Advanced search
1 file | 2.12 MB Add to list

The tomato genome sequence provides insights into fleshy fruit evolution

(2012) NATURE. 485(7400). p.635-641
Author
Organization
Project
Bioinformatics: from nucleotids to networks (N2N)
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.
Keywords
GENE, HISTORY, DIVERSIFICATION, LYCOPERSICON-ESCULENTUM, ARABIDOPSIS, ORTHOLOG, PATTERNS, SORGHUM, POTATO

Downloads

  • (...).pdf
    • full text
    • |
    • UGent only
    • |
    • PDF
    • |
    • 2.12 MB

Citation

Please use this url to cite or link to this publication:

MLA
Sato, Shusei, Satoshi Tabata, Hideki Hirakawa, et al. “The Tomato Genome Sequence Provides Insights into Fleshy Fruit Evolution.” NATURE 485.7400 (2012): 635–641. Print.
APA
Sato, S., Tabata, S., Hirakawa, H., Asamizu, E., Shirasawa, K., Isobe, S., Kaneko, T., et al. (2012). The tomato genome sequence provides insights into fleshy fruit evolution. NATURE, 485(7400), 635–641.
Chicago author-date
Sato, Shusei, Satoshi Tabata, Hideki Hirakawa, Erika Asamizu, Kenta Shirasawa, Sachiko Isobe, Takakazu Kaneko, et al. 2012. “The Tomato Genome Sequence Provides Insights into Fleshy Fruit Evolution.” Nature 485 (7400): 635–641.
Chicago author-date (all authors)
Sato, Shusei, 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, 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 KC 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, 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, Thomas Schiex, Céline Noirot, Arnaud Bellec, Christophe Klopp, Corinne Delalande, Hélène Berges, Jérôme Mariette, Pierre Frasse, Sonia Vautrin, Mohamed Zouine, Alain Latche, Christine Rousseau, Farid Regad, Jean-Claude Pech, Murielle Philippot, Mondher Bouzayen, Pierre Pericard, Sonia Osorio, Asunción 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, Modesto Orozco, Xavier Pastor, David Torrents, Keygene NV Marco GM van Schriek, Richard MC Feron, Jan van Oeveren, Peter de Heer, Lorena daPonte, Saskia Jacobs-Oomen, Mike Cariaso, Marcel Prins, Michiel JT van Eijk, Antoine Janssen, Mark JJ van Haaren, Sung-Hwan Jo, Jungeun 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 D Sherman, Hiroyuki Fukuoka, Satomi Negoro, Sarita Bhutty, Parul Chowdhury, Debasis Chattopadhyay, Erwin Datema, Sandra Smit, Eliog WM Schijlen, Jose van de Belt, Jan C van Haarst, Sander A Peters, Marjo J van Staveren, Marleen HC Henkens, Paul JW Mooyman, Thamara Hesselink, Roeland CHJ 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 Zuñiga, 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, Ramon Gonzalez, Jose Luis Goicoechea, Yeisoo Yu, David Kudrna, Kristi Collura, Marina Wissotski, Rod Wing, Heiko Schoof, 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, Chunmei Qu, Ruihua Shi, 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 GF Visser, René M Klein Lankhorst, Helen Beasley, Karen McLaren, Christine Nicholson, Claire Riddle, and Giulio Gianese. 2012. “The Tomato Genome Sequence Provides Insights into Fleshy Fruit Evolution.” Nature 485 (7400): 635–641.
Vancouver
1.
Sato S, Tabata S, Hirakawa H, Asamizu E, Shirasawa K, Isobe S, et al. The tomato genome sequence provides insights into fleshy fruit evolution. NATURE. 2012;485(7400):635–41.
IEEE
[1]
S. Sato et al., “The tomato genome sequence provides insights into fleshy fruit evolution,” NATURE, vol. 485, no. 7400, pp. 635–641, 2012.
@article{3036383,
  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       = {Sato, Shusei and Tabata, Satoshi and Hirakawa, Hideki and Asamizu, Erika and Shirasawa, Kenta and Isobe, Sachiko and Kaneko, Takakazu and Nakamura, Yasukazu and Shibata, Daisuke and Aoki, Koh and Egholm, Michael and Knight, James and Bogden, Robert and Li, Changbao and Shuang, Yang and Xu, Xun and Pan, Shengkai and Cheng, Shifeng and Liu, Xin and Ren, Yuanyuan and Wang, Jun and Albiero, Alessandro and Dal Pero, Francesca and Todesco, Sara and Van Eck, Joyce and Buels, Robert M and Bombarely, Aureliano and Gosselin, Joseph R and Huang, Minyun and Leto, Jonathan A and Menda, Naama and Strickler, Susan and Mao, Linyong and Gao, Shan and Tecle, Isaak Y and York, Thomas and Zheng, Yi and Vrebalov, Julia T and Lee, JeMin and Zhong, Silin and Mueller, Lukas A and Stiekema, Willem J and Ribeca, Paolo and Alioto, Tyler and Yang, Wencai and Huang, Sanwen and Du, Yongchen and Zhang, Zhonghua and Gao, Jianchang and Guo, Yanmei and Wang, Xiaoxuan and Li, Ying and He, Jun and Li, Chuanyou and Cheng, Zhukuan and Zuo, Jianru and Ren, Jianfeng and Zhao, Jiuhai and Yan, Liuhua and Jiang, Hongling and Wang, Bao and Li, Hongshuang and Li, Zhenjun and Fu, Fuyou and Chen, Bingtang and Han, Bin and Feng, Qi and Fan, Danlin and Wang, Ying and Ling, Hongqing and Xue, Yongbiao and Ware, Doreen and McCombie, W Richard and Lippman, Zachary B and Chia, Jer-Ming and Jiang, Ke and Pasternak, Shiran and Gelley, Laura and Kramer, Melissa and Anderson, Lorinda K and Chang, Song-Bin and Royer, Suzanne M and Shearer, Lindsay A and Stack, Stephen M and Rose, Jocelyn KC and Xu, Yimin and Eannetta, Nancy and Matas, Antonio J and McQuinn, Ryan and Tanksley, Steven D and Camara, Francisco and Guigó, Roderic and Rombauts, Stephane and Fawcett, Jeffrey and Van de Peer, Yves and Zamir, Dani and Liang, Chunbo and Spannagl, Manuel and Gundlach, Heidrun and Bruggmann, Remy and Mayer, Klaus and Jia, Zhiqi and Zhang, Junhong and Ye, Zhibiao and Bishop, Gerard J and Butcher, Sarah and Lopez-Cobollo, Rosa and Buchan, Daniel and Filippis, Ioannis and Abbott, James and Dixit, Rekha and Singh, Manju and Singh, Archana and Pal, Jitendra Kumar and Pandit, Awadhesh and Singh, Pradeep Kumar and Mahato, Ajay Kumar and Dogra, Vivek and Gaikwad, Kishor and Sharma, Tilak Raj and Mohapatra, Trilochan and Singh, Nagendra Kumar and Causse, Mathilde and Rothan, Christophe and Schiex, Thomas and Noirot, Céline and Bellec, Arnaud and Klopp, Christophe and Delalande, Corinne and Berges, Hélène and Mariette, Jérôme and Frasse, Pierre and Vautrin, Sonia and Zouine, Mohamed and Latche, Alain and Rousseau, Christine and Regad, Farid and Pech, Jean-Claude and Philippot, Murielle and Bouzayen, Mondher and Pericard, Pierre and Osorio, Sonia and Fernandez del Carmen, Asunción and Monforte, Antonio and Granell, Antonio and Fernandez-Muñoz, Rafael and Conte, Mariana and Lichtenstein, Gabriel and Carrari, Fernando and De Bellis, Gianluca and Fuligni, Fabio and Peano, Clelia and Grandillo, Silvana and Termolino, Pasquale and Pietrella, Marco and Fantini, Elio and Falcone, Giulia and Fiore, Alessia and Giuliano, Giovanni and Lopez, Loredana and Facella, Paolo and Perrotta, Gaetano and Daddiego, Loretta and Bryan, Glenn and Orozco, Modesto and Pastor, Xavier and Torrents, David and van Schriek, Keygene NV Marco GM and Feron, Richard MC and van Oeveren, Jan and de Heer, Peter and daPonte, Lorena and Jacobs-Oomen, Saskia and Cariaso, Mike and Prins, Marcel and van Eijk, Michiel JT and Janssen, Antoine and van Haaren, Mark JJ and Jo, Sung-Hwan and Kim, Jungeun and Kwon, Suk-Yoon and Kim, Sangmi and Koo, Dal-Hoe and Lee, Sanghyeob and Hur, Cheol-Goo and Clouser, Christopher and Rico, Alain and Hallab, Asis and Gebhardt, Christiane and Klee, Kathrin and Jöcker, Anika and Warfsmann, Jens and Göbel, Ulrike and Kawamura, Shingo and Yano, Kentaro and Sherman, Jamie D and Fukuoka, Hiroyuki and Negoro, Satomi and Bhutty, Sarita and Chowdhury, Parul and Chattopadhyay, Debasis and Datema, Erwin and Smit, Sandra and Schijlen, Eliog WM and van de Belt, Jose and van Haarst, Jan C and Peters, Sander A and van Staveren, Marjo J and Henkens, Marleen HC and Mooyman, Paul JW and Hesselink, Thamara and van Ham, Roeland CHJ and Jiang, Guoyong and Droege, Marcus and Choi, Doil and Kang, Byung-Cheol and Kim, Byung Dong and Park, Minkyu and Kim, Seungill and Yeom, Seon-In and Lee, Yong-Hwan and Choi, Yang-Do and Li, Guangcun and Gao, Jianwei and Liu, Yongsheng and Huang, Shengxiong and Fernandez-Pedrosa, Victoria and Collado, Carmen and Zuñiga, Sheila and Wang, Guoping and Cade, Rebecca and Dietrich, Robert A and Rogers, Jane and Knapp, Sandra and Fei, Zhangjun and White, Ruth A and Thannhauser, Theodore W and Giovannoni, James J and Angel Botella, Miguel and Gilbert, Louise and Gonzalez, Ramon and Goicoechea, Jose Luis and Yu, Yeisoo and Kudrna, David and Collura, Kristi and Wissotski, Marina and Wing, Rod and Schoof, Heiko and Meyers, Blake C and Gurazada, Aishwarya Bala and Green, Pamela J and Mathur, Saloni and Vyas, Shailendra and Solanke, Amolkumar U and Kumar, Rahul and Gupta, Vikrant and Sharma, Arun K and Khurana, Paramjit and Khurana, Jitendra P and Tyagi, Akhilesh K and Dalmay, Tamas and Mohorianu, Irina and Walts, Brandon and Chamala, Srikar and Barbazuk, W Brad and Li, Jingping and Guo, Hui and Lee, Tae-Ho and Wang, Yupeng and Zhang, Dong and Paterson, Andrew H and Wang, Xiyin and Tang, Haibao and Barone, Amalia and Chiusano, Maria Luisa and Ercolano, Maria Raffaella and D'Agostino, Nunzio and Di Filippo, Miriam and Traini, Alessandra and Sanseverino, Walter and Frusciante, Luigi and Seymour, Graham B and Elharam, Mounir and Fu, Ying and Hua, Axin and Kenton, Steven and Lewis, Jennifer and Lin, Shaoping and Najar, Fares and Lai, Hongshing and Qin, Baifang and Qu, Chunmei and Shi, Ruihua and White, Douglas and White, James and Xing, Yanbo and Yang, Keqin and Yi, Jing and Yao, Ziyun and Zhou, Liping and Roe, Bruce A and Vezzi, Alessandro and D'Angelo, Michela and Zimbello, Rosanna and Schiavon, Riccardo and Caniato, Elisa and Rigobello, Chiara and Campagna, Davide and Vitulo, Nicola and Valle, Giorgio and Nelson, David R and De Paoli, Emanuele and Szinay, Dora and de Jong, Hans H and Bai, Yuling and Visser, Richard GF and Lankhorst, René M Klein and Beasley, Helen and McLaren, Karen and Nicholson, Christine and Riddle, Claire and Gianese, Giulio},
  issn         = {0028-0836},
  journal      = {NATURE},
  keywords     = {GENE,HISTORY,DIVERSIFICATION,LYCOPERSICON-ESCULENTUM,ARABIDOPSIS,ORTHOLOG,PATTERNS,SORGHUM,POTATO},
  language     = {eng},
  number       = {7400},
  pages        = {635--641},
  title        = {The tomato genome sequence provides insights into fleshy fruit evolution},
  url          = {http://dx.doi.org/10.1038/nature11119},
  volume       = {485},
  year         = {2012},
}

Altmetric
View in Altmetric
Web of Science
Times cited: