Archive for May, 2010

Tap the Vein that Bleeds

May 30th, 2010

Sans titre

The Colorful Secret Of The Pea Aphid: To illustrate Moran & Jarvik’s study demonstrating an ancestral transfer of genes involved in carotenoid biosynthesis between fungus and aphids, I have taken this photo of aphids feeding on a Salix leaf.

Moran & Jarvik(2010) Lateral Transfer of Genes from Fungi Underlies Carotenoid Production in Aphids. Science 328, 624 – 627

“Bite the hand that feed/Tap the vein that bleeds” Post Blue – Meds: Placebo.

Photo: © F Martin

Slug Bites

May 30th, 2010

slug biteTranscript profiling of mushrooms, such as Coprinopsis cinereaLaccaria bicolor and Tuber melanosporum, have showed a striking accumulation of transcripts coding for various types of sugar-binding lectins in fruiting bodies. It has been suggested (e.g., by Markus Künzler at ETH-Zürich) that this accumulation of lectins, such as galectins, plays a role defense against fungivores. Clearly, mushrooms growing on the horse manure composting in the back of my garden are not accumulating enough lectins to deter slugs. Dozen of fruiting bodies have mushroomed today after the overnight rains … and now this is a slug feast.

For more info: Glycans and Lectins in the Defense of Fungi against Predators and Parasites (Institute of Microbiology, ETH).

Photo: © F Martin


May 30th, 2010

CB055265Great news!!! To increase the understanding of the role of soil biodiversity in ecosystem functioning, the European Commission (EC) awarded €7 million to our research project ECOFINDERS. This four year project, coordinated by INRA, aims to support European Union soil policy making by providing the necessary tools to design and implement strategies for sustainable use of soils.

The project will include:

  • Characterisation of the biodiversity of European soils and the normal operating range (NOR) according to soil types, threats, climatic zone and land use,
  • Determination of relationships between soil biodiversity, functioning and ecosystem services,
  • Quantification of the economic values of soil ecosystem services,
  • Evaluation of the impacts of human activities on soil biodiversity, functioning and services,
  • Design of policy-relevant and cost-effective indicators for monitoring soil biodiversity, functioning and ecosystem services.

To reach this overall aim, the project will pursue the following:

  • Describe the diversity of soil organisms (microorganisms and fauna) by using nextgen sequencing,
  • Decipher their interactions through trophic food webs,
  • Determine the role played by soil organisms in soil functioning and major ecosystem services: nutrient retention, carbon storage, water retention, soil structure regulation, resistance to pests and diseases, and regulation of above-ground diversity,
  • Assess the stability and resilience of ecosystems against threats in relation to their biodiversity: soil erosion and physical degradation, decline in organic content, loss of soil biodiversity, and soil contamination.

The 22 consortium partners will:

  • Develop and standardise phenotypic tools and procedures to measure the faunal biodiversity,
  • Design molecular methods to characterise the faunal diversity calibrated upon phenotypic traits,
  • Customise functional tools and methods to determine the functional diversity of fauna,
  • Establish high-throughput molecular assays for assessing microbial and faunal biodiversity,
  • Design, develop and establish a database aimed at mapping the European soil biodiversity and threats,
  • Establish cost-effective bioindicators to measure microbial and faunal diversity, their associated functions and the resulting ecosystem services,
  • Evaluate the economic added-value brought by these bioindicators in assessing the consequences of soil management policy for soil biodiversity and functioning,
  • Implement effective dissemination strategies to transfer the project knowledge and tools to soil stakeholders, notably but not exclusively regional, national and European policy-makers, and inform the general public about the issues associated with the sustainability of soil biodiversity.

My lab will focus on developing 454-based genotyping to survey the microbial communities — hundreds of creeping subterranean bugs will ended up in digits. Our on-going analysis of forest soil metagenomes will likely feed this large scale multi-year project.

Rust Never Sleeps

May 30th, 2010

rust1It is invisible to the naked eye, and can travel hundred kilometres a day destroying nearly everything in its path”  … the deadly mutant making news headlines has nothing to see with the merciless Predator, its nickname is UG99  (TTKSK), alias Puccinia graminis f. sp. tritici, a basidiomycetous fungal pathogen from the Pucciniales clade. Two new forms of Ug99  able to overcome the effects of wheat resistance genes have been detected in South Africa. The discovery of these new variants marks the first time that the stem rust fungus with virulence against crucial defense resistance mechanisms (it overcome the effects of the resistance genes Sr31 and Sr24) has moved south of its origins in Uganda in East Africa. Epidemiologists now worry that next stop of the deadly journey of this wind-borne cereal-killer may be the wheat fields, the breadbaskets of the Middle East and South Asia.

To know more about the stem rust threathening world food supply :

Photo: Another rust, the poplar foliar rust (© B Pêtre – INRA).

HGT: ‘un de plus’- Plant-to-plant gene transfer

May 29th, 2010

striga_hermonthica_referenceShirazu’s group published a brevia paper in the last issue of Science reporting a gene transfer between a crop plant, Sorghum, and its parasite plant Striga hermonthica. ESTs (transcript sequences) of the eudicot parasite witchweed contains a sequence highly similar to the putative cis-prenyltransferase gene of its monocot host, sorghum (Sorghum bicolor).

Yoshida et al. (2010) Horizontal Gene Transfer by the Parasitic Plant Striga hermonthica. Science 328, 1128.

Photo: Striga hermonthica © CIRAD

You Are What You Eat

May 22nd, 2010

cabbage-noriA nice post from by Karen Schwarzberg and Mike Gurney at Small Things Considered (The Microbe Blog) discussing a paper recently published in Nature by Hehemann et al. which reports that, in at least one particular instance, we do harbor bacteria adapted to the traditional diet of our culture. Porphyranases are glycosyl hydrolases cleaving sulphated polysaccharides of carrageenan and agar from marine algae. These enzymes found in marine bacteria are common in Japanese—and only Japanese—intestinal microbiota. The Japanese can digest their nori (Porphyra) thanks to specific strains of Bacteroides plebeius that they host. The initial acquisition of the β-porphyranase genes by B. plebeius was likely by horizontal transfer from a marine Bacteroidetes.

Hehemann, J., Correc, G., Barbeyron, T., Helbert, W., Czjzek, M., & Michel, G. (2010). Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota Nature, 464 (7290), 908-912 DOI: 10.1038/nature08937

See also my previous post on the gut metagenomics-inspired poem from the Cuttlefish Poet at The Digital Cuttlefish‘s “You are What you Eat.”

Photo: Cabbage Nori Rolls.©


May 22nd, 2010


ASM has launched mBio™, the Society’s first broad-scope, open-access online journal. Arturo Casadevall, the Founding Editor-in-Chief, says the new journal is a good choice for scientists who wish to publish cutting-edge research rapidly. Readers can get an inside glimpse of the latest via mBiosphere, the journal’s blog run by Merry Buckley.

Playing God

May 21st, 2010

2407ld1In the last issue of Science Online (May 20), Craig Venter reports the creation (= design, synthesis, and assembly) of a bacterial cell controlled by a chemically synthesized genome. The 1.08-Mbp Mycoplasma mycoides JCVI-syn1.0 genome was constructed from a digitized genome sequence information and its transplantation into a Mycoplasma capricolum recipient cell to create new Mycoplasma mycoides cells that are controlled only by the synthetic chromosome. Talking about this project, Venter said a couple of years ago: ““It will be one of the bright milestones in human history, changing our conceptual view of life.” Said Venter.” . Hum! Hum! … The first step towards Dr. Frankenstein’s dreams?

From Nicholas Wade’s paper in the New York Times:

Some other scientists said that aside from assembling a large piece of DNA, Dr. Venter has not broken new ground. “To my mind Craig has somewhat overplayed the importance of this,” said David Baltimore, a geneticist at Caltech. He described the result as “a technical tour de force,” a matter of scale rather than a scientific breakthrough.

“He has not created life, only mimicked it,” Dr. Baltimore said.

“My worry is that some people are going to draw the conclusion that they have created a new life form,” said Jim Collins, a bioengineer at Boston University. “What they have created is an organism with a synthesized natural genome. But it doesn’t represent the creation of life from scratch or the creation of a new life form,” he said.

Methylome Phylogeny

May 18th, 2010

Laccaria methylome


DNA cytosine methylation is a crucial process for the regulation of many cellular events in mammalian, plant and fungal development, although other eukaryotic species live well without this mechanism. Zilberman’s team at the University of California, Berkeley, is reporting the DNA methylation patterns of 17 organisms — five plants, seven animals and five fungi — in Science online. They have picked these species throughout the tree of life to reconstruct how methylation might have evolved. My pet fungus Laccaria bicolor, but also Coprinopsis cinerea and Postia placenta, are among the scrutinized fungi. The methylome (genome-wide methylation maps) for each species was generated by using high-throughput bisulphite Illumina sequencing. Zilberman suggests that the last common ancestor of plants, animals and fungi carried enzymes, DNA methyltransferases, that methylated both transposons and gene bodies.

In fungi, DNA methylation is concentrated in transposable elements (TEs), as observed in plants and vertebrates, and no methylation was observed in the middle of active genes. It however remains to be shown whether cytosine methylation takes place in dormant or active TEs. This nice methylome study was on my to-do list for Laccaria and Tuber genomes. Snif, snif !!!

Zemach, A., McDaniel, I. E., Silva, P. & Zilberman, D. (2010) Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation. Science 328, 916 – 919 .

Further readings:

Jeltsch A (2010) Phylogeny of Methylomes. Science 328, 837.

Katsnelson A (2010) Mapping methylation’s mysterious background. Nature | doi:10.1038/news.2010.185.

SciLifeLab Center for Sequencing Christmas Tree Genome:

May 14th, 2010

spruceNorway Spruce (Picea abies) is ecologically and economically the most important plant in Sweden.  This conifer is thus one of the biggest asset of the Sweden timber industries. Earlier this year the Wallenberg Foundation  announced it would provide about $10 million for the sequencing of the Norway spruce’s genome. Next week, a new genome center will open to host the  cutting-edge DNA sequencing machines which will decipher this giant tree genome. This center — one of Europe’s biggest — is part  of the Science for Life Laboratory (SciLifeLab), an unusual initiative spanning multiple Swedish research organizations and two sites, one in Stockholm and the other in nearby Uppsala.

The new lab should produce a rough draft of the genome of Spruce by 2013.

25 Mycorrhiza Genomes

May 13th, 2010

Exploring the Genome Diversity of Mycorrhizal Fungi to Unearth Symbiosis Evolution

TintinBy the end of May, we will submit a proposal to the JGI Community Sequencing Program 2011 for whole-genome shotgun sequencing and deep transcriptomics of 25 symbiotic mycorrhizal fungi aiming to develop a phylogeny-driven genomic encyclopedia of symbiotic fungi. This project will be developed under the umbrella of the JGI Fungal Genomics Program initiated in October 2009.

The analysis of the Laccaria bicolor and Tuber melanosporum genomes emphasized the importance of having sequence data for more than one representative of each phylum of ECM fungi. As today, only a few ECM species were targeted for genome sequencing because of an interest in a specific characteristic of the organism. The model species nominated by the ECM symbiosis community are Paxillus involutus (CSP 2008), Rhizopogon salebrosus (CSP 2009), and Pisolithus tinctorius and P. microcarpus (CSP 2010). They belong to the Boletales, a large phylum of symbiotic basidiomycetes. None of the sequence has been released yet.

In addition to the on-going sequencing of Pisolithus species, we now propose a two-year project to sequence the 23 following reference genomes for basidiomycetous and ascomycetous mycorrhizal fungi. These species have been selected based on their ecological and phylogenetic importance, ability to establish different types of mycorrhizal symbiosis, and the avalaibility of HMW DNA:

JGI Fungal Genome Programme (MycoCosm): The ascomycetous Cenococcum geophilum (Dothideomycetes) and basidiomycetous Hebeloma cylindrosporum (Agaricales, Cortinariaceae) ectomycorrhizal fungi have been selected within the JGI Fungal Genome Programme in October 2009. As of this writing, DNA has been extracted and shipped to JGI for sequencing.

Tier 1 [11 species]

Basidiomycotina: Amanita muscaria (Agaricales; Amanitaceae), Laccaria amethystina (Agaricales; Hydnangiaceae), Lactarius quietus (Russulales, oak-specific symbiont), Paxillus rubicundulus (Boletales, Paxilineae, alder-specific), Piloderma croceum (Atheliales), Suillus luteus (Boletales, Suillineae), Scleroderma citrinum (Boletales, Sclerodermataceae), Thelephora terrestris (Thelephorales), Sebacina vermifera (Sebacinales).

AscomycotinaMeliniomyces bicolor (Helotiales, forms both ericoid mycorrhizas and ectomycorrhizas), Rhizoscyphus ericeae (Helotiales, ericoid mycorrhizal fungus), Terfezia boudieri (Pezizales, Pezizaceae; forms both endo- and ectomycorrhizas).

Tier 2 [10 species]

Basidiomycotina: Boletus edulis (Boletales, Boletineae), Cantharellus cibarius (Cantharellales), Corticia cinnamomea (Hymenochaetales), Cortinarius glaucopus (Agaricales; Cortinariaceae), Gymnomyces xanthosporus (Russulales), Ramaria formosa (Gomphales), Tomentella sublilacina (Thelephorales), Tricholoma matsutake (Agaricales; Tricholomataceae), Tulasnella calospora (Cantharellales; Tulasnellaceae).

AscomycotinaMeliniomyces variabilis (Helotiales, root endophyte)

The Tier 1 taxa are proposed for sequencing in 2010. If sequencing capacity exists, Tier 2 taxa could be sequenced in 2011.

The proposed taxa include representatives of the major clades (orders or subclasses) of culturable Mycotina that contain mycorrhizal taxa. This phylogenetically based sample of the genomes that we propose would propel the field forward and allow us to answer fundamental questions about the evolution of this mutualism and the variation in function and interaction across the phylogenetic depth occupied by these organisms. The fact that mycorrhizal fungi appear to be independently derived from multiple saprobic lineages means that genomic data will provide independent assessments of what is required to become ectomycorrhizal. This initiative would be complementary to the project aiming to sequence the genome of the lignocellulose-degrading basidiomycetes submitted by Hibbett, Cullen, Eastwood and Martin to CSP2011.

Community Interest

The proposed genome sequences will be of great interest to diverse scientists with interests in 1) development and evolution of the mycorrhizal symbiosis; 2) carbon cycling and carbon sequestration in terrestrial ecosystems; 3) diverse aspects of fungal molecular biology; 4) molecular ecology of communities of mycorrhizal fungi; 5) plant health and domesticated bioenergy trees; 6) fungal phylogenetics; and 7) evolution of terrestrial ecosystems.

If you are interested by joining this exciting project and/or willing to provide a letter of support for this proposal, contact me.

Peeking through Caveman Bones

May 9th, 2010

63065In The Shelters of Stone (by JM Auel), Ayla meets the Zelandonii tribe of Jondalar, the Cro-Magnon hunk hosted in the shelter of stones (likely) along the Dordogne valley. But most regard her Neanderthal adoptive as subhuman “flatheads”. Neanderthal larynxes can’t quite manage language, and Ayla must convince the Cro-Magnon that Neanderthal sign language isn’t just arm-flapping. Both clans are skirmishing, and those who interbreed are deemed “abominations”. Although described by JM Auel, mating of Neanderthal (Homo neanderthalensis) with modern humans (Homo sapiens sapiens) has been hotly debated by Archaeologists for years; some claiming that the fossil record shows evidence of Neanderthal-human hybrids with mixed features, though not all palaeoanthropologists agree on this.

The Neanderthal Genome Consortium led by Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology is fueling the debate. In the 7 May 2010 special issue of Science, they report their current analysis of the draft genome of the Neanderthal. The sequence is an amazing accomplishment. It appears that Neanderthals mated with some modern humans after all and left their imprint in the human genome. Any modern human whose ancestral populations developed outside Africa has a little Neanderthal in them – between 1 and 4 per cent of their genome, Pääbo’s team estimates using population genetics statistics. In contrast to Auel’s description, the interbreeding did not occur in the Dordogne valley in southwestern France, but in the Middle East.

The sequenced genome (x1.3) is composed of over 3 billion nucleotides of three female Neanderthals  individuals from Vindija cave (Croatia) — dated to between 32,000 and 38,000 years ago. Green et al. used 454 Life Sciences GS FLX/Titanium and Illumina GAII platforms to generate 5.3 Gb of Neandertal DNA sequence from about 400 mg of bone powder. This likely represents 60 percent of the genome and it requires up to 600 lanes of Illumina GA. The Neanderthal bones were not well preserved, and more than 95 percent of the DNA extracted from them came from bacteria and other organisms that had colonized the bone. The DNA itself was degraded into small fragments and had been chemically modified in many places. The differences between Neanderthal and modern human genomes are so slight that the researchers suspect them to be functionally irrelevant. Only about 100 genes — surprisingly few — may have contributed to the evolution of modern humans since the split between Neanderthals and moderns. Further analysis is required to confirm this initial findings.

Technological sequencing and computing developments over the past decade have been the catalyst of dramatic innovation and progress. As reported earlier in this blog, massive Illumina sequencing has been used for sequencing small fungal genomes (Grosmania clavigera, Sordaria macrospora), the large genome of the giant panda (Ailuropoda melanoleura) and now the Neanderthal genome, and there are more to come … NextGen sequencing is driving the genomics field forward at a dizzying pace.

Additional readings:

A Draft Sequence of the Neandertal Genome By Richard E. Green et al. Science, 328 No. 5979, May 6, 2010.

Signs of Neanderthals Mating With Humans by Nicholas Wade (New York Times).

Neanderthal genome reveals interbreeding with humans by Ewen Callaway (New Scientist)

Neanderthal Genome Shows Most Humans Are Cavemen By Brandon Keim (Wired Science)

Neanderthal Genome Yields Insights Into Human Evolution and Evidence of Interbreeding With Modern Humans

Painting: ©

Another Big Tree Genome

May 7th, 2010

450px-Eucalyptus_grandis_(1)The preliminary 8X draft assembly of the Eucalyptus grandis genome, which is being sequenced by the US Department of Energy (DOE) Joint Genome Institute (JGI), is now available at the public Eucalyptus Genome Database (EucalyptusDB). Members of the Eucalyptus research community and the wider plant genomics community are invited to make use of this resource, which is already widely accessed.

Some notes on this release:

1. The genome browser in EucalyptusDB has been updated to Generic Genome Browser (GBrowse) version 2.0.

2. The browser for the preliminary 4.5X (checkpoint) assembly will remain accessible, but is currently also being updated to GBrowse 2.0.

3. The 8X assembly released on EucalyptusDB is the first draft assembly that incorporates all of the Sanger sequences produced for the E. grandis genome. The assembly is still being updated and the current release is therefore likely to be incomplete in some regions and will change in the next release. A more complete draft assembly and draft annotation will be released on Phytozome later in 2010.

4. The draft 8X assembly consists of 6043 genome scaffolds covering 693 Mbp. This total is somewhat inflated due to the fact that approximately 20% of the genome is currently assembling into two parallel haplotypes (both included in the 693 Mbp) due to very high heterozygosity in some regions of the E. grandis genome. This will be resolved in the next release of the genome assembly.

The initial analysis of a high quality draft E. grandis genome sequence will be published in 2011. The principal investigators and collaborators of the E. grandis Genome Project intend to publish genome-wide analyses of features such as genes, protein families, metabolic pathways, non-coding RNA and repetitive DNA in the main genome paper, associated papers and in subsequent publications. Interested persons are encouraged to contact the principle investigators (Zander Myburg, Dario Grattapaglia or Jerry Tuskan) to coordinate collaborative efforts aimed at producing such publications.

We also invite members of the Eucalyptus research community and all other interested persons to register as members on the EUCAGEN website.


Photo: Eucalyptus grandis (Maranoa Gardens, Melbourne) (© HelloMojo, Wikipedia).

Agaricus bisporus Genome

May 6th, 2010

The genome sequence of Agaricus bisporus var bisporus H97 (v. 2.0) is now publicly available via the Agaricus JGI portal

Cartoon: ©

Spring DOE JGI Newsletter

May 6th, 2010

jgi1The Spring 2010 edition of the DOE JGI newsletter, The Primer, is now available for download: Features include:

  • 5th DOE JGI User Meeting Keynotes
  • Paving the road to biofuels
  • Charting ocean communities

BTW videos of the User Meeting talks can be found here: You thus have a chance to see me on stage talking about Laccaria and Tuber genomes (

A Day Among Personal Genomes

May 4th, 2010

What will the world be like when your genome sequence costs less than a cell phone? A couple days ago Carl Zimmer, together with past and future Nobel-prize winners and biotech barons, went to the “Genome, Environments, and Traits” meeting at Cambridge, Mass. to find out. You can read his account in ‘A Day Among the Genomes‘.

Carl’s quote of the geneticist Daniel Macarthur (in  his ‘Genetic Future’ blog) about the limitations of (human) personal genomics likely applies to plants and fungi :

“…there are the variants that simply can’t be interpreted. This includes virtually everything seen outside protein-coding regions, and the majority of even those variants found inside coding regions. We simply don’t understand the biology of most genes well enough yet to be able to predict with confidence whether a novel variant will have a major impact on how that gene operates; and we have an even less complete picture of how genes work together to affect the risk of disease.”

Rooting or not Rooting?

May 4th, 2010

mutantA Postdoctoral Fellowship from the Kempe Foundation is available at UPSC (Sweden) and Tree-Microbe Interactions Department at INRA-Nancy (France) within the framework of the UPRA programme. This position is open competitively to applicants who wish to pursue research projects on tree root development, i.e. adventitious root formation.

Adventitious rooting (AR), i.e. the regeneration and development of roots on any organ but roots, is an essential step in the vegetative propagation of economically important horticultural and woody species. Easy-to-root and difficult-to-root genotypes are well known in the tree genus Populus and we propose to investigate the role of key regulatory genes identified in Arabidopsis by comparing their expression in two different poplar species: P. trichocarpa (easy-to-root) and P. tremula (difficult-to-root), during the AR initiation in stem cuttings. We will also aim to identify new genes regulating AR formation by comparing the transcriptome of both genotypes, after laser capture microdissection of the root-forming regions. Competences in molecular biology are required and knowledge in tree physiology and anatomy would be an advantage.

If you know of any potential applicants in the fields of plant development and tree molecular biology, please pass the details on to them.

Enquiries can be addressed to Catherine Bellini <> or Francis Martin <>.

Photo: Proliferation of adventitous roots in a poplar mutant (© Adeline Rigal – INRA)

Future of Computational Genomics

May 4th, 2010

240px-us-nih-nhgri-logosvgFollowing the Cloud Computing workshop and the NHGRI Informatics and Analysis Planning Meeting, Sean Eddy is sharing some of his personal views on the future of computational genomics research on his blog, Cryptogenomicon. Anyone with an interest in management of large-scale genomics data, standardized representations of sequence data, computing infrastructure, cloud computing and better software development cannot miss this very interesting post.

You are What you Eat

May 2nd, 2010

Brought to my attention by today Jonathan Eisen's tweet, I like this charming gut metagenomics-inspired poem from the Cuttlefish Poet at The Digital Cuttlefish's "You are What you Eat." 
Here is the first verse:

Bacteria are living, by the trillions, in your gut;
There's an ecosystem hidden in your skin 
It's a case of symbiosis, if an icky one, somewhat, 
Where both human and bacteria can win.

Banner image by Michael McRae. Banner layout Matt Hagglund

Yeast Aging

May 1st, 2010

wheals2Matecic and his colleagues have performed a microarray-based genetic screen to identify short- and long-lived mutants in budding yeast (Saccharomyces cerevisiae). These mutants have been identified from a population that contained each of the viable haploid gene deletion mutants from the yeast gene knockout collection that were pooled together and DNA barcoded. The genetic screen led to the identification of several pathways that regulate the yeast lifespan, including autophagy and de novo purine biosynthesis pathway. The recycling of cellular organelles via autophagy appears to play a key role in longevity. Additional genes appear to contribute to the caloric-restriction effect induced by restriction of either amino acids or sugar.

Matecic M, Smith DL Jr, Pan X, Maqani N, Bekiranov S, et al. (2010) A Microarray-Based Genetic Screen for Yeast Chronological Aging Factors. PLoS Genet 6(4): e1000921. doi:10.1371/journal.pgen.1000921