The tomato genome sequence provides insights into fleshy fruit evolution

Shusei Sato; Satoshi Tabata; Hideki Hirakawa; Erika Asamizu; Kenta Shirasawa; Sachiko Isobe; Takakazu Kaneko; Yasukazu Nakamura; Daisuke Shibata; Koh Aoki; Michael Egholm; James Knight; Robert Bogden; Changbao Li; Yang Shuang; Xun Xu; Shengkai Pan; Shifeng Cheng; Xin Liu; Yuanyuan Ren; Jun Wang; Alessandro Albiero; Francesca Dal Pero; Sara Todesco; Joyce Van Eck; Robert M. Buels; Aureliano Bombarely; Joseph R. Gosselin; Minyun Huang; Jonathan A. Leto; Naama Menda; Susan Strickler; Linyong Mao; Shan Gao; Isaak Y. Tecle; Thomas York; Yi Zheng; Julia T. Vrebalov; JeMin Lee; Silin Zhong; Lukas A. Mueller; Willem J. Stiekema; Paolo Ribeca; Tyler Alioto; Wencai Yang; Sanwen Huang; Yongchen Du; Zhonghua Zhang; Glenn Bryan; Andrew H. Paterson; Tomato Genome Consortium

doi:10.1038/nature11119

The tomato genome sequence provides insights into fleshy fruit evolution

Shusei Sato, Satoshi Tabata, Hideki Hirakawa, Erika Asamizu, Kenta Shirasawa, Sachiko Isobe, Takakazu Kaneko, Yasukazu Nakamura, Daisuke Shibata, Koh Aoki, Michael Egholm, James Knight, Robert Bogden, Changbao Li, Yang Shuang, Xun Xu, Shengkai Pan, Shifeng Cheng, Xin Liu, Yuanyuan RenJun Wang, Alessandro Albiero, Francesca Dal Pero, Sara Todesco, Joyce Van Eck, Robert M. Buels, Aureliano Bombarely, Joseph R. Gosselin, Minyun Huang, Jonathan A. Leto, Naama Menda, Susan Strickler, Linyong Mao, Shan Gao, Isaak Y. Tecle, Thomas York, Yi Zheng, Julia T. Vrebalov, JeMin Lee, Silin Zhong, Lukas A. Mueller, Willem J. Stiekema, Paolo Ribeca, Tyler Alioto, Wencai Yang, Sanwen Huang, Yongchen Du, Zhonghua Zhang, Glenn Bryan, Andrew H. Paterson, Tomato Genome Consortium

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

2464 Citations (Scopus)

Abstract

Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera(1) 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(2), 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.</p>

Original language	English
Pages (from-to)	635-641
Number of pages	7
Journal	Nature
Volume	485
Issue number	7400
DOIs	https://doi.org/10.1038/nature11119
Publication status	Published - 31 May 2012

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Sato, S., Tabata, S., Hirakawa, H., Asamizu, E., Shirasawa, K., Isobe, S., Kaneko, T., Nakamura, Y., Shibata, D., Aoki, K., Egholm, M., Knight, J., Bogden, R., Li, C., Shuang, Y., Xu, X., Pan, S., Cheng, S., Liu, X., ... Tomato Genome Consortium (2012). The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485(7400), 635-641. https://doi.org/10.1038/nature11119

@article{45aced88a46a4b81872ae76b4d2fa7ac,

title = "The tomato genome sequence provides insights into fleshy fruit evolution",

abstract = "Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera(1) 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(2), 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.",

author = "Shusei Sato and Satoshi Tabata and Hideki Hirakawa and Erika Asamizu and Kenta Shirasawa and Sachiko Isobe and Takakazu Kaneko and Yasukazu Nakamura and Daisuke Shibata and Koh Aoki and Michael Egholm and James Knight and Robert Bogden and Changbao Li and Yang Shuang and Xun Xu and Shengkai Pan and Shifeng Cheng and Xin Liu and Yuanyuan Ren and Jun Wang and Alessandro Albiero and {Dal Pero}, Francesca and Sara Todesco and {Van Eck}, Joyce and Buels, {Robert M.} and Aureliano Bombarely and Gosselin, {Joseph R.} and Minyun Huang and Leto, {Jonathan A.} and Naama Menda and Susan Strickler and Linyong Mao and Shan Gao and Tecle, {Isaak Y.} and Thomas York and Yi Zheng and Vrebalov, {Julia T.} and JeMin Lee and Silin Zhong and Mueller, {Lukas A.} and Stiekema, {Willem J.} and Paolo Ribeca and Tyler Alioto and Wencai Yang and Sanwen Huang and Yongchen Du and Zhonghua Zhang and Glenn Bryan and Paterson, {Andrew H.} and {Tomato Genome Consortium}",

year = "2012",

month = may,

day = "31",

doi = "10.1038/nature11119",

language = "English",

volume = "485",

pages = "635--641",

journal = "Nature",

issn = "0028-0836",

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Sato, S, Tabata, S, Hirakawa, H, Asamizu, E, Shirasawa, K, Isobe, S, Kaneko, T, Nakamura, Y, Shibata, D, Aoki, K, Egholm, M, Knight, J, Bogden, R, Li, C, Shuang, Y, Xu, X, Pan, S, Cheng, S, Liu, X, Ren, Y, Wang, J, Albiero, A, Dal Pero, F, Todesco, S, Van Eck, J, Buels, RM, Bombarely, A, Gosselin, JR, Huang, M, Leto, JA, Menda, N, Strickler, S, Mao, L, Gao, S, Tecle, IY, York, T, Zheng, Y, Vrebalov, JT, Lee, J, Zhong, S, Mueller, LA, Stiekema, WJ, Ribeca, P, Alioto, T, Yang, W, Huang, S, Du, Y, Zhang, Z, Bryan, G, Paterson, AH & Tomato Genome Consortium 2012, 'The tomato genome sequence provides insights into fleshy fruit evolution', Nature, vol. 485, no. 7400, pp. 635-641. https://doi.org/10.1038/nature11119

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AU - Sato, Shusei

AU - Tabata, Satoshi

AU - Hirakawa, Hideki

AU - Asamizu, Erika

AU - Shirasawa, Kenta

AU - Isobe, Sachiko

AU - Kaneko, Takakazu

AU - Nakamura, Yasukazu

AU - Shibata, Daisuke

AU - Aoki, Koh

AU - Egholm, Michael

AU - Knight, James

AU - Bogden, Robert

AU - Li, Changbao

AU - Shuang, Yang

AU - Xu, Xun

AU - Pan, Shengkai

AU - Cheng, Shifeng

AU - Liu, Xin

AU - Ren, Yuanyuan

AU - Wang, Jun

AU - Albiero, Alessandro

AU - Dal Pero, Francesca

AU - Todesco, Sara

AU - Van Eck, Joyce

AU - Buels, Robert M.

AU - Bombarely, Aureliano

AU - Gosselin, Joseph R.

AU - Huang, Minyun

AU - Leto, Jonathan A.

AU - Menda, Naama

AU - Strickler, Susan

AU - Mao, Linyong

AU - Gao, Shan

AU - Tecle, Isaak Y.

AU - York, Thomas

AU - Zheng, Yi

AU - Vrebalov, Julia T.

AU - Lee, JeMin

AU - Zhong, Silin

AU - Mueller, Lukas A.

AU - Stiekema, Willem J.

AU - Ribeca, Paolo

AU - Alioto, Tyler

AU - Yang, Wencai

AU - Huang, Sanwen

AU - Du, Yongchen

AU - Zhang, Zhonghua

AU - Bryan, Glenn

AU - Paterson, Andrew H.

AU - Tomato Genome Consortium

PY - 2012/5/31

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AB - Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera(1) 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(2), 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.

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DO - 10.1038/nature11119

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VL - 485

SP - 635

EP - 641

JO - Nature

JF - Nature

IS - 7400

ER -

The tomato genome sequence provides insights into fleshy fruit evolution

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