Archive for April, 2010

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.

Phyllosphere 2010

April 21st, 2010

logoThe 9th International Symposium on the Microbiology of Aerial Plant Surfaces will be held at the campus of Oregon State University from August 14-18, 2010. The meeting seeks to bring together researchers from the plant and the microbial side and will include the areas of aerobiology, anatomy, bacteriology, biochemistry, biological control, micro-meteorology, mycology, plant physiology, plant pathology, and molecular biology in order to further our understanding the ecology of foliar plant surfaces in both aquatic and terrestrial environments.

Another Grass Genome

April 19th, 2010

Bd-1Grasses swaying in the wind on a summer day can be seen on vast land areas on this planet. The grass family (Poaceae) comprises more than 10,000 species that cover several important natural and agricultural ecosystems. Rice, maize, sorghum, wheats and millets provide the staple food for billions of people. The rice (Ehrhartoideae subfamily) and sorghum (Panicoideae) genomes have been released. The genomes of most Pooideae, such as the bread wheat (17 Gb), are characterized by daunting size and complexity (polyploidy) which preclude their study. Brachypodium distachyon (the purple false brome) is a  Pooideae grass species native to southern Europe, northern Africa and southwestern Asia east to India. Thanks to the availability of germplasm and mutant collections, an efficient transformation system, a meiotic map, BAC libraries and microarrays, it has been promoted as a model grass. The Brachypodium distachyon Initiative published a draft Brachypodium genome sequence and annotation in the February 11, 2010 issue of Nature. Compared to other grasses, this genome is very compact (272 Mb), with transposable elements mainly located at the centromeres and syntenic breakpoints.  The comparison of this genome with the rice and sorghum genomes enabled the reconstruction of chromosome evolution across the grasses. It appears that the varying number of chromosomes found in the major grass subfamilies derives from an ancestral set of five chromosomes by nested insertions of whole chromosome into centromeres. A total of 25,532 protein-coding genes was predicted — a coding space similar to rice and sorghum. Most gene families are shared between these three grass species, indicating a recent common origin. This novel genome will likely allow important advance in grass genomics.

Photo: ©University of Massachusetts Amherst (Biology Department)

The genome of a songbird

April 18th, 2010

Zebra_finchThe zebra finch (Taeniopygia guttata) is a songbird belonging to the large avian order Passeriformes. As the lovely bird lives in trees, it deserves a slot in this blog. This songbird genome has been sequenced and assembled, and the main results are presented in the 1st of April issue of Nature.

Of the 1.2 gigabase (Gb) draft assembly, 1.0 Gb has been assigned to 33 chromosomes and three linkage groups, by using zebra finch genetic linkage and bacterial artificial chromosome (BAC) fingerprint maps. A total of 17,475 protein-coding genes were predicted from the zebra finch genome assembly using the Ensembl pipeline supplemented by Gpipe gene models. A major result of this study the demonstration that song behaviour engages gene regulatory networks in the songbird brain, altering the expression of long non-coding RNAs, microRNAs, transcription factors and their targets. This study also suggests rapid molecular evolution in the songbird lineage of genes that are regulated during song experience. These results indicate an active involvement of the genome in neural processes underlying vocal communication.

Warren et al. (2010) The genome of a songbird. Nature 464, 757-762.

Photo: © mediawiki.org

Cherry Blossoms

April 18th, 2010

Cherry tree blossoms

The long Lorraine Winter is gone … the cherry trees in my garden are blossoming ;-)

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).

Trees: the Life-Form of the Month

April 10th, 2010

old_oakIf you love trees as I do, you should read Olivia Judson’s recent post on the New York Times science blog:

“Trees figure in our mythologies and metaphors — the tree of life, the tree of knowledge — and we often imagine them to harbor spirits and sprites. They also figure in a big way in our reality: forests (still) cover about 30 percent of the planet’s land, and may make up as much as 80 percent of Earth’s biomass. That is, if you were to put all the organisms on the planet on a giant set of scales, trees would account for 80 percent of the total.

Better yet, trees harbor plenty of non-imaginary beings. Birds like starlings or blue tits nest in tree holes; others, like magpies and crows, build their nests high in the branches. Chimpanzees sleep in trees. A number of fungi — truffles, anyone? — associate with tree roots. Insects like wasps make houses (galls) in the leaves.

And if you half-close your eyes and dream a little, you can also see its roots, stretching deep beneath the grass, much as its branches and twigs stretch outwards towards the buildings and upwards towards the sky. And so on …..”

http://opinionator.blogs.nytimes.com/2010/04/06/tree-mendous/

Photo: Old oak near my home © FM

Chinese and Perigord Black Truffles

April 3rd, 2010

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A TV crew and a photograph from Reuters visited the lab on Thursday. We had a lot of fun in mimicking the DNA typing of the Chinese and Perigord black truffles . As we claimed: “DNA fingerprinting will help identify the regional origin of harvested truffles and set up the means to certify these products and detect any frauds”.

Photo: Claude Murat handling a T. indicum and  T. melanosporum in his right and left hand, respectively. © Reuters/INRA.