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 CB; Shuang Y; Xu X; Pan SK; Cheng SF; Liu X; Ren YY; Wang J; Albiero A; Dal Pero F; Todesco S; Van Eck J; Buels RM; Bombarely A; Gosselin JR; Huang MY; Leto JA; Menda N; Strickler S; Mao LY; Gao S; Tecle IY; York T; Zheng Y; Vrebalov JT; Lee J; Zhong SL; Mueller LA; Stiekema WJ; Ribeca P; Alioto T; Yang WC; Huang SW; Du YC; Zhang ZH; Gao JC; Guo YM; Wang XX; Li Y; He J; Li CY; Cheng ZK; Zuo JR; Ren JF; Zhao JH; Yan LH; Jiang HL; Wang B; Li HS; Li ZJ; Fu FY; Chen BT; Han B; Feng Q; Fan DL; Wang Y; Ling HQ; Xue YBA; 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 JKC; Xu YM; Eannetta N; Matas AJ; McQuinn R; Tanksley SD; Camara F; Guigo R; Rombauts S; Fawcett J; Van de Peer Y; Zamir D; Liang CB; Spannagl M; Gundlach H; Bruggmann R; Mayer K; Jia ZQ; Zhang JH; Ye ZBA; 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; Dogra V; Gaikwad K; Sharma TR; 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; Latche A; Rousseau C; Regad F; Pech JC; Philippot M; Bouzayen M; Pericard P; Osorio S; del Carmen AF; Monforte A; Granell A; Fernandez-Munoz 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; Perrotta G; Daddiego L; Bryan G; Orozco M; Pastor X; Torrents D; van Schriek KNVMGM; Feron RMC; van Oeveren J; de Heer P; daPonte L; Jacobs-Oomen S; Cariaso M; Prins M; van Eijk MJT; Janssen A; van Haaren MJJ; Jo SH; Kim J; Kwon SY; Kim S; Koo DH; Lee S; Hur CG; Clouser C; Rico A; Hallab A; Gebhardt C; Klee K; Jocker A; Warfsmann J; Gobel U; Kawamura S; Yano K; Sherman JD; Fukuoka H; Negoro S; Bhutty S; Chowdhury P; Chattopadhyay D; Datema E; Smit S; Schijlen EWM; van de Belt J; van Haarst JC; Peters SA; van Staveren MJ; Henkens MHC; Mooyman PJW; Hesselink T; van Ham RCHJ; Jiang GY; Droege M; Choi D; Kang BC; Kim BD; Park M; Kim S; Yeom SI; Lee YH; Choi YD; Li GC; Gao JW; Liu YS; Huang SX; Fernandez-Pedrosa V; Collado C; Zuniga S; Wang GP; Cade R; Dietrich RA; Rogers J; Knapp S; Fei ZJ; White RA; Thannhauser TW; Giovannoni JJ; Botella MA; Gilbert L; Gonzalez R; Goicoechea JL; Yu Y; Kudrna D; Collura K; Wissotski M; Wing R; Schoof H; Meyers BC; Gurazada AB; Green PJ; Mathur S; Vyas S; 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 JP; Guo H; Lee TH; Wang YP; Zhang D; Paterson AH; Wang XY; Tang HB; 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 SP; Najar F; Lai HS; Qin BF; Qu CM; Shi RH; White D; White J; Xing YB; Yang KQ; Yi J; Yao ZY; Zhou LP; 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 YL; Visser RGF; Lankhorst RMK; Beasley H; McLaren K; Nicholson C; Riddle C; Gianese G

Nature, Vol.485, No.7400, 635-641, 2012

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 CB, Shuang Y, Xu X, Pan SK, Cheng SF, Liu X, Ren YY, Wang J, Albiero A, Dal Pero F, Todesco S, Van Eck J, Buels RM, Bombarely A, Gosselin JR, Huang MY, Leto JA, Menda N, Strickler S, Mao LY, Gao S, Tecle IY, York T, Zheng Y, Vrebalov JT, Lee J, Zhong SL, Mueller LA, Stiekema WJ, Ribeca P, Alioto T, Yang WC, Huang SW, Du YC, Zhang ZH, Gao JC, Guo YM, Wang XX, Li Y, He J, Li CY, Cheng ZK, Zuo JR, Ren JF, Zhao JH, Yan LH, Jiang HL, Wang B, Li HS, Li ZJ, Fu FY, Chen BT, Han B, Feng Q, Fan DL, Wang Y, Ling HQ, Xue YBA, 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 JKC, Xu YM, Eannetta N, Matas AJ, McQuinn R, Tanksley SD, Camara F, Guigo R, Rombauts S, Fawcett J, Van de Peer Y, Zamir D, Liang CB, Spannagl M, Gundlach H, Bruggmann R, Mayer K, Jia ZQ, Zhang JH, Ye ZBA, 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, Dogra V, Gaikwad K, Sharma TR, 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, Latche A, Rousseau C, Regad F, Pech JC, Philippot M, Bouzayen M, Pericard P, Osorio S, del Carmen AF, Monforte A, Granell A, Fernandez-Munoz 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, Perrotta G, Daddiego L, Bryan G, Orozco M, Pastor X, Torrents D, van Schriek KNVMGM, Feron RMC, van Oeveren J, de Heer P, daPonte L, Jacobs-Oomen S, Cariaso M, Prins M, van Eijk MJT, Janssen A, van Haaren MJJ, Jo SH, Kim J, Kwon SY, Kim S, Koo DH, Lee S, Hur CG, Clouser C, Rico A, Hallab A, Gebhardt C, Klee K, Jocker A, Warfsmann J, Gobel U, Kawamura S, Yano K, Sherman JD, Fukuoka H, Negoro S, Bhutty S, Chowdhury P, Chattopadhyay D, Datema E, Smit S, Schijlen EWM, van de Belt J, van Haarst JC, Peters SA, van Staveren MJ, Henkens MHC, Mooyman PJW, Hesselink T, van Ham RCHJ, Jiang GY, Droege M, Choi D, Kang BC, Kim BD, Park M, Kim S, Yeom SI, Lee YH, Choi YD, Li GC, Gao JW, Liu YS, Huang SX, Fernandez-Pedrosa V, Collado C, Zuniga S, Wang GP, Cade R, Dietrich RA, Rogers J, Knapp S, Fei ZJ, White RA, Thannhauser TW, Giovannoni JJ, Botella MA, Gilbert L, Gonzalez R, Goicoechea JL, Yu Y, Kudrna D, Collura K, Wissotski M, Wing R, Schoof H, Meyers BC, Gurazada AB, Green PJ, Mathur S, Vyas S, 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 JP, Guo H, Lee TH, Wang YP, Zhang D, Paterson AH, Wang XY, Tang HB, 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 SP, Najar F, Lai HS, Qin BF, Qu CM, Shi RH, White D, White J, Xing YB, Yang KQ, Yi J, Yao ZY, Zhou LP, 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 YL, Visser RGF, Lankhorst RMK, 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 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.