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 Rm, Bombarely A, Gosselin Jr, Huang M, Leto Ja, Menda N, Strickler S, Mao L, Gao S, Tecle Iy, York T, Zheng Y, Vrebalov Jt, Lee J, Zhong S, Mueller La, Stiekema Wj, 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, Feng Q, Fan D, Wang Y, Ling H, Xue Y, Ware D, Mccombie Wr, Lippman Zb, Chia Jm, Jiang K, Pasternak S, Gelley L, Kramer M, Anderson Lk, Chang Sb, Royer Sm, Shearer La, Stack Sm, Rose Jk, Xu Y, Eannetta N, Matas Aj, Mcquinn R, Tanksley Sd, 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 Gj, Butcher S, Lopez-cobollo R, Buchan D, Filippis I, Abbott J, Dixit R, Singh M, Singh A, Pal Jk, Pandit A, Singh Pk, Mahato Ak, Gaikwad Vd, Sharma Rr, Mohapatra T, Singh Nk, Causse M, Rothan C, Schiex T, Noirot C, Bellec A, Klopp C, Delalande C, Berges H, Mariette J, Frasse P, Vautrin S, Zouine M, Latché A, Rousseau C, Regad F, Pech Jc, Philippot M, Bouzayen M, Pericard P, Osorio S, Fernandez Del Carmen A, 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, Fiore A, Giuliano G, Lopez L, Facella P, Perotta G, Daddiego L, Bryan G, Orozco M, Pastor X, Torrents D, Van Schriek Mg, Feron Rm, Van Oeveren J, De Heer P, Daponte L, Jacobs-oomen S, Cariaso M, Prins M, Van Eijk Mj, Janssen A, Van Haaren Mj, Jungeun Kim Sh, Kwon Sy, Kim S, Koo Dh, Lee S, Hur Cg, Clouser C, Rico A, Hallab A, Gebhardt C, Klee K, Jöcker A, Warfsmann J, Göbel U, Kawamura S, Yano K, Sherman Jd, Fukuoka H, Negoro S, Bhutty S, Chowdhury P, Chattopadhyay D, Datema E, Smit S, Schijlen Eg, Van De Belt J, Van Haarst Jc, Peters Sa, Van Staveren Ma, Henkens Mh, Mooyman Pj, Hesselink T, Van Ham Rc, Jiang G, Droege M, Choi D, Kang Bc, Kim Bd, Park M, Kim S, Yeom Si, Lee Yh, Choi Yd, Li G, Gao J, Liu Y, Huang S, Fernandez-pedrosa V, Collado C, Zuñiga S, Wang G, Cade R, Dietrich Ra, Rogers J, Knapp S, Fei Z, White Ra, Thannhauser Tw, Giovannoni Jj, Botella Ma, Gilbert L, Gonzalez R, Goicoechea Jl, Yu Y, Kudrna D, Collura K, Wissotski M, Wing R, Meyers Bc, Gurazada Ab, Green Pj, Vyas Sm, Solanke Au, Kumar R, Gupta V, Sharma Ak, Khurana P, Khurana Jp, Tyagi Ak, Dalmay T, Mohorianu I, Walts B, Chamala S, Barbazuk Wb, Li J, Guo H, Lee Th, Wang Y, Zhang D, Paterson Ah, Wang X, Tang H, Barone A, Chiusano Ml, Ercolano Mr, D’agostino N, Di Filippo M, Traini A, Sanseverino W, Frusciante L, Seymour Gb, Elharam M, Fu Y, Hua A, Kenton S, Lewis J, Lin S, Najar F, Lai H, Qin B, Qu C, Shi R, White D, White J, Xing Y, Yang K, Yi J, Yao Z, Zhou L, Roe Ba, Vezzi A, D’angelo M, Zimbello R, Schiavon R, Caniato E, Rigobello C, Campagna D, Vitulo N, Valle G, Nelson Dr, De Paoli E, Szinay D, De Jong Hh, Bai Y, Visser Rg, Klein R, Beasley H, Mclaren K, Nicholson C, Riddle C, Gianese G
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.
