The tomato genome sequence provides insights into fleshy fruit evolution

被引：2299

作者：

Sato, Shusei ^{[1
]}

Tabata, Satoshi ^{[1
]}

Hirakawa, Hideki ^{[1
]}

Asamizu, Erika ^{[1
]}

Shirasawa, Kenta ^{[1
]}

Isobe, Sachiko ^{[1
]}

Kaneko, Takakazu ^{[1
]}

Nakamura, Yasukazu ^{[1
]}

Shibata, Daisuke ^{[1
]}

Aoki, Koh ^{[1
]}

Egholm, Michael ^{[2
]}

Knight, James ^{[2
]}

Bogden, Robert ^{[3
]}

Li, Changbao ^{[4
,6
]}

Shuang, Yang ^{[5
]}

Xu, Xun ^{[5
]}

Pan, Shengkai ^{[5
]}

Cheng, Shifeng ^{[5
]}

Liu, Xin ^{[5
]}

Ren, Yuanyuan ^{[5
]}

Wang, Jun ^{[5
]}

Albiero, Alessandro ^{[7
]}

Dal Pero, Francesca ^{[7
]}

Todesco, Sara ^{[7
]}

Van Eck, Joyce ^{[8
]}

Buels, Robert M. ^{[8
]}

Bombarely, Aureliano ^{[8
]}

Gosselin, Joseph R. ^{[8
]}

Huang, Minyun ^{[8
]}

Leto, Jonathan A. ^{[8
]}

Menda, Naama ^{[8
]}

Strickler, Susan ^{[8
]}

Mao, Linyong ^{[8
]}

Gao, Shan ^{[8
]}

Tecle, Isaak Y. ^{[8
]}

York, Thomas ^{[8
]}

Zheng, Yi ^{[8
]}

Vrebalov, Julia T. ^{[8
]}

Lee, JeMin ^{[8
]}

Zhong, Silin ^{[8
]}

Mueller, Lukas A. ^{[8
]}

Stiekema, Willem J. ^{[9
]}

Ribeca, Paolo ^{[10
]}

Alioto, Tyler ^{[10
]}

Yang, Wencai ^{[11
]}

Huang, Sanwen ^{[12
]}

Du, Yongchen ^{[12
]}

Zhang, Zhonghua ^{[12
]}

Gao, Jianchang ^{[12
]}

Guo, Yanmei ^{[12
]}

机构：

[1] Kazusa DNA Res Inst, 2-6-7 Kazusa Kamatari, Kisarazu, Chiba 2920818, Japan

[2] 454 Life Sci, Branford, CT 06405 USA

[3] Amplicon Express Inc, Pullman, WA 99163 USA

[4] Beijing Acad Agr & Forestry Sci, Beijing Vegetable Res Ctr, Beijing 100097, Peoples R China

[5] BGI Shenzhen, Shenzhen 518083, Peoples R China

[6] Chinese Acad Sci, Natl Ctr Gene Res, Shanghai 200233, Peoples R China

[7] BMR Genom SrL, I-35131 Padua, Italy

[8] Cornell Univ, Boyce Thompson Inst Plant Res, Ithaca, NY 14853 USA

[9] Ctr BioSyst Genom, NL-6700 AB Wageningen, Netherlands

[10] CNAG, Barcelona 08028, Spain

[11] China Agr Univ, Coll Agron & Biotechnol, Dept Vegetable Sci, Beijing 100193, Peoples R China

[12] Chinese Acad Agr Sci, Inst Vegetables & Flowers, Sinodutch Joint Lab Hort Genom Technol, Key Lab Hort Crops Genet Improvement,Minist Agr, Beijing 100081, Peoples R China

[13] Chinese Acad Sci, Inst Genet & Dev Biol, State Key Lab Plant Genom, Beijing 100101, Peoples R China

[14] Chinese Acad Sci, Inst Genet & Dev Biol, Natl Ctr Plant Gene Res, Beijing 100101, Peoples R China

[15] Chinese Acad Sci, Wuhan Bot Garden, Wuhan 430074, Peoples R China

[16] Chinese Acad Sci, Inst Genet & Dev Biol, State Key Lab Plant Cell & Chromosome Engn, Beijing 100101, Peoples R China

[17] Chinese Acad Sci, Inst Genet & Dev Biol, Mol & Dev Biol Lab, Beijing 100080, Peoples R China

[18] Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA

[19] Colorado State Univ, Dept Biol, Ft Collins, CO 80523 USA

[20] Natl Taiwan Univ, Dept Agron, Taipei 107, Taiwan

[21] Cornell Univ, Dept Plant Biol, Ithaca, NY 14853 USA

[22] Univ Pompeu Fabra, CRG, Genome Bioinformat Lab, GRIB IMIM, Barcelona 08003, Spain

[23] Univ Ghent VIB, Dept Plant Biotechnol & Bioinformat, Dept Plant Syst Biol, B-9052 Ghent, Belgium

[24] Hebrew Univ Jerusalem, Fac Agr, IL-76100 Rehovot, Israel

[25] Heilongjiang Acad Agr Sci, Inst Ind Crops, Harbin 150086, Peoples R China

[26] Helmholtz Ctr Hlth & Environm, Inst Bioinformat & Syst Biol MIPS, D-85764 Neuherberg, Germany

[27] Henan Agr Univ, Coll Hort, Zhengzhou 450002, Peoples R China

[28] Huazhong Agr Univ, Natl Key Lab Crop Genet Improvement, Wuhan 430070, Peoples R China

[29] Univ London Imperial Coll Sci Technol & Med, Dept Life Sci, London SW7 1AZ, England

[30] Indian Agr Res Inst, NRC Plant Biotechnol, New Delhi 110012, India

[31] INRA, Genet & Ameliorat Fruits & Legumes UR1052, F-84143 Montfavet, France

[32] INRA, Biol Fruit & Pathol, F-33883 Villenave Dornon, France

[33] INRA, Unite Biometrie & Intelligence Artificielle UR 87, F-31320 Castanet Tolosan, France

[34] INRA CNRGV, F-31326 Castanet Tolosan, France

[35] INRA, Biometrie & Intelligence Artificielle UR875, F-31326 Castanet Tolosan, France

[36] Univ Toulouse, Inst Natl Polytech Toulouse ENSAT, F-31326 Castanet Tolosan, France

[37] Inst Biol Mol & Celular Plantas CSIC UPV, Valencia 46022, Spain

[38] Univ Malaga, CSIC, UMA, IHSM,Inst Hortofruticultura Subtrop & Mediterrane, Algarrobo Costa 29750, Malaga, Spain

[39] Natl Res Council Italy, Inst Biomed Technol, I-20090 Milan, Italy

[40] Natl Res Council Italy, Inst Plant Genet, Res Div Portici, I-80055 Naples, Italy

[41] ENEA, Casaccia Res Ctr, I-00123 Rome, Italy

[42] Scuola Super Sant Anna, I-56127 Pisa, Italy

[43] ENEA, Trisaia Res Ctr, I-75026 Rotondella, Matera, Italy

[44] James Hutton Inst, Dundee DD2 5DA, Scotland

[45] Barcelona Supercomp Ctr, Barcelona 08034, Spain

[46] Inst Biomed Res, Barcelona 08028, Spain

[47] Pg Lluis Co, ICREA, Barcelona 08010, Spain

[48] Keygene NV, NL-6708 PW Wageningen, Netherlands

[49] Korea Res Inst Biosci & Biotechnol, Plant Syst Engn Res Ctr, Taejon 305806, South Korea

[50] Life Technol, Beverly, MA 01915 USA

来源：

NATURE | 2012年 / 485卷 / 7400期

基金：

英国生物技术与生命科学研究理事会; 美国国家科学基金会;

关键词：

LYCOPERSICON-ESCULENTUM; GENE; DIVERSIFICATION; ARABIDOPSIS; PATTERNS; ORTHOLOG; HISTORY; SORGHUM; POTATO;

D O I：

10.1038/nature11119

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页码：635 / 641

页数：7

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