ARS | Publication request: The Genome of the Cucumber, Cucumis Sativus L

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 1, 2009
Publication Date: November 1, 2009
Citation: Huang, S., Li, R., Zhang, Z., Li, L., Gu, X., Fan, W., Lucas, W., Wang, X., Xie, B., Ni, P., Ren, Y., Zhu, H., Li, J., Lin, K., Jin, W., Fei, Z., Li, G., Staub, J.E., Kilian, A., Van Der Vossen, E.A., 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., Wu, Z., Zhang, J., Cai, Q., Bai, Y., Zhao, B., Han, Y., Li, Y., Li, X., Wang, S., Shi, Q., Liu, S., Cho, W.K., Kim, J., 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. 41(12):1275-1281.

Interpretive Summary: Cucurbit vegetable species include squash, watermelon, melon, and cucumber. Agricultural production of cucurbits uses 9 million hectares of land and yields 184 million tons of vegetables, fruits and seeds annually. Cucumber is the third most widely grown vegetable crop worldwide. It has also been used as a model crop for many genetic studies. Despite the agricultural and biological importance of cucurbits, knowledge of their genetics (the inheritance of horticulturally important traits) and genome (the location and DNA composition of genes which control traits) is currently very limited. The genome of cucumber is made up of a linear order of DNA that is called a sequence. A study was designed to determine the order of the DNA sequence in cucumber to learn more about its genome or the nature of horticulturally important traits. The sequenced cucumber genome affords insight into traits such as its sex expression, disease resistance, bitterness in fruits, and ‘fresh green’ odor. The cucumber genome was sequenced. The cucumber genome provides a valuable resource for developing improved cultivars and for studying its evolution. The information obtained from this study adds dramatically to our knowledge of cucumber genetics and will allow plant breeders to be more effective in developing strategies for cucumber improvement. This increase in effectiveness will result in the development of improved cultivars that will increase the global competitiveness of the U.S. grower.

Technical 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.