The tomato genome sequence provides insights into fleshy fruit evolution

作者：Hideki Hirakawa, Erika Asamizu, K Shirasawa, Sachiko Isobe, Takakazu Kaneko, Yasukazu Nakamura, Daisuke Shibata, Koh Aoki, Michael Egholm, James Knight, Robert Bogden, Changbao Li, Qi Feng, Danlin Fan, Shuang Yang, Xun Xu, Shengkai Pan, Shifeng Cheng, Xin Liu, Yuanyuan Ren, Jun Wang, Alessandro Albiero, Francesca Dal Pero, Sara Todesco, Joyce Van Eck, Robert Buels, Aureliano Bombarely, J. Gosselin, Minyun Huang, Jonathan A. Leto, Naama Menda, Susan R. Strickler, Linyong Mao, Shan Gao, Isaak Tecle, Thomas York, Yi Zheng, Julia Vrebalov, Je Min Lee, Silin Zhong, Ruth A. White, Theodore W. Thannhauser, Willem J. Stiekema, Paolo Ribeca, Tyler Alioto, Wencai Yang, Zhonghua Zhang, Jianchang Gao, Yanmei Guo, Xiaoxuan Wang, Ying Li, Jun He, Jianfeng Ren, Jiuhai Zhao, Liuhua Yan, Hongling Jiang, Bao Wang, Hongshuang Li, Zhenjun Li, Fuyou Fu, Bingtang Chen, Jer-Ming Chia, Ke Jiang, Shiran Pasternak, Laura Gelley, Melissa Kramer, Lorinda K. Anderson, Suzanne M. Royer, L.A. Shearer, Song‐Bin Chang, Rose Jc, Yimin Xu, Nancy T. Eannetta, Antonio J. Matas, Ryan P. McQuinn, Francisco Câmara, R Guigó, Stéphane Rombauts, Jeffrey A. Fawcett, Dani Zamir, Chunbo Liang, M. Spannagl, Heidrun Gundlach, Rémy Bruggmann, Zhiqi Jia, Jun Zhang, Zhibiao Ye, Rosa Lopez-Cobollo, Daniel Buchan, Ioannis Filippis, James Abbott, Rekha Dixit, Dr M K Singh, Archana Singh, Jitendra Kumar Pal, Awadhesh Pandit, P. K. Singh, Ajay Kumar Mahato, Vivek Dogra, Kishor Gaikwad, Tilak Raj Sharma, Trilochan Mohapatra, Mathilde Causse, Christophe Rothan, Céline Noirot, Arnaud Bellec, Hélène Bergès, Sonia Vautrin, Christophe Klopp, Jérôme Mariette, Corinne Delalande, Pierre Frasse, Mohamed Zouine, Alain Latché, Christine Rousseau, Farid Regad, Pech Jc, Murielle Philippot, Pierre Péricard, Sonia Osorio, Asun Fernández‐del‐Carmen, Antonio J. Monforte, R. Fernández-Muñoz, Mariana Conte, Gabriel Lichtenstein, Fabio Fuligni, Clelia Peano, Silvana Grandillo, Pasquale Termolino, Marco Pietrella, Elio Fantini, Giulia Falcone, Alessia Fiore, Loredana Lopez, Paolo Facella, Gaetano Perrotta, Loretta Daddiego, Modesto Orozco, Xavier Pastor, David Torrents, Marco G.M. Van Schriek, Richard Feron, Jan van Oeveren, Peter de Heer, Lorena daPonte, Saskia Jacobs-Oomen, Mike Cariaso, Marcel Prins, Antoine Janssen, M. J. J. van Haaren, Erwin Datema, Sung-Hwan Jo, Jung‐Eun Kim, Suk‐Yoon Kwon, Sangmi Kim, Dal-Hoe Koo, Sanghyeob Lee, Cheol-Goo Hur, Christopher Clouser, Alain Rico, Asis Hallab, Christiane Gebhardt, Kathrin Klee, Anika Jöcker, Jens Warfsmann, Ulrike Göbel, Shingo Kawamura, Kentaro Yano, Jamie Sherman, Satomi Negoro, Sarita Bhutty, Parul Chowdhury, Sandra Smit, Elio Schijlen, José van de Belt, Jan C. van Haarst, Sander Peters, M. J. van Staveren, Marleen H.C. Henkens, Paul Mooyman, Thamara Hesselink, Guoyong Jiang, Marcus Droege, Byung-Cheol Kang, Byung Dong Kim, Minkyu Park, Seungill Kim, Seon‐In Yeom, Yong-Hwan Lee, Choi Yang-Do, Guangcun Li, JS Gao, Yongsheng Liu, Huang, Victoria Fernández‐Pedrosa, C. Trueba Collado, Sheila Zuñiga, Guoping Wang, Rebecca Cade, Robert Dietrich, Sandra Knapp, Miguel A. Botella, Louise Gilbert, Ramón González, José Luis Goicoechea, Yeisoo Yu, David Kudrna, Kristi Collura, Marina Wissotski, Aishwarya Bala Gurazada, Pamela J. Green, Saloni Mathur, Shailendra Vyas, Amolkumar U. Solanke, Rahul Kumar, Vikrant Gupta, Arun Kumar Sharma, Paramjit Khurana, Irina Mohorianu, Brandon Walts, Srikar Chamala, W. Brad Barbazuk, Jingping Li, Hui Guo, Tae-Ho Lee, Yupeng Wang, Dong Zhang, Haibao Tang, Amalia Barone, Maria Luisa Chiusano, Maria Raffaella Ercolano, Nunzio D’Agostino, Miriam Di Filippo, Alessandra Traini, Walter Sanseverino, Mounir Elharam, Ying Fu, Axin Hua, Steven Kenton, Jennifer Lewis, Shaoping Lin, Fares Z. Najar, Hongshing Lai, Baifang Qin, Chunmei Qu, Ruihua Shi, Douglas White, James D. White, Yanbo Xing, Keqin Yang, Jing Yi, Ziyun Yao, Liping Zhou, Alessandro Vezzi, Michela D’Angelo, Rosanna Zimbello, Riccardo Schiavon, Elisa Caniato, Chiara Rigobello, Davide Campagna, Nicola Vitulo, David R. Nelson, Emanuele De Paoli, Dóra Szinay, Yuling Bai, Richard G. F. Visser, Helen Beasley, Karen McLaren, Christine Nicholson, Claire Riddle, Giulio Gianese · 发表于：Nature · 年份：2012 · DOI：10.1038/nature11119 · 被引用次数：3406 · 研究领域：Plant Pathogens and Resistance、Genomics and Phylogenetic Studies、Chromosomal and Genetic Variations

This paper reports the genome sequence of domesticated tomato, a major crop plant, and a draft sequence for its closest wild relative; comparative genomics reveal very little divergence between the two genomes but some important differences with the potato genome, another important food crop in the genus Solanum. 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.