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.

An integrated molecular cytogenetic map of Cucumis sativus L. chromosome 2

“…Thus, the centromeres have been left as gap in the sequence maps in most model eukaryotes. rDNA sequences and several types of satellite sequences primarily located in the centromeric and telomeric regions comprised the majority of unassembled reads in cucumber genome shotgun sequences [1]. FISH is a powerful technique to delineate the structure and DNA composition of such genomic regions [9].…”

“…The cucumber genome has been sequenced using a novel combination of traditional Sanger and next-generation Illumina GA sequencing technologies [1]. Illumina GA sequencing technology has significantly improved high throughput sequencing efforts at reasonable cost.…”

“…However, an intrinsic characteristic of the technology is short read lengths (~50 bp), which prevents their direct application for de novo genomic assembly. Within a total of 72.2-fold genome coverage generated for cucumber genome, Sanger reads provided 3.9-fold coverage and Illumina GA reads provided 68.3-fold coverage [1]. The total length of assembled cucumber genome was 243.5 Mb which is 30% smaller compared to cucumber genome size.…”

Advances in genomics for flatfish aquaculture

“…Although limited information about sequencing strategies and assemblies is still available, length reads and strategies to orientate adequately the scaffolds and contigs are critical. For the Senegalese sole, as in other de novo eukaryotic genomes published until now, a two-step strategy is being followed: scaffolding using matepair (Illumina Ò ) and long paired-end libraries (454) with insert sizes comprised between 2 kb and 20 kb, followed by massive whole-genome shotgun sequencing (454 and Illumina paired-ends) to be assembled into smaller contigs (Huang et al 2009;Dalloul et al 2010;Li et al 2010;Suen et al 2011;Woycicki et al 2011). However, de novo assembly of large and complex eukaryotic genomes is still challenging due to repetitive DNA and, in fish, by additional whole-genome duplication (WGD) events that occurred in the teleost lineage (3R and 4R in salmonids).…”

The tomato genome: implications for plant breeding, genomics and evolution

“…Eudicots (Box 1), the largest group in flowering plants, are composed of two major clades, the Eurosids and Euasterids. Genome sequences of many members of group Eurosids, such as Arabidopsis , grape, poplar, medicago, cucumber, and so on, have already been published [3,13,29-31]. However, members of the group Euasterids, which has many plants of economic importance, were not represented in the list of known plant genome sequences until the release of the potato ( Solanum tuberosum ) genome belonging to the family Solanaceae [6].…”