Abstract
Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.
Original language | English (US) |
---|---|
Pages (from-to) | 635-641 |
Number of pages | 7 |
Journal | Nature |
Volume | 485 |
Issue number | 7400 |
DOIs | |
State | Published - 2012 |
ASJC Scopus subject areas
- General
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In: Nature, Vol. 485, No. 7400, 2012, p. 635-641.
Research output: Contribution to journal › Article › peer-review
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TY - JOUR
T1 - The tomato genome sequence provides insights into fleshy fruit evolution
AU - Sato, Shusei
AU - Tabata, Satoshi
AU - Hirakawa, Hideki
AU - Asamizu, Erika
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AU - Wang, Xiaoxuan
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AU - Cheng, Zhukuan
AU - Zuo, Jianru
AU - Ren, Jianfeng
AU - Zhao, Jiuhai
AU - Yan, Liuhua
AU - Jiang, Hongling
AU - Wang, Bao
AU - Li, Hongshuang
AU - Li, Zhenjun
AU - Fu, Fuyou
AU - Chen, Bingtang
AU - Han, Bin
AU - Feng, Qi
AU - Fan, Danlin
AU - Wang, Ying
AU - Ling, Hongqing
AU - Xue, Yongbiao
AU - Ware, Doreen
AU - Richard McCombie, W.
AU - Lippman, Zachary B.
AU - Chia, Jer Ming
AU - Jiang, Ke
AU - Pasternak, Shiran
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AU - Rombauts, Stephane
AU - Fawcett, Jeffrey
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AU - Zamir, Dani
AU - Liang, Chunbo
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AU - Bruggmann, Remy
AU - Mayer, Klaus
AU - Jia, Zhiqi
AU - Zhang, Junhong
AU - Ye, Zhibiao
AU - Bishop, Gerard J.
AU - Butcher, Sarah
AU - Lopez-Cobollo, Rosa
AU - Buchan, Daniel
AU - Filippis, Ioannis
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AU - Dixit, Institute Rekha
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AU - Frasse, Pierre
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AU - Monforte, Antonio
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AU - Conte, Mariana
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AU - Carrari, Fernando
AU - De Bellis, Gianluca
AU - Fuligni, Fabio
AU - Peano, Clelia
AU - Grandillo, Silvana
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AU - Pietrella, Marco
AU - Fantini, Elio
AU - Falcone, Giulia
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AU - Orozco, Biology Modesto
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AU - Jacobs-Oomen, Saskia
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AU - Van Haaren, J. J.
AU - -HwanJo, Sung
AU - Kim, Jungeun
AU - Kwon, Suk Yoon
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AU - Koo, Dal Hoe
AU - Lee, Sanghyeob
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AU - Rico, Alain
AU - Hallab, Asis
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AU - Klee, Kathrin
AU - Jöcker, Anika
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AU - Göbel, Ulrike
AU - Kawamura, Shingo
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AU - Sherman, Jamie D.
AU - Fukuoka, Hiroyuki
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AU - Bhutty, Sarita
AU - Chowdhury, Parul
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AU - Datema, Erwin
AU - Smit, Sandra
AU - Schijlen, Elio G.W.M.
AU - Van De Belt, Jose
AU - Van Haarst, Jan C.
AU - Peters, Sander A.
AU - Van Staveren, Marjo J.
AU - Henkens, Marleen H.C.
AU - Mooyman, Paul J.W.
AU - Hesselink, Thamara
AU - Van Ham, Roeland C.H.J.
AU - Jiang, Guoyong
AU - Droege, Marcus
AU - Choi, Doil
AU - Kang, Byung Cheol
AU - Kim, Byung Dong
AU - Park, Minkyu
AU - Kim, Seungill
AU - Yeom, Seon In
AU - Lee, Yong Hwan
AU - Choi, Yang Do
AU - Li, Guangcun
AU - Gao, Jianwei
AU - Liu, Yongsheng
AU - Huang, Shengxiong
AU - Fernandez-Pedrosa, Victoria
AU - Collado, Carmen
AU - Zuñ Iga, Sheila
AU - Wang, Guoping
AU - Cade, Rebecca
AU - Dietrich, Robert A.
AU - Rogers, Jane
AU - Knapp, Sandra
AU - Fei, Zhangjun
AU - White, Ruth A.
AU - Thannhauser, Theodore W.
AU - Giovannoni, James J.
AU - Botella, Miguel Angel
AU - Gilbert, Louise
AU - Gonzalez, Fabra Ramon
AU - Goicoechea, Jose Luis
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AU - Kudrna, David
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AU - Wing, Rod
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AU - Solanke, Amolkumar U.
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AU - Gupta, Vikrant
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AU - Khurana, Jitendra P.
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AU - Dalmay, Tamas
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AU - Chamala, Srikar
AU - Barbazuk, W. Brad
AU - Li, Jingping
AU - Guo, Hui
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AU - Wang, Yupeng
AU - Zhang, Dong
AU - Paterson, Andrew H.
AU - Wang, Xiyin
AU - Tang, Haibao
AU - Barone, Amalia
AU - Chiusano, Maria Luisa
AU - Ercolano, Maria Raffaella
AU - D'Agostino, Nunzio
AU - Di Filippo, Miriam
AU - Traini, Alessandra
AU - Sanseverino, Walter
AU - Frusciante, Luigi
AU - Seymour, Graham B.
AU - Elharam, Mounir
AU - Fu, Ying
AU - Hua, Axin
AU - Kenton, Steven
AU - Lewis, Jennifer
AU - Lin, Shaoping
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AU - Lai, Hongshing
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AU - Qu, Chunmei
AU - White, Douglas
AU - White, James
AU - Xing, Yanbo
AU - Yang, Keqin
AU - Yi, Jing
AU - Yao, Ziyun
AU - Zhou, Liping
AU - Roe, Bruce A.
AU - Vezzi, Alessandro
AU - D'Angelo, Michela
AU - Zimbello, Rosanna
AU - Schiavon, Riccardo
AU - Caniato, Elisa
AU - Rigobello, Chiara
AU - Campagna, Davide
AU - Vitulo, Nicola
AU - Valle, Giorgio
AU - Nelson, David R.
AU - De Paoli, Emanuele
AU - Szinay, Dora
AU - De Jong, Hans H.
AU - Bai, Yuling
AU - Visser, Richard G.F.
AU - Lankhorst, Reném Klein
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AU - McLaren, Karen
AU - Nicholson, Christine
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AU - Gianese, Giulio
N1 - Funding Information: Acknowledgements This work was supported by: Argentina: INTA and CONICET. Belgium: Flemish Institute for Biotechnology and Ghent University. China: The State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences; Ministry of Science and Technology (2006AA10A116, 2004CB720405, 2006CB101907, 2007DFB30080) Ministry of Agriculture (‘948’ Program: 2007-Z5); National Natural Science Foundation (36171319); Postdoctoral Science Foundation (20070420446). European Union: FP6 Integrated ProjectEU-SOL PL 016214. France: Institute National de la Recherche Agronomique and Agence Nationale de la Recherche. Germany: the Max Planck Society. India: Department of Biotechnology, Government of India; Indian Council of Agricultural Research. Italy: Ministry of Research (FIRB-SOL, FIRB-Parallelomics, ItaLyco and GenoPOM projects); Ministry of Agriculture (Agronanotech and Biomassval projects); FILAS foundation; ENEA; CNR-ENEA project L. 191/2009. Japan: Kazusa DNA Research Institute Foundation and National Institute of Vegetable and Tea Science. Korea: KRIBB Basic Research Fund and Crop Functional Genomics Research Center (CFGC), MEST. Netherlands: Centrefor BioSystemsGenomics,Netherlands Organizationfor Scientific Research. Spain: Fundación Genoma España; Cajamar; FEPEX; Fundación Séneca; ICIA; IFAPA; Fundación Manrique de Lara; Instituto Nacional de Bioinformatica. UK: BBSRC grant BB/C509731/1; DEFRA; SEERAD. USA: NSF (DBI-0116076; DBI-0421634; DBI-0606595; IOS-0923312; DBI-0820612; DBI-0605659; DEB-0316614; DBI 0849896 and MCB 1021718); USDA (2007-02773 and 2007-35300-19739); USDA-ARS. We acknowledge the Potato Genome Sequencing Consortium for sharing data before publication; potato RNA-Seq data was provided by C. R. Buell from the NSF-funded Potato Genome Sequence and Annotation project; tomato RNA-Seq data by the USDA-funded SolCAP project, N. Sinha and J. Maloof; the Amplicon Express team for BAC pooling services; construction of the Whole Genome Profiling (WGP) physical map was supported by EnzaZaden, RijkZwaan, Vilmorin & Cie, and Takii & Co. Keygene N.V. owns patents and patent applications covering its AFLP and Whole Genome Profiling technologies; AFLP and Keygene are registered trademarks of Keygene N.V. The following individuals are also acknowledged for their contribution to the work described: J. Park, B. Wang, C. Niu, D. Liu, F. Cojutti, S.Pescarolo, A.Zambon, G.Xiao, J. Chen, J.Shi, L.Zhang, L.Zeng, M.Caccamo, D.Bolser, D. Martin, M. Gonzalez, P. A. Bedinger, P. A. Covey, P. Pachori, R. R. Pousada, S. Hakim, S. Sims, V. Cahais, W. Long, X. Zhou, Y. Lu, W. Haso, C. Lai, S. Lepp, C. Peluso, H. Teramu, H. De Jong, R. Lizarralde, E. R. May and Z. Li. M. Zabeau is thanked for his support and encouragement and S. van den Brink for her secretarial support. We dedicate this work to the late C. Rick whopioneered tomato genetics, collection of wild germplasm and the distribution of seed and knowledge.
PY - 2012
Y1 - 2012
N2 - Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.
AB - Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.
UR - http://www.scopus.com/inward/record.url?scp=84863693752&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84863693752&partnerID=8YFLogxK
U2 - 10.1038/nature11119
DO - 10.1038/nature11119
M3 - Article
C2 - 22660326
AN - SCOPUS:84863693752
SN - 0028-0836
VL - 485
SP - 635
EP - 641
JO - Nature
JF - Nature
IS - 7400
ER -