Posts Tagged ‘plant evolution’

Concombre à la Crème & Cucumber Genome

April 25th, 2010

concombre_marketerWhen 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.

Ren et al. (2010) An Integrated Genetic and Cytogenetic Map of the Cucumber Genome. PLoS ONE 4(6): e5795. doi:10.1371/journal.pone.0005795.

Huang et al. (2009) The genome of the cucumber, : Cucumis sativus: L. Nature Genetics 41, 1275 – 1281.

Peach Genome Released: “un jus de première qualité”

April 11th, 2010

Peach flowerThe draft of the genome sequence of Peach (Prunus persica) (cultivar ‘Lovell’) has been released on April 1st by the International Peach Genome Initiative. This consortium, under the direction of Drs Bryon Sosinski, Ignazio Verde and Daniel Rokhsar, includes numerous researchers from countries around the globe including the US, Italy, Spain and Chile.

The genome is available online at the Genome Database for Rosaceae, JGI Phytozome and Istituto di Genomica Applicata (IGA).

Peach (Prunus persica) is considered one of the genetically most well characterized species in the Rosaceae, and it has distinct advantages that make it suitable as a model genome species for Prunus as well as for other species in the Rosaceae. While some Prunus species, such as cultivated plums and sour cherries, are polyploid, peach is a diploid with n = 8 and has a comparatively small genome currently estimated to be ~220-230 Mbp based upon the peach v1.0 assembly.

Assembly v1.0 currently consists of 8 pseudomolecules (scaffolds) representing the 8 chromosomes. The genome sequencing consisted of approximately 7.7 fold whole genome shotgun sequencing employing the Sanger methodology, and was assembled using Arachne. The assembled peach scaffolds cover nearly 99% of the peach genome, with over 92% having confirmed orientation. To further validate the quality of the assembly, 74,757 Prunus ESTs were queried against the genome — only ~2% were missing;  28,689 transcripts and 27,852 genes have been predicted.

Together, with the poplar and euclayptus genomes, the peach genome is being used to identify genes that are critical for deciduous tree growth and development.

Photo: Peach flower (© FM).

The first legume species with a complete genome sequence

February 14th, 2010

soybeanThe face of Legume genetics has changed in early 2008  with the release of the complete draft assembly of the soybean [Glycine max (L.) Merr.] genome delivered by a triogency group [National Science Foundation (NSF), United States Department of Energy (US DOE), and United States Department of Agriculture (USDA)]. The genome project was initiated by by a consortium led by Gary Stacey, Randy Shoemaker, Scott Jackson, Jeremy Schmutz, and Dan Rokhsar. DOE JGI’s interest in sequencing the soybean genome stems from its role as a major source of biodiesel, a renewable, alternative fuel with the highest energy content of any alternative fuel. The genome data can be accessed at the Phytozome genome portal and the main features of this crop genome are discussed in the 14th January issue of Nature. The 1.1-gigabase genome containing 46,430 protein-coding genes has been sequenced by a whole-genome shotgun approach and integrated with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. Repeated elements make up ~59% of the assembled genome.

Soybean’s set of chromosomes has been duplicated at least twice, approximately 59 million years ago the first time and then again about 13 million years ago and, as consequence, soybean plants still have multiple copies of almost three-quarters of their genes. Mining this coding space allowed the identification of genes involved in the nitrogen-fixing symbiosis. Interestingly, the number of genes involved in lipid signalling, degradation of storage lipids, and membrane lipid synthesis were two- to threefold higher in soybean than Arabidopsis, indicating that these areas of acyl lipid synthesis are more complex in soybean.

As emphasized by the authors: “Soybean, one of the most important global sources of protein and oil, is now the first legume species with a complete genome sequence. It is, therefore, a key reference for the more than 20,000 legume species, and for the remarkable evolutionary innovation of nitrogen-fixing symbiosis”. The genome sequence has provided access to the first resistance gene for the devastating disease Asian Soybean Rust.

Schmutz et al. (2010) Genome sequence of the palaeopolyploid soybean. Nature 463, 178-183.

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