The tomato genome sequence provides insights into fleshy fruit evolution
Kenta Shirasawa(Kazusa DNA Research Institute), Sachiko Isobe(Kazusa DNA Research Institute), Takakazu Kaneko(Kazusa DNA Research Institute), Hideki Hirakawa(Kazusa DNA Research Institute), Koh Aoki(Kazusa DNA Research Institute), Yasukazu Nakamura(Kazusa DNA Research Institute), Daisuke Shibata(Kazusa DNA Research Institute), Erika Asamizu(Kazusa DNA Research Institute), James Knight(Enzo Life Sciences (United States)), Michael Egholm (Enzo Life Sciences (United States)), Robert Bogden(Roche (Switzerland)), Changbao Li(Roche (Switzerland)), Qi Feng(National Center for Gene Research), Danlin Fan(Chinese Academy of Sciences), Changbao Li(National Center for Gene Research), Jun Wang(BGI Group (China)), Xin Liu(BGI Group (China)), Shifeng Cheng(BGI Group (China)), Shuang Yang(BGI Group (China)), Xun Xu(BGI Group (China)), Yuanyuan Ren(BGI Group (China)), Shengkai Pan(BGI Group (China)), Alessandro Albiero(Biomolecular Research Genomics (Italy)), Francesca Dal Pero(Biomolecular Research Genomics (Italy)), Sara Todesco(Cornell University), J. Gosselin(Cornell University), JeMin Lee(Cornell University), Jonathan A. Leto(Cornell University), Linyong Mao(Cornell University), Susan R. Strickler(Cornell University), Isaak Tecle(Cornell University), Aureliano Bombarely(Cornell University), Shan Gao(Cornell University), Minyun Huang(Cornell University), Robert Buels(Cornell University), Naama Menda(Cornell University), Yi Zheng(Cornell University), Julia Vrebalov(Cornell University), Silin Zhong(Cornell University), A. York(Cornell University), Joyce Van Eck(Cornell University), Theodore W. Thannhauser(Cornell University), Ruth A. White(Cornell University), Willem J. Stiekema(Centre for BioSystems Genomics), Paolo Ribeca(Centro Nacional de Análisis Genómico), Tyler Alioto(Centro Nacional de Análisis Genómico), Wencai Yang(China Agricultural University), Zhonghua Zhang(Institute of Vegetables and Flowers), Xiaoxuan Wang(Institute of Vegetables and Flowers), Jun He(Institute of Vegetables and Flowers), Yanmei Guo(Institute of Vegetables and Flowers), Ying Li(Institute of Vegetables and Flowers), Jianchang Gao(Shandong Academy of Agricultural Sciences), Jianfeng Ren(State Key Laboratory of Plant Genomics), Hongling Jiang(State Key Laboratory of Plant Genomics), Hongshuang Li(State Key Laboratory of Plant Genomics), Liuhua Yan(State Key Laboratory of Plant Genomics), Jiuhai Zhao(State Key Laboratory of Plant Genomics), Fuyou Fu(State Key Laboratory of Plant Genomics), Zhenjun Li(State Key Laboratory of Plant Genomics), Bao Wang(State Key Laboratory of Plant Genomics), Bingtang Chen(State Key Laboratory of Plant Genomics), Ke Jiang(Cold Spring Harbor Laboratory), Jer-Ming Chia(Cold Spring Harbor Laboratory), Melissa Kramer(Cold Spring Harbor Laboratory), Shiran Pasternak(Chinese Academy of Sciences), Laura Gelley(Chinese Academy of Sciences), L.A. Shearer(Colorado State University), Lorinda K. Anderson(Chinese Academy of Sciences), Suzanne M. Royer(Colorado State University), Song-Bin Chang(National Taiwan University), Jocelyn K. C. Rose(Cornell University), Nancy T. Eannetta(Cornell University), Ryan P. McQuinn(Cornell University), Antonio J. Matas(Cornell University), Yimin Xu(Cornell University), Francisco Camara (Centre for Genomic Regulation), Roderic Guigó(Centre for Genomic Regulation), Stéphane Rombauts(VIB-UGent Center for Plant Systems Biology), Jeffrey A. Fawcett(VIB-UGent Center for Plant Systems Biology), Dani Zamir(Hebrew University of Jerusalem), Chunbo Liang(Heilongjiang Academy of Sciences), Rémy Bruggmann(Institute of Bioinformatics and Systems Biology), M. Spannagl(National Taiwan University), Heidrun Gundlach(Cornell University), Zhiqi Jia(Cornell University), Zhibiao Ye(Huazhong Agricultural University), Junhong Zhang (Huazhong Agricultural University), Ioannis Filippis(Cornell University), Daniel Buchan(Cornell University), James Abbott(Universitat Pompeu Fabra), Rosa López-Cobollo(Universitat Pompeu Fabra), Rekha Dixit(Ghent University Hospital), Jitendra Kumar Pal(Ghent University Hospital), Vivek Dogra(Ghent University Hospital), Awadhesh Pandit(Hebrew University of Jerusalem), Tilak Raj Sharma(Indian Agricultural Research Institute), Trilochan Mohapatra(Indian Agricultural Research Institute), Kishor Gaikwad(Indian Agricultural Research Institute), Manju Singh(Indian Agricultural Research Institute), Ajay Kumar Mahato(Indian Agricultural Research Institute), Archana Singh(Indian Agricultural Research Institute), Pradeep Kumar Singh(Huazhong Agricultural University), Mathilde Causse(Huazhong Agricultural University), Christophe Rothan(Biologie du Fruit et Pathologie), Céline Noirot(Génétique Physiologie et Systèmes d'Elevage), Hélène Bergès(Génétique Physiologie et Systèmes d'Elevage), Arnaud Bellec(Génétique Physiologie et Systèmes d'Elevage), Sonia Vautrin(Génétique Physiologie et Systèmes d'Elevage), Christophe Klopp(Génétique Physiologie et Systèmes d'Elevage), Jérôme Mariette(Génétique Physiologie et Systèmes d'Elevage), Mohamed Zouine(Institut National Polytechnique de Toulouse), Pierre Frasse(Institut National Polytechnique de Toulouse), Alain Latché(Institut National Polytechnique de Toulouse), Christine Rousseau(Institut National Polytechnique de Toulouse), Jean-Claude Pech(Institut National Polytechnique de Toulouse), Farid Regad(Institut National Polytechnique de Toulouse), Corinne Delalande(Institut National Polytechnique de Toulouse), Murielle Philippot(Institut National Polytechnique de Toulouse), Sonia Osorio(Instituto de Biología Molecular y Celular de Plantas), Antonio J. Monforte(Instituto de Biología Molecular y Celular de Plantas), Pierre Péricard(Instituto de Biología Molecular y Celular de Plantas), Asunción Fernandez del Carmen(Instituto de Biología Molecular y Celular de Plantas), R. Fernández-Muñoz(Institut National de la Recherche Agronomique), Gabriel Lichtenstein(Institut National de la Recherche Agronomique), Mariana Conte(Institut National de la Recherche Agronomique), Clelia Peano(Institut National Polytechnique de Toulouse), Fabio Fuligni(Institut National de la Recherche Agronomique), Pasquale Termolino(Institut National de la Recherche Agronomique), Silvana Grandillo(Institut National Polytechnique de Toulouse), Elio Fantini(National Agency for New Technologies, Energy and Sustainable Economic Development), Giulia Falcone(National Agency for New Technologies, Energy and Sustainable Economic Development), Alessia Fiore(National Agency for New Technologies, Energy and Sustainable Economic Development), Marco Pietrella(National Agency for New Technologies, Energy and Sustainable Economic Development), Marco Pietrella(National Agency for New Technologies, Energy and Sustainable Economic Development), Paolo Facella(National Agency for New Technologies, Energy and Sustainable Economic Development), Loretta Daddiego(National Agency for New Technologies, Energy and Sustainable Economic Development), Gaetano Perrotta(National Agency for New Technologies, Energy and Sustainable Economic Development), Loredana Lopez(National Agency for New Technologies, Energy and Sustainable Economic Development), David Torrents(Institució Catalana de Recerca i Estudis Avançats), Xavier Pastor (Consejo Superior de Investigaciones Científicas), Modesto Orozco(Consejo Superior de Investigaciones Científicas), Modesto Orozco(Consejo Superior de Investigaciones Científicas), David Torrents(Institució Catalana de Recerca i Estudis Avançats), Peter de Heer(Agro Business Park), Erwin Datema(Agro Business Park), Marcel Prins(Agro Business Park), Mike Cariaso(National Academies of Sciences, Engineering, and Medicine), Marco G.M. Van Schriek(National Academies of Sciences, Engineering, and Medicine), Jan van Oeveren(National Academies of Sciences, Engineering, and Medicine), Saskia Jacobs-Oomen(Agro Business Park), Mark J. J. van Haaren(Agro Business Park), Richard Feron(Scuola Superiore Sant'Anna), Antoine Janssen(Agro Business Park), Lorena daPonte(Agro Business Park), Jung‐Eun Kim(Korea Research Institute of Bioscience and Biotechnology), Sangmi Kim(Seoul National University), Dal-Hoe Koo(Korea Research Institute of Bioscience and Biotechnology), Sung-Hwan Jo(Korea Research Institute of Bioscience and Biotechnology), Cheol-Goo Hur(Korea Research Institute of Bioscience and Biotechnology), Sanghyeob Lee(Korea Research Institute of Bioscience and Biotechnology), Suk-Yoon Kwon(James Hutton Institute), Christopher R. Clouser(Thermo Fisher Scientific (Norway)), Alain Rico(National University of Food Technologies), Asis Hallab(Max Planck Institute for Plant Breeding Research), Christiane Gebhardt(Max Planck Institute for Plant Breeding Research), Jens Warfsmann(Max Planck Institute for Plant Breeding Research), Kathrin Klee(Max Planck Institute for Plant Breeding Research), Ulrike Göbel(Max Planck Institute for Plant Breeding Research), Anika Jöcker(Max Planck Institute for Plant Breeding Research), Shingo Kawamura(Meiji University), Kentaro Yano(Meiji University), Jamie Sherman(Montana State University), Satomi Negoro(Institute of Vegetable and Floriculture Science), Sarita Bhutty(National Institute of Plant Genome Research), Parul Chowdhury(National Institute of Plant Genome Research), Sandra Smit(Research International (United States)), Thamara Hesselink(Research International (United States)), M. J. van Staveren(Research International (United States)), Paul Mooyman(Research International (United States)), José van de Belt(Research International (United States)), Erwin Datema(Agro Business Park), Jan C. van Haarst(Research International (United States)), Marleen H.C. Henkens(Research International (United States)), Sander Peters(Max Planck Society), Elio Schijlen(Max Planck Society), Guoyong Jiang(Qingdao Agricultural University), Marcus Droege(Roche (Switzerland)), Seungill Kim(Seoul National University), Byung-Cheol Kang(Seoul National University), Byung Dong Kim(Seoul National University), Seon-In Yeom (Seoul National University), Minkyu Park(Seoul National University), Yong-Hwan Lee(Seoul National University), Yang-Do Choi(Seoul National University), Guangcun Li(Shandong Academy of Agricultural Sciences), Jianwei Gao(Shandong Academy of Agricultural Sciences), Shengxiong Huang(Sichuan University), Yongsheng Liu(Sichuan University), C. Trueba Collado(Sistemas Genómicos), Victoria Fernández‐Pedrosa(Sistemas Genómicos), Sheila Zuñiga(Sistemas Genómicos), Guoping Wang(South China Agricultural University), Rebecca Cade(North Carolina Biotechnology Center), Robert Dietrich(North Carolina Biotechnology Center), Sandra Knapp(Natural History Museum), Ruth A. White(Cornell University), Theodore W. Thannhauser(Cornell University), Miguel A. Botella(Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora"), Louise Gilbert(Qingdao Agricultural University), Ramon Gonzalez(Roche (Switzerland)), Kristi Collura(University of Arizona), José Luis Goicoechea(University of Arizona), Yeisoo Yu(University of Arizona), David Kudrna(University of Arizona), Marina Wissotski(University of Arizona), P. J. Green(Seoul National University), Aishwarya Bala Gurazada(Seoul National University), Arun Kumar Sharma(University of Delhi), Amolkumar U. Solanke(University of Delhi), Shailendra Vyas(University of Delhi), Vikrant Gupta(University of Delhi), Rahul Kumar(University of Delhi), Saloni Mathur(University of Delhi), Paramjit Khurana(University of Delhi), Irina Mohorianu(University of East Anglia), Brandon Walts(South China Agricultural University), W. Brad Barbazuk(Cancer Genetics (United States)), Srikar Chamala(Cancer Genetics (United States)), Dong Zhang(University of Georgia), Tae-Ho Lee(Natural History Museum), Haibao Tang(J. Craig Venter Institute), Hui Guo(United States Department of Agriculture), Yupeng Wang(United States Department of Agriculture), Jingping Li(United States Department of Agriculture), Haibao Tang(J. Craig Venter Institute), Maria Luisa Chiusano(Consejo Superior de Investigaciones Científicas), Alessandra Traini(Department of Agricultural Sciences), Walter Sanseverino(Department of Agricultural Sciences), Nunzio D’Agostino(Department of Agricultural Sciences), Maria Raffaella Ercolano(Department of Agricultural Sciences), Amalia Barone(Department of Agricultural Sciences), Miriam Di Filippo(Department of Agricultural Sciences), Fares Z. Najar(University of Bonn), Mounir Elharam(University of Delaware), Baifang Qin(University of Delaware), Jennifer A. Lewis(University of Delaware), Chunmei Qu(University of Delhi), Ziyun Yao(University of Delhi), Hongshing Lai(University of Delhi), Axin Hua(University of Delhi), Ruihua Shi(University of Delhi), Keqin Yang(University of Delhi), Liping Zhou(University of Delhi), Ying Fu(University of Delhi), Douglas White(University of Delhi), James D. White(University of East Anglia), Yanbo Xing(University of East Anglia), Steven Kenton(University of Florida), Shaoping Lin(University of Florida), Jing Yi(University of Florida), Chiara Rigobello(University of Padua), Davide Campagna(University of Padua), Elisa Caniato(University of Padua), Nicola Vitulo(University of Padua), Riccardo Schiavon(University of Padua), Michela D’Angelo(University of Padua), Alessandro Vezzi(North China University of Science and Technology), Rosanna Zimbello(J. Craig Venter Institute), David R. Nelson(University of Tennessee Health Science Center), Emanuele De Paoli(University of Udine), Dora Szinay(Graduate School Experimental Plant Sciences), Yuling Bai(Graduate School Experimental Plant Sciences), Dora Szinay(Graduate School Experimental Plant Sciences), Richard G. F. Visser(Graduate School Experimental Plant Sciences), Helen Beasley(Wellcome Sanger Institute), Christine Nicholson(Wellcome Sanger Institute), Karen McLaren(University of Nottingham), Claire Riddle(Wellcome Sanger Institute), Giulio Gianese(National Agency for New Technologies, Energy and Sustainable Economic Development)
Cited by 3,365Open Access
Abstract
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.
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