AU - Lin, Haining

AU - Massa, Alicia N.

AU - Geoffroy, Michael

AU - Lundback, Steven

AU - DellaPenna, Dean

AU - Buell, C. Robin

AU - Sharma, Sanjeev Kumar

AU - Marshall, David F.

AU - Waugh, Robbie

AU - Bryan, Glenn J.

AU - Destefanis, Marialaura

AU - Nagy, Istvan

AU - Milbourne, Dan

AU - Thomson, Susan J.

AU - Fiers, Mark

AU - Jacobs, Jeanne M.E.

AU - Nielsen, Kare L.

AU - Sønderkær, Mads

AU - Iovene, Marina

AU - Torres, Giovana A.

AU - Jiang, Jiming

AU - Veilleux, Richard E.

AU - Bachem, Christian W.B.

AU - De Boer, Jan

AU - Borm, Theo

AU - Kloosterman, Bjorn

AU - Van Eck, Herman

AU - Datema, Erwin

AU - Hekkert, Baste Lintel

AU - Goverse, Aska

AU - Van Ham, Roeland C.H.J.

AU - Visser, Richard G.F.

PY - 2011/7/14

Y1 - 2011/7/14

N2 - Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop.

AB - Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop.

UR - http://www.scopus.com/inward/record.url?scp=79960422847&partnerID=8YFLogxK

U2 - 10.1038/nature10158

DO - 10.1038/nature10158

M3 - Artículo

C2 - 21743474

AN - SCOPUS:79960422847

SN - 0028-0836

VL - 475

SP - 189

EP - 195

JO - Nature

JF - Nature

IS - 7355

ER -

Genome sequence and analysis of the tuber crop potato

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