The genome of the cucumber, Cucumis sativus L

Sanwen Huang; Ruiqiang Li; Zhonghua Zhang; Li Li; Xingfang Gu; Wei Fan; William J Lucas; Xiaowu Wang; Bingyan Xie; Peixiang Ni; Yuanyuan Ren; Hongmei Zhu; Jun Li; Kui Lin; Weiwei Jin; Zhangjun Fei; Guangcun Li; Jack Staub; Andrzej Kilian; Edwin A G van der Vossen; Yang Wu; Jie Guo; Jun He; Zhiqi Jia; Yi Ren; Geng Tian; Yao Lu; Jue Ruan; Wubin Qian; Mingwei Wang; Quanfei Huang; Bo Li; Zhaoling Xuan; Jianjun Cao; null Asan; Zhigang Wu; Juanbin Zhang; Qingle Cai; Yinqi Bai; Bowen Zhao; Yonghua Han; Ying Li; Xuefeng Li; Shenhao Wang; Qiuxiang Shi; Shiqiang Liu; Won Kyong Cho; Jae-Yean Kim; Yong Xu; Katarzyna Heller-Uszynska; Han Miao; Zhouchao Cheng; Shengping Zhang; Jian Wu; Yuhong Yang; Houxiang Kang; Man Li; Huiqing Liang; Xiaoli Ren; Zhongbin Shi; Ming Wen; Min Jian; Hailong Yang; Guojie Zhang; Zhentao Yang; Rui Chen; Shifang Liu; Jianwen Li; Lijia Ma; Hui Liu; Yan Zhou; Jing Zhao; Xiaodong Fang; Guoqing Li; Lin Fang; Yingrui Li; Dongyuan Liu; Hongkun Zheng; Yong Zhang; Nan Qin; Zhuo Li; Guohua Yang; Shuang Yang; Lars Bolund; Karsten Kristiansen; Hancheng Zheng; Shaochuan Li; Xiuqing Zhang; Huanming Yang; Jian Wang; Rifei Sun; Baoxi Zhang; Shuzhi Jiang; Jun Wang; Yongchen Du; Songgang Li

doi:10.1038/ng.475

The genome of the cucumber, Cucumis sativus L

Sanwen Huang, Ruiqiang Li, Zhonghua Zhang, Li Li, Xingfang Gu, Wei Fan, William J Lucas, Xiaowu Wang, Bingyan Xie, Peixiang Ni, Yuanyuan Ren, Hongmei Zhu, Jun Li, Kui Lin, Weiwei Jin, Zhangjun Fei, Guangcun Li, Jack Staub, Andrzej Kilian, Edwin A G van der VossenYang Wu, Jie Guo, Jun He, Zhiqi Jia, Yi Ren, Geng Tian, Yao Lu, Jue Ruan, Wubin Qian, Mingwei Wang, Quanfei Huang, Bo Li, Zhaoling Xuan, Jianjun Cao, Asan, Zhigang Wu, Juanbin Zhang, Qingle Cai, Yinqi Bai, Bowen Zhao, Yonghua Han, Ying Li, Xuefeng Li, Shenhao Wang, Qiuxiang Shi, Shiqiang Liu, Won Kyong Cho, Jae-Yean Kim, Yong Xu, Katarzyna Heller-Uszynska, Han Miao, Zhouchao Cheng, Shengping Zhang, Jian Wu, Yuhong Yang, Houxiang Kang, Man Li, Huiqing Liang, Xiaoli Ren, Zhongbin Shi, Ming Wen, Min Jian, Hailong Yang, Guojie Zhang, Zhentao Yang, Rui Chen, Shifang Liu, Jianwen Li, Lijia Ma, Hui Liu, Yan Zhou, Jing Zhao, Xiaodong Fang, Guoqing Li, Lin Fang, Yingrui Li, Dongyuan Liu, Hongkun Zheng, Yong Zhang, Nan Qin, Zhuo Li, Guohua Yang, Shuang Yang, Lars Bolund, Karsten Kristiansen, Hancheng Zheng, Shaochuan Li, Xiuqing Zhang, Huanming Yang, Jian Wang, Rifei Sun, Baoxi Zhang, Shuzhi Jiang, Jun Wang, Yongchen Du, Songgang Li

Department of Biology

935 Citations (Scopus)

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 sativus var. 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.

Original language	English
Journal	Nature Genetics
Volume	41
Issue number	12
Pages (from-to)	1275-81
Number of pages	6
ISSN	1061-4036
DOIs	https://doi.org/10.1038/ng.475
Publication status	Published - 2009

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Huang, S, Li, R, Zhang, Z, Li, L, Gu, X, Fan, W, Lucas, WJ, Wang, X, Xie, B, Ni, P, Ren, Y, Zhu, H, Li, J, Lin, K, Jin, W, Fei, Z, Li, G, Staub, J, Kilian, A, van der Vossen, EAG, Wu, Y, Guo, J, He, J, Jia, Z, Ren, Y, Tian, G, Lu, Y, Ruan, J, Qian, W, Wang, M, Huang, Q, Li, B, Xuan, Z, Cao, J, Asan, Wu, Z, Zhang, J, Cai, Q, Bai, Y, Zhao, B, Han, Y, Li, Y, Li, X, Wang, S, Shi, Q, Liu, S, Cho, WK, Kim, J-Y, Xu, Y, Heller-Uszynska, K, Miao, H, Cheng, Z, Zhang, S, Wu, J, Yang, Y, Kang, H, Li, M, Liang, H, Ren, X, Shi, Z, Wen, M, Jian, M, Yang, H, Zhang, G, Yang, Z, Chen, R, Liu, S, Li, J, Ma, L, Liu, H, Zhou, Y, Zhao, J, Fang, X, Li, G, Fang, L, Li, Y, Liu, D, Zheng, H, Zhang, Y, Qin, N, Li, Z, Yang, G, Yang, S, Bolund, L, Kristiansen, K, Zheng, H, Li, S, Zhang, X, Yang, H, Wang, J, Sun, R, Zhang, B, Jiang, S, Wang, J, Du, Y & Li, S 2009, 'The genome of the cucumber, Cucumis sativus L', Nature Genetics, vol. 41, no. 12, pp. 1275-81. https://doi.org/10.1038/ng.475

@article{73603a90a5ee11df928f000ea68e967b,

title = "The genome of the cucumber, Cucumis sativus L",

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 sativus var. 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.",

author = "Sanwen Huang and Ruiqiang Li and Zhonghua Zhang and Li Li and Xingfang Gu and Wei Fan and Lucas, {William J} and Xiaowu Wang and Bingyan Xie and Peixiang Ni and Yuanyuan Ren and Hongmei Zhu and Jun Li and Kui Lin and Weiwei Jin and Zhangjun Fei and Guangcun Li and Jack Staub and Andrzej Kilian and {van der Vossen}, {Edwin A G} and Yang Wu and Jie Guo and Jun He and Zhiqi Jia and Yi Ren and Geng Tian and Yao Lu and Jue Ruan and Wubin Qian and Mingwei Wang and Quanfei Huang and Bo Li and Zhaoling Xuan and Jianjun Cao and Asan and Zhigang Wu and Juanbin Zhang and Qingle Cai and Yinqi Bai and Bowen Zhao and Yonghua Han and Ying Li and Xuefeng Li and Shenhao Wang and Qiuxiang Shi and Shiqiang Liu and Cho, {Won Kyong} and Jae-Yean Kim and Yong Xu and Katarzyna Heller-Uszynska and Han Miao and Zhouchao Cheng and Shengping Zhang and Jian Wu and Yuhong Yang and Houxiang Kang and Man Li and Huiqing Liang and Xiaoli Ren and Zhongbin Shi and Ming Wen and Min Jian and Hailong Yang and Guojie Zhang and Zhentao Yang and Rui Chen and Shifang Liu and Jianwen Li and Lijia Ma and Hui Liu and Yan Zhou and Jing Zhao and Xiaodong Fang and Guoqing Li and Lin Fang and Yingrui Li and Dongyuan Liu and Hongkun Zheng and Yong Zhang and Nan Qin and Zhuo Li and Guohua Yang and Shuang Yang and Lars Bolund and Karsten Kristiansen and Hancheng Zheng and Shaochuan Li and Xiuqing Zhang and Huanming Yang and Jian Wang and Rifei Sun and Baoxi Zhang and Shuzhi Jiang and Jun Wang and Yongchen Du and Songgang Li",

note = "Keywords: Cucumis sativus; DNA Transposable Elements; DNA, Plant; Gene Duplication; Genes, Plant; Genome, Plant; Immunity, Innate; Molecular Sequence Data; Plant Diseases; Repetitive Sequences, Nucleic Acid; Synteny",

year = "2009",

doi = "10.1038/ng.475",

language = "English",

volume = "41",

pages = "1275--81",

journal = "Nature: New biology",

issn = "1061-4036",

publisher = "nature publishing group",

number = "12",

}

TY - JOUR

T1 - The genome of the cucumber, Cucumis sativus L

AU - Huang, Sanwen

AU - Li, Ruiqiang

AU - Zhang, Zhonghua

AU - Li, Li

AU - Gu, Xingfang

AU - Fan, Wei

AU - Lucas, William J

AU - Wang, Xiaowu

AU - Xie, Bingyan

AU - Ni, Peixiang

AU - Ren, Yuanyuan

AU - Zhu, Hongmei

AU - Li, Jun

AU - Lin, Kui

AU - Jin, Weiwei

AU - Fei, Zhangjun

AU - Li, Guangcun

AU - Staub, Jack

AU - Kilian, Andrzej

AU - van der Vossen, Edwin A G

AU - Wu, Yang

AU - Guo, Jie

AU - He, Jun

AU - Jia, Zhiqi

AU - Ren, Yi

AU - Tian, Geng

AU - Lu, Yao

AU - Ruan, Jue

AU - Qian, Wubin

AU - Wang, Mingwei

AU - Huang, Quanfei

AU - Li, Bo

AU - Xuan, Zhaoling

AU - Cao, Jianjun

AU - Asan, null

AU - Wu, Zhigang

AU - Zhang, Juanbin

AU - Cai, Qingle

AU - Bai, Yinqi

AU - Zhao, Bowen

AU - Han, Yonghua

AU - Li, Ying

AU - Li, Xuefeng

AU - Wang, Shenhao

AU - Shi, Qiuxiang

AU - Liu, Shiqiang

AU - Cho, Won Kyong

AU - Kim, Jae-Yean

AU - Xu, Yong

AU - Heller-Uszynska, Katarzyna

AU - Miao, Han

AU - Cheng, Zhouchao

AU - Zhang, Shengping

AU - Wu, Jian

AU - Yang, Yuhong

AU - Kang, Houxiang

AU - Li, Man

AU - Liang, Huiqing

AU - Ren, Xiaoli

AU - Shi, Zhongbin

AU - Wen, Ming

AU - Jian, Min

AU - Yang, Hailong

AU - Zhang, Guojie

AU - Yang, Zhentao

AU - Chen, Rui

AU - Liu, Shifang

AU - Li, Jianwen

AU - Ma, Lijia

AU - Liu, Hui

AU - Zhou, Yan

AU - Zhao, Jing

AU - Fang, Xiaodong

AU - Li, Guoqing

AU - Fang, Lin

AU - Li, Yingrui

AU - Liu, Dongyuan

AU - Zheng, Hongkun

AU - Zhang, Yong

AU - Qin, Nan

AU - Li, Zhuo

AU - Yang, Guohua

AU - Yang, Shuang

AU - Bolund, Lars

AU - Kristiansen, Karsten

AU - Zheng, Hancheng

AU - Li, Shaochuan

AU - Zhang, Xiuqing

AU - Yang, Huanming

AU - Wang, Jian

AU - Sun, Rifei

AU - Zhang, Baoxi

AU - Jiang, Shuzhi

AU - Wang, Jun

AU - Du, Yongchen

AU - Li, Songgang

N1 - Keywords: Cucumis sativus; DNA Transposable Elements; DNA, Plant; Gene Duplication; Genes, Plant; Genome, Plant; Immunity, Innate; Molecular Sequence Data; Plant Diseases; Repetitive Sequences, Nucleic Acid; Synteny

PY - 2009

Y1 - 2009

N2 - 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 sativus var. 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.

AB - 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 sativus var. 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.

U2 - 10.1038/ng.475

DO - 10.1038/ng.475

M3 - Journal article

C2 - 19881527

SN - 1061-4036

VL - 41

SP - 1275

EP - 1281

JO - Nature: New biology

JF - Nature: New biology

IS - 12

ER -

The genome of the cucumber, Cucumis sativus L

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