Genome sequence and analysis of the tuber crop potato

Potato Genome Sequencing Consortium

Research output: Contribution to journalArticle

1045 Citations (Scopus)

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 languageEnglish
Pages (from-to)189-95
Number of pages7
JournalNature
Volume475
Issue number7355
DOIs
Publication statusPrint publication - 10 Jul 2011
Externally publishedYes

Fingerprint

Solanum tuberosum
Sequence Analysis
Genome
Clone Cells
Tissue Expansion
Genes
Angiosperms
Food Supply
Diploidy
Gene Expression
Food
Mutation
Proteins
Inbreeding Depression

Bibliographical note

©2011 Macmillan Publishers Limited. All rights reserved

Keywords

  • Evolution, Molecular
  • Gene Duplication
  • Gene Expression Regulation, Plant
  • Genes, Plant/genetics
  • Genetic Variation
  • Genome, Plant/genetics
  • Genomics
  • Haplotypes/genetics
  • Heterozygote
  • Homozygote
  • Immunity, Innate
  • Inbreeding
  • Molecular Sequence Annotation
  • Molecular Sequence Data
  • Plant Diseases/genetics
  • Ploidies
  • Solanum tuberosum/genetics

Cite this

Potato Genome Sequencing Consortium (2011). Genome sequence and analysis of the tuber crop potato. Nature, 475(7355), 189-95. https://doi.org/10.1038/nature10158
Potato Genome Sequencing Consortium. / Genome sequence and analysis of the tuber crop potato. In: Nature. 2011 ; Vol. 475, No. 7355. pp. 189-95.
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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.",
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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 Skryabin, {Konstantin G} 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 Marshall, {David F} and Bryan, {Glenn J} and {Potato Genome Sequencing Consortium}",
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Potato Genome Sequencing Consortium 2011, 'Genome sequence and analysis of the tuber crop potato', Nature, vol. 475, no. 7355, pp. 189-95. https://doi.org/10.1038/nature10158

Genome sequence and analysis of the tuber crop potato. / Potato Genome Sequencing Consortium.

In: Nature, Vol. 475, No. 7355, 10.07.2011, p. 189-95.

Research output: Contribution to journalArticle

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, Konstantin 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 - Marshall, David F

AU - Bryan, Glenn J

AU - Potato Genome Sequencing Consortium

N1 - ©2011 Macmillan Publishers Limited. All rights reserved

PY - 2011/7/10

Y1 - 2011/7/10

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.

KW - Evolution, Molecular

KW - Gene Duplication

KW - Gene Expression Regulation, Plant

KW - Genes, Plant/genetics

KW - Genetic Variation

KW - Genome, Plant/genetics

KW - Genomics

KW - Haplotypes/genetics

KW - Heterozygote

KW - Homozygote

KW - Immunity, Innate

KW - Inbreeding

KW - Molecular Sequence Annotation

KW - Molecular Sequence Data

KW - Plant Diseases/genetics

KW - Ploidies

KW - Solanum tuberosum/genetics

U2 - 10.1038/nature10158

DO - 10.1038/nature10158

M3 - Article

C2 - 21743474

VL - 475

SP - 189

EP - 195

JO - Nature

JF - Nature

SN - 0028-0836

IS - 7355

ER -

Potato Genome Sequencing Consortium. Genome sequence and analysis of the tuber crop potato. Nature. 2011 Jul 10;475(7355):189-95. https://doi.org/10.1038/nature10158