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, Jianchang Gao, Yanmei Guo, Xiaoxuan Wang, Ying Li, Jun He, Chuanyou Li, Zhukuan Cheng, Jianru Zuo, Jianfeng Ren, Jiuhai Zhao, Liuhua Yan, Hongling Jiang, Bao Wang, Hongshuang Li, Zhenjun Li, Fuyou Fu, Bingtang Chen, Bin Han, Qi Feng, Danlin Fan, Ying Wang, Hongqing Ling, Yongbiao Xue, Doreen Ware, W. Richard McCombie, Zachary B. Lippman, Jer Ming Chia, Ke Jiang, Shiran Pasternak, Laura Gelley, Melissa Kramer, Lorinda K. Anderson, Song Bin Chang, Suzanne M. Royer, Lindsay A. Shearer, Stephen M. Stack, Jocelyn K.C. Rose, Yimin Xu, Nancy Eannetta, Antonio J. Matas, Ryan McQuinn, Steven D. Tanksley, Francisco Camara, Roderic Guigó, Stephane Rombauts, Jeffrey Fawcett, Yves Van De Peer, Dani Zamir, Chunbo Liang, Manuel Spannagl, Heidrun Gundlach, Remy Bruggmann, Klaus Mayer, Zhiqi Jia, Junhong Zhang, Zhibiao Ye, Gerard J. Bishop, Sarah Butcher, Rosa Lopez-Cobollo, Daniel Buchan, Ioannis Filippis, James Abbott, Institute Rekha Dixit, Manju Singh, Archana Singh, Jitendra Kumar Pal, Awadhesh Pandit, Pradeep Kumar Singh, Ajay Kumar Mahato, Vivek Dogra, Kishor Gaikwad, Tilak Raj Sharma, Trilochan Mohapatra, Nagendra Kumar Singh, Mathilde Causse, Christophe Rothan, Celine Noirot, Arnaud Bellec, Christophe Klopp, Corinne Delalande, Helene Berges, Jerome Mariette, Pierre Frasse, Sonia Vautrin, Toulouse Mohamed Zouine, Alain Latché, Christine Rousseau, Farid Regad, Jean Claude Pech, Murielle Philippot, Mondher Bouzayen, Pierre Pericard, Sonia Osorio, Asuncion Fernandez Del Carmen, Antonio Monforte, Antonio Granell, Rafael Fernandez-Muñoz, Mariana Conte, Gabriel Lichtenstein, Fernando Carrari, Gianluca De Bellis, Fabio Fuligni, Clelia Peano, Silvana Grandillo, Pasquale Termolino, Marco Pietrella, Elio Fantini, Giulia Falcone, Alessia Fiore, Giovanni Giuliano, Loredana Lopez, Paolo Facella, Gaetano Perrotta, Loretta Daddiego, Glenn Bryan, Biology Modesto Orozco, Xavier Pastor, David Torrents, Marco G.M. Van Schriek, Richard M.C. Feron, Jan Van Oeveren, Peter De Heer, Lorena Da Ponte, Saskia Jacobs-Oomen, Mike Cariaso, Marcel Prins, Michiel J.T. Van Eijk, Antoine Janssen, J. J. Van Haaren, Sung -HwanJo, Jungeun Kim, Suk Yoon Kwon, Sangmi Kim, Dal Hoe Koo, Sanghyeob Lee, Christopher Clouser, Alain Rico, Asis Hallab, Christiane Gebhardt, Kathrin Klee, Anika Jöcker, Jens Warfsmann, Ulrike Göbel, Shingo Kawamura, Kentaro Yano, Jamie D. Sherman, Hiroyuki Fukuoka, Satomi Negoro, Sarita Bhutty, Parul Chowdhury, Debasis Chattopadhyay, Erwin Datema, Sandra Smit, Elio G.W.M. Schijlen, Jose Van De Belt, Jan C. Van Haarst, Sander A. Peters, Marjo J. Van Staveren, Marleen H.C. Henkens, Paul J.W. Mooyman, Thamara Hesselink, Roeland C.H.J. Van Ham, Guoyong Jiang, Marcus Droege, Doil Choi, Byung Cheol Kang, Byung Dong Kim, Minkyu Park, Seungill Kim, Seon In Yeom, Yong Hwan Lee, Yang Do Choi, Guangcun Li, Jianwei Gao, Yongsheng Liu, Shengxiong Huang, Victoria Fernandez-Pedrosa, Carmen Collado, Sheila Zuñ Iga, Guoping Wang, Rebecca Cade, Robert A. Dietrich, Jane Rogers, Sandra Knapp, Zhangjun Fei, Ruth A. White, Theodore W. Thannhauser, James J. Giovannoni, Miguel Angel Botella, Louise Gilbert, Fabra Ramon Gonzalez, Jose Luis Goicoechea, Yeisoo Yu, David Kudrna, Kristi Collura, Marina Wissotski, Rod Wing, Blake C. Meyers, Aishwarya Bala Gurazada, Pamela J. Green, Saloni Mathur, Shailendra Vyas, Amolkumar U. Solanke, Rahul Kumar, Vikrant Gupta, Arun K. Sharma, Paramjit Khurana, Jitendra P. Khurana, Akhilesh K. Tyagi, Tamas Dalmay, Irina Mohorianu, Brandon Walts, Srikar Chamala, W. Brad Barbazuk, Jingping Li, Hui Guo, Tae Ho Lee, Yupeng Wang, Dong Zhang, Andrew H. Paterson, Xiyin Wang, Haibao Tang, Amalia Barone, Maria Luisa Chiusano, Maria Raffaella Ercolano, Nunzio D'Agostino, Miriam Di Filippo, Alessandra Traini, Walter Sanseverino, Luigi Frusciante, Graham B. Seymour, Mounir Elharam, Ying Fu, Axin Hua, Steven Kenton, Jennifer Lewis, Shaoping Lin, Fares Najar, Hongshing Lai, Baifang Qin, Ruihua Shi, Chunmei Qu, Douglas White, James White, Yanbo Xing, Keqin Yang, Jing Yi, Ziyun Yao, Liping Zhou, Bruce A. Roe, Alessandro Vezzi, Michela D'Angelo, Rosanna Zimbello, Riccardo Schiavon, Elisa Caniato, Chiara Rigobello, Davide Campagna, Nicola Vitulo, Giorgio Valle, David R. Nelson, Emanuele De Paoli, Dora Szinay, Hans H. De Jong, Yuling Bai, Richard G.F. Visser, Reném Klein Lankhorst, Helen Beasley, Karen McLaren, Christine Nicholson, Claire Riddle, Giulio Gianese

Research output: Contribution to journalArticle

1715 Scopus citations

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 languageEnglish (US)
Pages (from-to)635-641
Number of pages7
JournalNature
Volume485
Issue number7400
DOIs
StatePublished - 2012

ASJC Scopus subject areas

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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., ... Gianese, G. (2012). The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485(7400), 635-641. https://doi.org/10.1038/nature11119