Archive for November, 2011

Zwerg & Fliegenpilz

November 19th, 2011

Zwerg und Fliegenpilz

The Fly Agaric, Amanita muscaria, is amongst the most easily recognised “toadstool”. This mushroom is frequently depicted in fairy stories and on greeting cards. It is often associated with gnomes or ‘lutins’. – Zenodot Verlagsgesellschaft mbH


Effectors in Plant-Microbe Interactions

November 17th, 2011

Just got a copy of our book on Effectors in Plant-Microbe Interactions by Sophien Kamoun and I. It looks georgious … although the photo on the cover page is reminiscent of ‘The Eye of Sauron‘ as portrayed in Peter Jackson’s Lord of the Ringsmovie  trilogy.

Search inside this book at


Unraveling the secrets of the mother of plant root endosymbioses

November 17th, 2011

Glomus intraradices, alias G. irregulare, is a widespread arbuscular mycorrhizal fungus (AMF) (Glomeromycota) found in different ecosystems throughout the world, including temperate and tropical locations. As a symbiont G. intraradices is highly effective in mobilizing, taking up and transferring mineral nutrients from soils to plants, and it readily colonizes many plant species including agriculturally important species such as wheat, alfalfa, rice, and key model plants such as Medicago truncatula, Lotus japonicum, and Populus trichocarpa. For these reasons G. intraradices is among the most studied AMF and is the prime ingredient in several commercially available inocula. G. intraradices can also be grown in vitro in dual culture with transformed carrot roots. G. intraradices is also the only species whose spores are available commercially in pure form in large quantities.

From an evolutionary standpoint, the AMF are unique obligate symbionts with coenocytic hyphae (lacking cellular structure) that transport organelles and nutrients over long distances. The concept of an individual does not apply, raising substantial questions about natural selection and population genetics of these highly unusual organisms.

To provide long-awaited insights into the molecular basis of symbiosis-associated traits, the Glomus Genome Consortium investigated the transcriptome from G. intraradices (strain DAOM 197198). From >437,000 ESTs, we generated a set of 25,906 nonredundant virtual transcripts (NRVTs) transcribed in germinated spores, extraradical mycelium and symbiotic roots using Sanger and 454 sequencing. These NRVTs were then used to construct an oligoarray for investigating gene expression.

Take-home points:

  • We identified transcripts coding for the meiotic recombination machinery, as well as meiosis-specific proteins, suggesting that the lack of a known sexual cycle in G. intraradices is not a result of major deletions of genes essential for sexual reproduction and meiosis.
  • Induced expression of genes encoding membrane transporters, such as ammonium and phosphate transporters, and small secreted proteins in intraradical mycelium, together with the lack of expression of hydrolytic enzymes acting on plant cell wall polysaccharides (e.g. cellulases, pectin lyases), are all features of G. intraradices that are shared with ectomycorrhizal symbionts and obligate biotrophic pathogens.

Our results illuminate the genetic basis of symbiosis-related traits of the most ancient lineage of plant biotrophs, hopefully advancing future research on these agriculturally and ecologically important symbionts.

Next challenge: Assembling the highly polymorphic genome sequence of G. intraradices.

Read more …

Parniske M (2008) Arbuscular mycorrhiza: the mother of plant root endosymbioses. Nature Reviews Microbiology 6, 763-775.

Bonfante P, Genre A (2010) Mechanisms underlying beneficial plant-fungus interactions in mycorrhizal symbiosis. Nature Communications 1: 4

Photo: The most beautiful photo of G. intraradices arbuscules, branching profusingly in its host plant cell (Thanks to Yves Piché, Laval University).

Shigeru Ban’s musHRoom

November 13th, 2011


Yesterday, I visited the recent modern arts museum ‘Centre Pompidou-Metz‘ in Metz. The building is remarkable for its wooden roof structure, one of the largest and most complex built to date, which was inspired by a Chinese hat found in Paris by the japanese architect Shigeru Ban … a Chinese hat or a gigantic mushroom?

From Wikipedia: ‘The Centre Pompidou Metz is a museum of modern and contemporary arts designed by architects Shigeru Ban and Jean de Gastines and located in Metz, capital of Lorraine, France. It is built in the Amphitheatre District, near the Metz railway station and the German Imperial District. The Centre Pompidou-Metz is a branch of Pompidou arts centre of Paris, and features temporary exhibitions from the large collection of the French National Museum of Modern Art, the largest European collection of 20th and 21st century arts. The museum is the largest temporary exhibition space outside Paris in France . The building was inaugurated on May  2010.’

Photo: Centre Pompidou-Metz (© F Martin)


JGI Fungal Genome Program update

November 12th, 2011

Some news from the JGI Fungal Genome Program By Igor Grigoriev:

CSP2012 results were recently announced and eight new fungal projects were selected for the next year in tight competition with others. The winners included large scale genome sequencing projects (1000+ Fungal Genomes, thermophiles, Colletotrichum), functional genomics of model fungal organisms (Schizophyllum commune, Coprinopsis cinerea) and exploration of fungal systems (lichens, cow rumen guts, forest soils), all in good alignment with our strategic goals. We published a summary of CSP11 portfolio and Genomic Encyclopedia of Fungi in New Phytologist and Mycology journals.

In order to discuss ongoing projects and better coordinate in future we would like to organize a fungal jamboree (tentatively on Mar 19, 2012) just before the JGI User meeting in Walnut Creek (Mar 20-22, 2012). The meeting will focus on bringing larger research community into discussions of the Genomic Encyclopedia of Fungi, 1000 fungal genomes, and fungal systems/metagenomics.

The latest version of MycoCosm now offers 100+ fungal genomes to public. Since this is a relatively new system, we would like to get feedback from you and your colleagues using a 5 minutes online survey. This will help us to better assess your experience and needs and share this feedback with DOE, which will reveiw JGI programs next month. Please share this survey with your colleagues and ask them to complete it by the next week.

Photo: The polypore Fomitopsis pinicola (© F Martin).

1000 Fungal Genomes Project

November 11th, 2011


Our proposal to sequence 1000+ fungal genomes has been funded by the Joint Genome Institute (JGI) of the Department of Energy. Our consortium in collaboration with JGI has embarked on a five-year project to sequence 1000 fungal genomes from across the Fungal Tree of Life. The guiding principle for sampling in F1000 is at the end of the project to have 2 representatives from all fungal families or family-level clades. This will require a lot of coordination across several JGI CSP projects, e.g. our Mycorrhizal Genome Initiative, the Forest Soil Metatranscriptome Project and the Saprotrophic Agaricomycotina project, and interactions with the community and systematics experts of given groups.

The team comprises Joseph Spatafora (Oregon State University), Jason Stajich (University of California at Riverside), Kevin McCluskey (Fungal Genetics Stock Center), Pedro Crous (Centraal Bureau voor Schimmelcultures, Netherlands), Gillian Turgeon (Cornell University), Daniel Lindner (USDA Forest Service), Kerry O’Donnell and Todd Ward (USDA ARS), Antonis Rokas (Vanderbilt University), Louise Glass (University of California at Berkeley), Betsy Arnold (University of Arizona), Igor Grigoriev (JGI DOE) and myself.

The ‘1000 Fungal Genomes‘ site, set up by Jason Stajich’s group, represents a gathering of the information about the project and will link to additional resources tracking the progress of the project.

DOE JGI 2012 Community Sequencing Program Portfolio

November 4th, 2011

Trillions Served: Massive, Complex Projects Dominate DOE JGI 2012 Community Sequencing Program Portfolio.

‘The 2012 Community Sequencing Program (CSP) call invited researchers to submit proposals for projects that advance capabilities in fields such as plant-microbe interactions, microbes involved in carbon capture and greenhouse gas emission, and metagenomics—the characterization of complex collections of microbes from particular environmental niches. The total allocation for the coming year’s CSP portfolio will exceed 30 trillion bases (terabases or Tb), a 100-fold increase compared with just two years ago, when just a third of a terabase was allocated to more than 70 projects. This amounts to the equivalent of at least 10,000 human genomes in data …’ Read more


Photo:  The boreal forest, one of the ecosystem investigated by the CSP 2012 program. Denali Natl Park, Alaska  (© F Martin)