Genomic data for the domestic cucumber (Cucumis sativus var. sativus L.).

Dataset type: Genomic, Transcriptomic
Data released on November 12, 2011

Here we present genomic data for the domestic cucumber (Cucumis sativus var. sativus L.). The cucumber is a member of the Cucurbitaceae or cucurbit family, a family of great agricultural and horticultural importance that also includes species such as melons, gourds and squashes. A biologically interesting as well as an economically relevant species, it is used as a model system for plant sex determination and vascular biology studies. The domestic cucumber has seven pairs of chromosomes and a haploid genome of 367 Mb, a smaller genome for the Cucurbitaceae family. The genome was sequenced and assembled with N50 contig and scaffold sizes of 19.8 Kb and 1.14 Mb, respectively. Using the genetic map, 72.8% of the assembled sequences were anchored onto the 7 chromosomes. A total of 26,682 genes were predicted in the current cucumber genome.

Additional details

Read the peer-reviewed publication(s):

Han, Y. H., Zhang, Z. H., Liu, J. H., Lu, J. Y., Huang, S. W., & Jin, W. W. (2008). Distribution of the tandem repeat sequences and karyotyping in cucumber (Cucumis sativus L.) by fluorescence in situ hybridization. Cytogenetic and Genome Research, 122(1), 80–88. doi:10.1159/000151320 (PubMed: 18931490)
Huang, S., Li, R., Zhang, Z., Li, L., Gu, X., Fan, W., … Ni, P. (2009). The genome of the cucumber, Cucumis sativus L. Nature Genetics, 41(12), 1275–1281. doi:10.1038/ng.475 (PubMed: 19881527)
Ren, Y., Zhang, Z., Liu, J., Staub, J. E., Han, Y., Cheng, Z., … Huang, S. (2009). An Integrated Genetic and Cytogenetic Map of the Cucumber Genome. PLoS ONE, 4(6), e5795. doi:10.1371/journal.pone.0005795 (PubMed: 19495411)

Genome browser:

Accessions (data generated as part of this study):

BioProject: PRJNA33619

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Cucumber869827Cucumber Cucumis sativus var. sativus
Displaying 1-1 of 1 Sample(s).

File NameSample IDData TypeFile FormatSizeRelease Date 
CucumberOtherEXCEL31.5 KB2011-11-12
CucumberOtherEXCEL29.5 KB2011-11-12
CucumberOtherEXCEL42.5 KB2011-11-12
CucumberOtherEXCEL31 KB2011-11-12
CucumberOtherEXCEL41.5 KB2011-11-12
CucumberOtherEXCEL46 KB2011-11-12
CucumberOtherEXCEL33.5 KB2011-11-12
CucumberOtherEXCEL223.5 KB2011-11-12
CucumberSequence assemblyFASTA67.08 MB2011-11-12
CucumberOtherEXCEL864 KB2011-11-12
Displaying 1-10 of 16 File(s).
Date Action