Nature Genetics

http://www.nature.com/ng/journal/vaop/ncurrent/abs/ng.475.html

Article abstract

Nature Genetics 
Published online: 1 November 2009 | doi:10.1038/ng.475

The genome of the cucumber, Cucumis sativus L.

Sanwen Huang1,19, Ruiqiang Li2,3,19, Zhonghua Zhang1,19, Li Li2,19, Xingfang Gu1,19, Wei Fan2,19, William J Lucas4,19, Xiaowu Wang1, Bingyan Xie1, Peixiang Ni2, Yuanyuan Ren2, Hongmei Zhu2, Jun Li2, Kui Lin5, Weiwei Jin6, Zhangjun Fei7, Guangcun Li8, Jack Staub9, Andrzej Kilian10, Edwin A G van der Vossen11, Yang Wu5, Jie Guo5, Jun He1, Zhiqi Jia1, Yi Ren1, Geng Tian2, Yao Lu2, Jue Ruan2,12, Wubin Qian2, Mingwei Wang2, Quanfei Huang2, Bo Li2, Zhaoling Xuan2, Jianjun Cao2, Asan2, Zhigang Wu2, Juanbin Zhang2, Qingle Cai2, Yinqi Bai2, Bowen Zhao13, Yonghua Han6, Ying Li1, Xuefeng Li1, Shenhao Wang1, Qiuxiang Shi1, Shiqiang Liu1, Won Kyong Cho14, Jae-Yean Kim14, Yong Xu15, Katarzyna Heller-Uszynska10, Han Miao1, Zhouchao Cheng1, Shengping Zhang1, Jian Wu1, Yuhong Yang1, Houxiang Kang1, Man Li1, Huiqing Liang2, Xiaoli Ren2, Zhongbin Shi2, Ming Wen2, Min Jian2, Hailong Yang2, Guojie Zhang2,12, Zhentao Yang2, Rui Chen2, Shifang Liu2, Jianwen Li2, Lijia Ma2,12, Hui Liu2, Yan Zhou2, Jing Zhao2, Xiaodong Fang2, Guoqing Li2, Lin Fang2, Yingrui Li2,12, Dongyuan Liu2, Hongkun Zheng2,3, Yong Zhang2, Nan Qin2, Zhuo Li2, Guohua Yang2, Shuang Yang2, Lars Bolund2,16, Karsten Kristiansen17, Hancheng Zheng2,18, Shaochuan Li2,18, Xiuqing Zhang2, Huanming Yang2, Jian Wang2, Rifei Sun1, Baoxi Zhang1, Shuzhi Jiang1, Jun Wang2,17, Yongchen Du1 & Songgang Li2

Abstract

Cucumber is an economically important crop as well as a model system for sex determination studies and plant vascular biology. Here we report the draft genome sequence of Cucumis sativusvar. sativus L., assembled using a novel combination of traditional Sanger and next-generation Illumina GA sequencing technologies to obtain 72.2-fold genome coverage. The absence of recent whole-genome duplication, along with the presence of few tandem duplications, explains the small number of genes in the cucumber. Our study establishes that five of the cucumber's seven chromosomes arose from fusions of ten ancestral chromosomes after divergence from Cucumis melo. The sequenced cucumber genome affords insight into traits such as its sex expression, disease resistance, biosynthesis of cucurbitacin and 'fresh green' odor. We also identify 686 gene clusters related to phloem function. The cucumber genome provides a valuable resource for developing elite cultivars and for studying the evolution and function of the plant vascular system.

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  1. Key Laboratory of Horticultural Crops Genetic Improvement of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics Technology, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
  2. BGI-Shenzhen, Shenzhen, China.
  3. Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
  4. Department of Plant Biology, College of Biological Sciences, University of California, Davis, California, USA.
  5. College of Life Sciences, Beijing Normal University, Beijing, China.
  6. National Maize Improvement Center of China, Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China.
  7. Boyce Thompson Institute and USDA Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, New York, USA.
  8. High-Tech Research Center, Shandong Academy of Agricultural Sciences, Jinan, China.
  9. US Department of Agriculture, Agricultural Research Service, Vegetable Crops Research Unit, Department of Horticulture, University of Wisconsin, Madison, Wisconsin, USA.
  10. Diversity Arrays Technology, Canberra, Australia.
  11. Wageningen UR Plant Breeding, Wageningen, The Netherlands.
  12. The Graduate University of Chinese Academy of Sciences, Beijing, China.
  13. High School Affiliated to Renmin University of China, Beijing, China.
  14. Division of Applied Life Science (BK21 and WCU program), PMBBRC and EB-NCRC, Gyeongsang National University, Jinju, Republic of Korea.
  15. National Engineering Research Center for Vegetables, Beijing, China.
  16. Institute of Human Genetics, University of Aarhus, Aarhus, Denmark.
  17. Department of Biology, University of Copenhagen, Copenhagen, Denmark.
  18. South China University of Technology, Guangzhou, China.
  19. These authors contributed equally to this work.

Correspondence to: Yongchen Du1 e-mail: yongchen.du@mail.caas.net.cn

Correspondence to: Sanwen Huang1,19 e-mail: huangsanwen@caas.net.cn

Correspondence to: Jun Wang2,17 e-mail: wangj@genomics.org.cn

Correspondence to: Songgang Li2 e-mail: lisg@genomics.org.cn



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