The tomato genome sequence provides insights into fleshy fruit evolution

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.; Ren, Y.; Wang, J.; Albiero, A.; Dal Pero, F.; Todesco, S.; Van Eck, J.; Buels, R.M.; Bombarely, A.; Gosselin, J.R.; Huang, M.; Leto, J.A.; Menda, N.; Strickler, S.; Mao, L.; Gao, S.; Tecle, I.Y.; York, T.; Zheng, Y.; Vrebalov, J.T.; Lee, J.; Zhong, S.; Mueller, L.A.; Stiekema, W.J.; Ribeca, P.; Alioto, T.; Yang, W.; Huang, S.; Du, Y.; Zhang, Z.; Gao, J.; Guo, Y.; Wang, X.; Li, Y.; He, J.; Li, C.; Cheng, Z.; Zuo, J.; Ren, J.; Zhao, J.; Yan, L.; Jiang, H.; Wang, B.; Li, H.; Li, Z.; Fu, F.; Chen, B.; Han, B.; Feng, Q.; Fan, D.; Wang, Y.; Ling, H.; Xue, Y.; Ware, D.; Richard McCombie, W.; Lippman, Z.B.; Chia, J.-M.; Jiang, K.; Pasternak, S.; Gelley, L.; Kramer, M.; Anderson, L.K.; Chang, S.-B.; Royer, S.M.; Shearer, L.A.; Stack, S.M.; Rose, J.K.C.; Xu, Y.; Eannetta, N.; Matas, A.J.; McQuinn, R.; Tanksley, S.D.; Camara, F.; Guigó, R.; Rombauts, S.; Fawcett, J.; Van De Peer, Y.; Zamir, D.; Liang, C.; Spannagl, M.; Gundlach, H.; Bruggmann, R.; Mayer, K.; Jia, Z.; Zhang, J.; Ye, Z.; Bishop, G.J.; Butcher, S.; Lopez-Cobollo, R.; Buchan, D.; Filippis, I.; Abbott, J.; Dixit, I.R.; Singh, M.; Singh, A.; Pal, J.K.; Pandit, A.; Singh, P.K.; Mahato, A.K.; Dogra, V.; Gaikwad, K.; Sharma, T.R.; Mohapatra, T.; Singh, N.K.; Causse, M.; Rothan, C.; Noirot, C.; Bellec, A.; Klopp, C.; Delalande, C.; Berges, H.; Mariette, J.; Frasse, P.; Vautrin, S.; Zouine, T.M.; Latché, A.; Rousseau, C.; Regad, F.; Pech, J.-C.; Philippot, M.; Bouzayen, M.; Pericard, P.; Osorio, S.; Del Carmen, A.F.; Monforte, A.; Granell, A.; Fernandez-Muñoz, R.; Conte, M.; Lichtenstein, G.; Carrari, F.; De Bellis, G.; Fuligni, F.; Peano, C.; Grandillo, S.; Termolino, P.; Pietrella, M.; Fantini, E.; Falcone, G.; Alessia Fiore; Giovanni Giuliano; Lopez, L.; Facella, P.; Gaetano Perrotta; Daddiego, L.; Bryan, G.; Orozco, B.M.; Pastor, X.; Torrents, D.; Van Schriek, M.G.M.; Feron, R.M.C.; Van Oeveren, J.; De Heer, P.; Da Ponte, L.; Jacobs-Oomen, S.; Cariaso, M.; Prins, M.; Van Eijk, M.J.T.; Janssen, A.; Van Haaren, J.J.; -HwanJo, S.; Kim, J.; Kwon, S.-Y.; Kim, S.; Koo, D.-H.; Lee, S.; Clouser, C.; Rico, A.; Hallab, A.; Gebhardt, C.; Klee, K.; Jöcker, A.; Warfsmann, J.; Göbel, U.; Kawamura, S.; Yano, K.; Sherman, J.D.; Fukuoka, H.; Negoro, S.; Bhutty, S.; Chowdhury, P.; Chattopadhyay, D.; Datema, E.; Smit, S.; Schijlen, E.G.W.M.; Van De Belt, J.; Van Haarst, J.C.; Peters, S.A.; Van Staveren, M.J.; Henkens, M.H.C.; Mooyman, P.J.W.; Hesselink, T.; Van Ham, R.C.H.J.; Jiang, G.; Droege, M.; Choi, D.; Kang, B.-C.; Kim, B.D.; Park, M.; Kim, S.; Yeom, S.-I.; Lee, Y.-H.; Choi, Y.-D.; Li, G.; Gao, J.; Liu, Y.; Huang, S.; Fernandez-Pedrosa, V.; Collado, C.; Zuñ Iga, S.; Wang, G.; Cade, R.; Dietrich, R.A.; Rogers, J.; Knapp, S.; Fei, Z.; White, R.A.; Thannhauser, T.W.; Giovannoni, J.J.; Botella, M.A.; Gilbert, L.; Gonzalez, F.R.; Goicoechea, J.L.; Yu, Y.; Kudrna, D.; Collura, K.; Wissotski, M.; Wing, R.; Meyers, B.C.; Gurazada, A.B.; Green, P.J.; Mathur, S.; Vyas, S.; Solanke, A.U.; Kumar, R.; Gupta, V.; Sharma, A.K.; Khurana, P.; Khurana, J.P.; Tyagi, A.K.; Dalmay, T.; Mohorianu, I.; Walts, B.; Chamala, S.; Barbazuk, W.B.; Li, J.; Guo, H.; Lee, T.-H.; Wang, Y.; Zhang, D.; Paterson, A.H.; Wang, X.; Tang, H.; Barone, A.; Chiusano, M.L.; Ercolano, M.R.; D'Agostino, N.; Di Filippo, M.; Traini, A.; Sanseverino, W.; Frusciante, L.; Seymour, G.B.; Elharam, M.; Fu, Y.; Hua, A.; Kenton, S.; Lewis, J.; Lin, S.; Najar, F.; Lai, H.; Qin, B.; Shi, R.; Qu, C.; White, D.; White, J.; Xing, Y.; Yang, K.; Yi, J.; Yao, Z.; Zhou, L.; Roe, B.A.; Vezzi, A.; D'Angelo, M.; Zimbello, R.; Schiavon, R.; Caniato, E.; Rigobello, C.; Campagna, D.; Vitulo, N.; Valle, G.; Nelson, D.R.; De Paoli, E.; Szinay, D.; De Jong, H.H.; Bai, Y.; Visser, R.G.F.; Lankhorst, R.K.; Beasley, H.; McLaren, K.; Nicholson, C.; Riddle, C.; Gianese, G.

Title	The tomato genome sequence provides insights into fleshy fruit evolution
Publication Type	Articolo su Rivista peer-reviewed
Year of Publication	2012
Authors	Sato, S., Tabata S., Hirakawa H., Asamizu E., Shirasawa K., Isobe S., Kaneko T., Nakamura Y., Shibata D., Aoki K., et al.
Journal	Nature
Volume	485
Pagination	635-641
ISSN	00280836
Keywords	Arabidopsis, article, color, DNA, DNA sequence, Evolution, fruit, fruit (structure), fruit color, fruit flesh, gene sequence, genetic parameters, Genetic variability, Genetic Variation, genetics, Genome, genome triplication, Genomics, Lycopersicon esculentum, Molecular, molecular evolution, molecular genetics, Molecular Sequence Data, nonhuman, nucleotide, Phylogeny, physiology, Plant, plant evolution, plant genetics, plant genome, plant RNA, potato, priority journal, promoter region, qualitative analysis, RNA, RNA analysis, Sequence Analysis, Solanum tuberosum, soybean, Soybeans, synteny, Tomato
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. © 2012 Macmillan Publishers Limited.
Notes	cited By 2082
URL	https://www.scopus.com/inward/record.uri?eid=2-s2.0-84863693752&doi=10.1038%2fnature11119&partnerID=40&md5=bf22c44d467345c551466d864299bc3d
DOI	10.1038/nature11119
Citation Key	Sato2012635