When the hot weather hits, nothing is more cooling than a cucumber salad. Unlike the somewhat seedy American cucumbers with thick, bitter skins, cucumbers from my garden are thin-skinned and practically seedless, so you can just slice them and eat them, without peeling. You can also gently toss together the sliced cucumbers in bowl with a little bit of fresh cream (or yogurt if you’re on diet), salt and pepper to taste. Right before serving, sprinkle on crumbled bits of feta cheese.
Why talking about my garden cucumbers? Because in a paper appearing online today in PLoS ONE, researchers from China and the US reported that they have come up with an integrated genetic and cytogenetic map of cucumber (Cucumis sativus). Researchers from the Chinese Academy of Agricultural Sciences, the China Agricultural University, and the US Department of Agriculture’s Agricultural Research Service used whole genome shotgun sequencing to come up with nearly 1,000 polymorphic simple sequence repeat markers in cucumber. Using these markers, along with cytogenetic data, they then created a high-density linkage map that will be used for future genetic and genomic studies in cucumbers and related pumpkins, squash, melon and watermelon.
The Cucurbitaceae family comprises about 120 genera and 800 species, including many economically important vegetable and fruit crops such as cucumber (Cucumis sativus L.), melon (C. melo L.), watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai), squash and pumpkin (Cucurbita spp.)
The genome of the cucumber (cultivar Chinese Long 9930) has been published a few months ago in Nature Genetics. The genome sequencing was done by the Beijing Genomics Institute-Shenzhen and the Cucumber Genome Initiative (CuGI). It was coordinated by Sanwen Huang of the Chinese Academy of Agricultural Science and included the Genome Center at BGI, UC Davis as well as several laboratories in China and others in the U.S., Denmark, the Netherlands, Australia and South Korea.
BGI applied a hybrid strategy for the whole genome sequencing that takes advantage of read length and paired-end of the conventional Sanger sequencing and of the extra-high throughput of the next generation Illumina GA sequencing (~72X coverage). They have finished 4x Sanger sequencing of the genome and preliminary assembly showed 90% the genome was covered. The total length of the genome assembly was 243.5 Mb, whereas the genome size estimated by flow cytometry was 367 Mb. The 30% non-assembled genome are transposable elements and rRNA sequences. In addition, ~410K EST was generated from cDNA samples using Roche 454 sequencing to facilitate protein-coding gene annotation. The gene-prediction methods predicted 26,682 protein-coding genes in 15,669 gene families. The cucumber gene repertoire contains the smallest number of tandem duplications (479), much smaller than grapevine (5,382). These low number of genes and tandem duplications is likely resulting from a lack of whole genome duplication.
The genome analysis showed that five of the seven cucumber’s chromosomes arose from ten ancestral chromosomes shared after divergence from melon (C. melo), and gene-coding stretches of DNA share about 95 percent similarity to melon. The cucumber genome will also provide insights into traits such as disease and pest-resistance, the “fresh green” odor of the fruit, bitter flavors and sex expression.
The cucumber genome is bursting with transposons and repetitive sequences — many of which have not been detected in previously sequenced genomes. Note also that this study identified 800 phloem proteins in the this genome, but only 61 NBS-containing resistance genes (against 398 in poplar has we’ve shown). Lipoxygenase (LOX) enzymes might be a complementary system to cope with biotic stress.
The cucumber is the seventh plant to have its genome sequence published, following the well-studied model plant Arabidopsis thaliana, the poplar tree, grapevine, papaya, and the crops rice and sorghum.
Additional information available at: Cucurbit Genomics Database.