The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions

被引：662

作者：

Guo, Shaogui ^{[1
,2
]}

Zhang, Jianguo ^{[3
,4
]}

Sun, Honghe ^{[1
,2
,5
]}

Salse, Jerome ^{[6
]}

Lucas, William J. ^{[7
]}

Zhang, Haiying ^{[1
]}

Zheng, Yi ^{[2
]}

Mao, Linyong ^{[2
]}

Ren, Yi ^{[1
]}

Wang, Zhiwen ^{[3
]}

Min, Jiumeng ^{[3
]}

Guo, Xiaosen ^{[3
]}

Murat, Florent ^{[6
]}

Ham, Byung-Kook ^{[7
]}

Zhang, Zhaoliang ^{[7
]}

Gao, Shan ^{[2
]}

Huang, Mingyun ^{[2
]}

Xu, Yimin ^{[2
]}

Zhong, Silin ^{[2
]}

Bombarely, Aureliano ^{[2
]}

Mueller, Lukas A. ^{[2
]}

Zhao, Hong ^{[1
]}

He, Hongju ^{[1
]}

Zhang, Yan ^{[1
]}

Zhang, Zhonghua ^{[8
]}

Huang, Sanwen ^{[8
]}

Tan, Tao ^{[9
]}

Pang, Erli ^{[9
]}

Lin, Kui ^{[9
]}

Hu, Qun ^{[10
]}

Kuang, Hanhui ^{[10
]}

Ni, Peixiang ^{[3
,4
]}

Wang, Bo ^{[3
]}

Liu, Jingan ^{[1
]}

Kou, Qinghe ^{[1
]}

Hou, Wenju ^{[1
]}

Zou, Xiaohua ^{[1
]}

Jiang, Jiao ^{[1
]}

Gong, Guoyi ^{[1
]}

Klee, Kathrin ^{[11
]}

Schoof, Heiko ^{[11
]}

Huang, Ying ^{[3
]}

Hu, Xuesong ^{[3
]}

Dong, Shanshan ^{[3
]}

Liang, Dequan ^{[3
]}

Wang, Juan ^{[3
]}

Wu, Kui ^{[3
]}

Xia, Yang ^{[1
]}

Zhao, Xiang ^{[3
]}

Zheng, Zequn ^{[3
]}

机构：

[1] Beijing Acad Agr & Forestry Sci, Natl Engn Res Ctr Vegetables, Key Lab Biol & Genet Improvement Hort Crops N Chi, Beijing, Peoples R China

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

[3] Beijing Genom Inst Shenzhen, Shenzhen, Peoples R China

[4] Fudan Univ, T Life Res, Shanghai 200433, Peoples R China

[5] Beijing Agr Univ, Coll Plant Sci & Technol, Beijing 100094, Peoples R China

[6] INRA, Unites Mixtes Rech 1095, Genet Divers & Ecophysiol Cereals, Clermont Ferrand, France

[7] Univ Calif Davis, Dept Plant Biol, Coll Biol Sci, Davis, CA 95616 USA

[8] Chinese Acad Agr Sci, Inst Vegetables & Flowers, Beijing 100193, Peoples R China

[9] Beijing Normal Univ, Coll Life Sci, Beijing 100875, Peoples R China

[10] Huazhong Agr Univ, Coll Hort & Forestry, Wuhan, Peoples R China

[11] Univ Bonn, Inst Nutzpflanzenwissensch & Ressource, Bonn, Germany

[12] Xinjiang Acad Agr Sci, Urumqi, Peoples R China

[13] Beijing Novogene Bioinformat Technol Co Ltd, Beijing, Peoples R China

[14] ARS, USDA, US Vegetable Lab, Charleston, SC USA

[15] USDA, Robert W Holley Ctr Agr & Hlth, Ithaca, NY USA

[16] Univ Copenhagen, Dept Biol, Copenhagen, Denmark

来源：

NATURE GENETICS | 2013年 / 45卷 / 01期

基金：

美国国家科学基金会; 北京市自然科学基金; 中国国家自然科学基金; 美国食品与农业研究所;

关键词：

MADS-BOX GENE; DNA-SEQUENCES; FRUIT; RNA; PLANT; IDENTIFICATION; EXPRESSION; RICE; CLASSIFICATION; RECONSTRUCTION;

D O I：

10.1038/ng.2470

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

Watermelon, Citrullus lanatus, is an important cucurbit crop grown throughout the world. Here we report a high-quality draft genome sequence of the east Asia watermelon cultivar 97103 (2n = 2x = 22) containing 23,440 predicted protein-coding genes. Comparative genomics analysis provided an evolutionary scenario for the origin of the 11 watermelon chromosomes derived from a 7-chromosome paleohexaploid eudicot ancestor. Resequencing of 20 watermelon accessions representing three different C. lanatus subspecies produced numerous haplotypes and identified the extent of genetic diversity and population structure of watermelon germplasm. Genomic regions that were preferentially selected during domestication were identified. Many disease-resistance genes were also found to be lost during domestication. In addition, integrative genomic and transcriptomic analyses yielded important insights into aspects of phloem-based vascular signaling in common between watermelon and cucumber and identified genes crucial to valuable fruit-quality traits, including sugar accumulation and citrulline metabolism.

引用

页码：51 / +

页数：10

共 76 条

[1] Palaeogenomics of plants: synteny-based modelling of extinct ancestors [J].

Abrouk, Michael ;

Murat, Florent ;

Pont, Caroline ;

Messing, Joachim ;

Jackson, Scott ;

Faraut, Thomas ;

Tannier, Eric ;

Plomion, Christophe ;

Cooke, Richard ;

Feuillet, Catherine ;

Salse, Jerome .

TRENDS IN PLANT SCIENCE, 2010, 15 (09) :479-487

[2] De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera) [J].

Al-Dous, Eman K. ;

George, Binu ;

Al-Mahmoud, Maryam E. ;

Al-Jaber, Moneera Y. ;

Wang, Hao ;

Salameh, Yasmeen M. ;

Al-Azwani, Eman K. ;

Chaluvadi, Srinivasa ;

Pontaroli, Ana C. ;

DeBarry, Jeremy ;

Arondel, Vincent ;

Ohlrogge, John ;

Saie, Imad J. ;

Suliman-Elmeer, Khaled M. ;

Bennetzen, Jeffrey L. ;

Kruegger, Robert R. ;

Malek, Joel A. .

NATURE BIOTECHNOLOGY, 2011, 29 (06) :521-U84

[3]

Anders S., 2010, GENOME BIOL, V11, pR106, DOI [10.1186/gb-2010-11-10-r106, DOI 10.1186/gb-2010-11-10-r106]

[4] The genome of Theobroma cacao [J].

Argout, Xavier ;

Salse, Jerome ;

Aury, Jean-Marc ;

Guiltinan, Mark J. ;

Droc, Gaetan ;

Gouzy, Jerome ;

Allegre, Mathilde ;

Chaparro, Cristian ;

Legavre, Thierry ;

Maximova, Siela N. ;

Abrouk, Michael ;

Murat, Florent ;

Fouet, Olivier ;

Poulain, Julie ;

Ruiz, Manuel ;

Roguet, Yolande ;

Rodier-Goud, Maguy ;

Barbosa-Neto, Jose Fernandes ;

Sabot, Francois ;

Kudrna, Dave ;

Ammiraju, Jetty Siva S. ;

Schuster, Stephan C. ;

Carlson, John E. ;

Sallet, Erika ;

Schiex, Thomas ;

Dievart, Anne ;

Kramer, Melissa ;

Gelley, Laura ;

Shi, Zi ;

Berard, Aurelie ;

Viot, Christopher ;

Boccara, Michel ;

Risterucci, Ange Marie ;

Guignon, Valentin ;

Sabau, Xavier ;

Axtell, Michael J. ;

Ma, Zhaorong ;

Zhang, Yufan ;

Brown, Spencer ;

Bourge, Mickael ;

Golser, Wolfgang ;

Song, Xiang ;

Clement, Didier ;

Rivallan, Ronan ;

Tahi, Mathias ;

Akaza, Joseph Moroh ;

Pitollat, Bertrand ;

Gramacho, Karina ;

D'Hont, Angelique ;

Brunel, Dominique .

NATURE GENETICS, 2011, 43 (02) :101-108

[5]

Arumuganathan K., 1991, Plant Mol Biol Rep, V9, P208, DOI [10.1007/BF02672069, DOI 10.1007/BF02672069]

[6] CONTROLLING THE FALSE DISCOVERY RATE - A PRACTICAL AND POWERFUL APPROACH TO MULTIPLE TESTING [J].

BENJAMINI, Y ;

HOCHBERG, Y .

JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY, 1995, 57 (01) :289-300

[7] GeneWise and genomewise [J].

Birney, E ;

Clamp, M ;

Durbin, R .

GENOME RESEARCH, 2004, 14 (05) :988-995

[8] GO::TermFinder - open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes [J].

Boyle, EI ;

Weng, SA ;

Gollub, J ;

Jin, H ;

Botstein, D ;

Cherry, JM ;

Sherlock, G .

BIOINFORMATICS, 2004, 20 (18) :3710-3715

[9]

BROWN AC, 1985, J AM SOC HORTIC SCI, V110, P683

[10] Watermelon consumption increases plasma arginine concentrations in adults [J].

Collins, Julie K. ;

Wu, Guoyao ;

Perkins-Veazie, Penelope ;

Spears, Karen ;

Claypool, P. Larry ;

Baker, Robert A. ;

Clevidence, Beverly A. .

NUTRITION, 2007, 23 (03) :261-266

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