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.
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References
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Acknowledgements
We thank L. Goodman for assistance in editing the manuscript and R. Quatrano, L. Kochian, L. Comai, V. Sundaresan, S. Kamoun and S. Renner for critical readings of the manuscript. This work was funded by the Chinese Ministry of Agriculture (948 program), Ministry of Science and Technology (2006DFA32140, 2007CB815701, 2007CB815703 and 2007CB815705) and Ministry of Finance (1251610601001); the National Natural Science Foundation of China (30871707 and 30725008); the Chinese Academy of Agricultural Sciences (seed grant to S.H.); the Chinese Academy of Science (GJHZ0701-6 and KSCX2-YWN-023); the US Department of Agriculture (National Research Initiative grant 2006-35304-17346 to W.J.L.); the National Science Foundation (grant IOS-07-15513 to W.J.L.); and the Korea Science and Engineering Foundation–Ministry of Education, Science and Technology (WCU R33-10002 and BK21 grants to J.-Y.K.). WKC was partly supported by grants from the Environmental Biotechnology National Core Research Center (R15-2003-012-01003-0) and National Research Laboratory (2009-0066339). This work was also supported by the Shenzhen Municipal and Yantian District Governments and the Society of Entrepreneurs & Ecology. D. Qu and Z. Fang of the Chinese Academy of Agricultural Sciences provided management support for this work.
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S.H., Y.D., Jun Wang and Songgang Li managed the project. S.H., Z.Z., W.J.L., X.G. and R.L. designed the analyses. X.G., H.M., L.L., Yuanyuan Ren, G.T., Y. Lu, Z.X., J.C., A., Z.W., J. Zhang, H. Liang, X.R., M.J., Hailong Yang, R.C., Shifang Liu and X.Z. conducted DNA preparation and sequencing. X.W., B.X., K.L., W.J., Guangcun Li, Z.F., J.S., A.K., E.A.G.v.d.V. and Y.X. contributed new reagents and analytic tools. S.H., Z.Z., W.J.L., X.G., R.L., X.W., B.X., K.L., W.J., J.H., Z.J., Yi Ren, Ying Li, X.L., S.W., Q.S., W.K.C., J.-Y.K., K.H.-U., H.M., Z.C., S.Z., J. Wu, Y.Y., H.K., Y.W., J.G., Y.H., M.L., B. Zhao, Shiqiang Liu, W.F., P.N., H. Zhu, Jun Li, J.R., W.Q., M. Wang, Q.H., B.L., Q.C., Y.B., Z.S., M. Wen, G.Z., Z.Y., Jianwen Li, L.M., H. Liu., Y. Zhou, J. Zhao, X.F., Guoqing Li, L.F., Yingrui Li, D.L., Hancheng Zheng and Shaochuan Li conducted the data analyses. S.H., R.L., Z.Z. and W.J.L. wrote the paper. Y.D., R.S., B. Zhang., S.J., G.Y., S.Y., Hongkun Zheng, Y. Zhang, N.Q., Z.L., L.B., K.K., Huanming Yang and Jian Wang revised the paper.
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Supplementary Figures 1–20 and Supplementary Tables 1–17, 20. (PDF 2463 kb)
Supplementary Table 18
Phylogenetic relationships of GH20-oxidase genes in cucumber (Csa), Arabidopsis (At), papaya (evm.Tu), poplar (Poptr), grapevine (GSVIVP), rice (BGIOSGA), pumpkin and watermelon. (XLS 440 kb)
Supplementary Table 19
Phylogenetic relationships of expansins in cucumber (Csa), Arabidopsis (At), papaya (evm.Tu), poplar (Poptr) and grapevine (GSVIVP). (XLS 412 kb)
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Huang, S., Li, R., Zhang, Z. et al. The genome of the cucumber, Cucumis sativus L.. Nat Genet 41, 1275–1281 (2009). https://doi.org/10.1038/ng.475
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DOI: https://doi.org/10.1038/ng.475
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