Press Release

Cucumber genome sequenced

November 1, 2009

The genome of the cucumber, an economically important crop, has been sequenced and was published online this week in Nature Genetics*.

The cucumber is part of the cucurbit botanical family, which also includes melon, watermelon, squash and pumpkin. Altogether, cucurbit crops utilize nine million hectares of land and yield 184 million tons of fruit, vegetables and seed each year. The cucumber is the seventh plant to have its genome sequenced, following the well-studied plant model Arabidopsis thaliana, the poplar tree, grapevine, papaya, and the crops rice and sorghum.

In 2009, the cucumber genome initiative was established to unveil the genetic code of this important vegetable. Dr. Sanwen Huang from the Chinese Academy of Agricultural Science coordinated the international consortium, which includes also the genome centre BGI-Shenzhen, two other Chinese universities, and three universities in US and one each in the Netherlands, Australia, and South Korea.

Sanwen Huang and colleagues used both traditional DNA sequencing methods and next-generation sequencing (NGS) technologies to assemble the cucumber genome. This was the first time next-generation sequencing data was used in the initial assembly of a plant genome. This is possible due to a novel assembly algorithm that was developed by BGI to handle short reads from NGS. The cucumber genome is 350 million base pairs, similar to the rice genome, which is 389 million base pairs.

The cucumber genome affords insight into several important biological and agronomical traits, such as sex expression, pest and disease resistance, biosynthesis of the bitter staff, cucurbitacin, and 'fresh green' odor of the fruits. 

Cucumber and melon are closely related species. Cucumber has 7 chromosomes, while melon has 12. The study establishes that 5 of the 7 cucumber chromosomes arose from 10 ancestral chromosomes after its divergence from melon. Genic regions of cucumber and melon have a similarity of 95%, making the cucumber genome sequence useful to biological study and genetic improvement of melon and probably other cucurbits as well. 

The cucurbits are also model plants for the study of vascular biology. Equivalent to the animal arterial system, phloem delivers nutrients and signaling molecular to developing organs. Collectively, 800 phloem proteins were identified in the cucumber genome, which will offer us a better understanding of the function of phloem. 

In summary, the sequenced genome will be a resource for plant breeders developing elite varieties of cucurbits and will also be useful for studying different aspects of plant development. 

Author contact:
Sanwen Huang (Chinese Academy of Agricultural Sciences, Beijing, China)
Tel: +86 10 8210 9512; E-mail:;

*Huang et al. (2009) The genome of the cucumber, Cucumis sativus L. Nature Genetics. Published online: 01 November 2009 | doi:10.1038/ng.475