Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 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 pimpinellifolium2, 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.
The tomato genome sequence provides insights into fleshy fruit evolution / S. Sato, S. Tabata, H. Hirakawa, E. Asamizu, K. Shirasawa, S. Isobe, T. Kaneko, Y. Nakamura, D. Shibata, K. Aoki, M. Egholm, J. Knight, R. Bogden, C. Li, Y. Shuang, X. Xu, S. Pan, S. Cheng, X. Liu, Y. Ren, J. Wang, A. Albiero, D. Pero Francesca, S. Todesco, V. Eck Joyce, M. Buels Robert, A. Bombarely, R. Gosselin Joseph, M. Huang, A. Leto Jonathan, N. Menda, S. Strickler, L. Mao, S. Gao, Y. Tecle Isaak, T. York, Y. Zheng, T. Vrebalov Julia, J. Lee, S. Zhong, A. Mueller Lukas, J. Stiekema Willem, P. Ribeca, T. Alioto, W. Yang, S. Huang, Y. Du, Z. Zhang, J. Gao, Y. Guo, X. Wang, Y. Li, J. He, C. Li, Z. Cheng, J. Zuo, J. Ren, J. Zhao, L. Yan, H. Jiang, B. Wang, H. Li, Z. Li, F. Fu, B. Chen, B. Han, Q. Feng, D. Fan, Y. Wang, H. Ling, Y. Xue, D. Ware, R. McCombie W., B. Lippman Zachary, J. Chia, K. Jiang, S. Pasternak, L. Gelley, M. Kramer, K. Anderson Lorinda, S. Chang, M. Royer Suzanne, A. Shearer Lindsay, M. Stack Stephen, K.C. Rose Jocelyn, Y. Xu, N. Eannetta, J. Matas Antonio, R. Mcquinn, D. Tanksley Steven, F. Camara, R. Guigó, S. Rombauts, J. Fawcett, D. Peer Yves Van, D. Zamir, C. Liang, M. Spannagl, H. Gundlach, R. Bruggmann, K. Mayer, Z. Jia, J. Zhang, Z. Ye, J. Bishop Gerard, S. Butcher, R. Lopez-Cobollo, D. Buchan, I. Filippis, J. Abbott, R. Dixit, M. Singh, A. Singh, K. Pal Jitendra, A. Pandit, K. Singh Pradeep, K. Mahato Ajay, V. Dogra, K. Gaikwad, R. Sharma Tilak, T. Mohapatra, K. Singh Nagendra, M. Causse, C. Rothan, T. Schiex, C. Noirot, A. Bellec, C. Klopp, C. Delalande, H. Berges, J. Mariette, P. Frasse, S. Vautrin, M. Zouine, A. Latché, C. Rousseau, F. Regad, Philippot, M. Jean-Claude Pech, M. Bouzayen, P. Pericard, S. Osorio, D. Carmen Asunción Fernandez, A. Monforte, A. Granell, R. Fernandez-Muñoz, M. Conte, G. Lichtenstein, F. Carrari, D. Bellis Gianluca, F. Fuligni, C. Peano, S. Grandillo, P. Termolino, M. Pietrella, E. Fantini, G. Falcone, A. Fiore, G. Giuliano, L. Lopez, P. Facella, G. Perrotta, L. Daddiego, G. Bryan, M. Orozco, X. Pastor, D. Torrents, V. Schriek Marco G. M., M.C. Feron Richard, V. Oeveren Jan, D. Heer Peter, L. Daponte, S. Jacobs-Oomen, M. Cariaso, M. Prins, V. Eijk Michiel J. T., A. Janssen, V. Haaren Mark J. J., S. Jo, J. Kim, S. Kwon, S. Kim, D. Koo, S. Lee, C. Hur, C. Clouser, A. Rico, A. Hallab, C. Gebhardt, K. Klee, A. Jöcker, J. Warfsmann, U. Göbel, S. Kawamura, K. Yano, D. Sherman Jamie, H. Fukuoka, S. Negoro, S. Bhutty, P. Chowdhury, D. Chattopadhyay, E. Datema, S. Smit, G.W.M. Schijlen Elio, D. Belt Jose van, V. Haarst Jan C., A. Peters Sander, V. Staveren Marjo J., H.C. Henkens Marleen, J.W. Mooyman Paul, T. Hesselink, V. Ham Roeland C. H. J., G. Jiang, M. Droege, D. Choi, B. Kang, D. Kim Byung, M. Park, S. Kim, S. Yeom, Y. Lee, Y. Choi, G. Li, J. Gao, Y. Liu, S. Huang, V. Fernandez-Pedrosa, C. Collado, S. Zuñiga, G. Wang, R. Cade, A. Dietrich Robert, J. Rogers, S. Knapp, Z. Fei, A. White Ruth, W. Thannhauser Theodore, J. Giovannoni James, A. Botella Miguel, L. Gilbert, R. Gonzalez, L. Goicoechea Jose, Y. Yu, D. Kudrna, K. Collura, M. Wissotski, R. Wing, H. Schoof, C. Meyers Blake, B. Gurazada Aishwarya, J. Green Pamela, S. Mathur, S. Vyas, U. Solanke Amolkumar, R. Kumar, K. Vikrant Gupta Arun, P. Khurana, P. Khurana Jitendra, K. Tyagi Akhilesh, T. Dalmay, I. Mohorianu, B. Walts, S. Chamala, B. Barbazuk W., J. Li, H. Guo, T. Lee, Y. Wang, D. Zhang, H. Paterson Andrew, X. Wang, H. Tang, A. Barone, L. Chiusano Maria, R. Ercolano Maria, N. D’Agostino, D. Filippo Miriam, A. Traini, W. Sanseverino, L. Frusciante, B. Seymour Graham, M. Elharam, Y. Fu, A. Hua, S. Kenton, J. Lewis, S. Lin, F. Najar, H. Lai, B. Qin, C. Qu, R. Shi, D. White, J. White, Y. Xing, K. Yang, J. Yi, Z. Yao, L. Zhou, A. Roe Bruce, A. Vezzi, M. D’Angelo, R. Zimbello, R. Schiavon, E. Caniato, C. Rigobello, D. Campagna, N. Vitulo, G. Valle, R. Nelson David, D. Paoli Emanuele, D. Szinay, D. Jong Hans H., Y. Bai, G.F. Visser Richard, K. Lankhorst René M., H. Beasley, K. Mclaren, C. Nicholson, C. Riddle, G. Gianese. - In: NATURE. - ISSN 0028-0836. - 485:7400(2012), pp. 635-641. [10.1038/nature11119]
The tomato genome sequence provides insights into fleshy fruit evolution
A. Bombarely;R. Schiavon;
2012
Abstract
Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 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 pimpinellifolium2, 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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