Posts Tagged ‘Workshop’

Exploring the Mycorrhizal Genomes

September 9th, 2012


I hope you are wrapping up a good summer. I’m touching base to update you on our Mycorrhizal Genomics Initiative (MGI).

The list of taxa of mycorrhizal fungi for the first series of analyses aiming to identify symbiotic traits has now been “frozen”. Thanks to Igor Grigoriev’s JGI team, this list includes an outstanding series of annotated genomes and transcriptomes from ectomycorrhizal, ericoid and orchid symbionts:

  • Amanita muscaria Koide
  • Hebeloma cylindrosporum h7  (v2.0),
  • Laccaria bicolor (v2.0),
  • Oidiodendron maius Zn,
  • Paxillus involutus,
  • Paxillus rubicundulus,
  • Piloderma croceum F 1598,
  • Pisolithus microcarpus 441,
  • Pisolithus tinctorius 270,
  • Scleroderma citrinum FougA,
  • Sebacina vermifera MAFF 305830,
  • Suillus luteus UH-Slu-Lm8-n1,
  • Tulasnella calospora AL13/4D,

In addition, the following available transcriptomes will also be mined for symbiotic-related features:

  • Cenococcum geophilum
  • Cortinarius glaucopus,
  • Laccaria amethystina 08-1,
  • Lactarius quietus,
  • Meliniomyces bicolor,
  • Meliniomyces variabilis, and
  • Tricholoma matsutake 945.

Finally, we will add the unpublished genomes of five saprotrophic agaricomycotina (including leaf-litter species) that we will use for identifying potential common genomic features in litter-borne and mycorrhizal fungi:

  • Jaapia argillacea MUCL-33604,
  • Hydnomerulium pinastri MD-312,
  • Plicaturopsis crispa FD-325 SS-3,
  • Hypholoma sublateritium FD-334 SS-4, and
  • Gymnopus luxurians FD-317 M1

JGI has (or will soon) publicly released the web portals with the annotation for the above-mentioned fungal species. Visit the JGI Mycocosm database. In addition, we have released web sites for the corresponding transcriptome annotation at the Mycorhiza Genomics Initiative portal [restricted].

To make good use of this tremendous genomic resource, we are organizing the 2nd MGI Workshop at the INRA-Nancy center in Champenoux (France), on November 13-14, 2012. The aim of the workshop is to bring together the consortium teams for discussing our findings. The format of the workshop will be roughly equally split between informal presentations summarizing the current findings and brainstorming about how to take advantage of the genome sequences to inform our understanding of symbiosis and fungal biology.

On the following days, we will organize a New Phytologist Workshop entitled ‘ Bridging Mycorrhizal Genomics, Metagenomics & Forest Ecology‘. The workshop will also take place at INRA-Nancy over two days (Thursday 15 & Friday 16 November). The aim is to bring together a small group of MGI PI’s, fungal biologists and ecologists (20-25 attendees) to explore the future use of mycorrhizal genomes in order to both maximize the efficacy with which the community utilizes these technological breakthroughs in biology, ecology, phylogenetics, and forestry.

Photo: Larch Bolete (Suillus grevellei) (Boletales), a close relative of the sequenced slippery Jack (Suillus luteus) (© F Martin).

MOMY in Woods Hole

February 17th, 2012

Dear Mycology Investigator,

The Molecular Mycology summer course at the Marine Biological Laboratories in Woods Hole provides an opportunity for researchers to learn new concepts and techniques relating to the study fungal pathogenesis and the discovery of novel antifungal strategies. Many course graduates are now leading medical mycology research efforts around the world. We depend upon the members of the medical mycology community to encourage outstanding applicants. We hope that you can identify at least one prospective course participant who would benefit from the experience and encourage them to apply.

This dynamic course provides state-of-the-art training in molecular methods and assays for studying fungal pathogens and fungi-host interactions. In addition, it provides opportunities to interact with colleagues from academia and industry with different areas of expertise relevant to the study of fungal diseases. The upcoming Molecular Mycology course promises to be exceptional. See the course website to see the list of interactive visiting and resident faculty who will make up the course curriculum.

Laboratory exercises, demos, lectures, and informal panel discussions make up the curriculum. Laboratory exercises focus on Candida, Aspergillus, and Cryptococcus, and include genetic manipulation, discussion of new genetic tools, genetic screening strategies, cell culture and animal models, host response assays, antifungal susceptibility assays and live cell imaging of fungi. Additional topics include current research problems and strategies in medical mycology and topics relating to careers in fungal pathogenesis. Among the topics to be addressed in lectures include new animal models, immunology and fungal diseases, and fungi within microbial communities.

The course is an intensive, two-week research training program, and its content is designed for advanced graduate students, post-docs, fellows, early independent investigators or PIs new to the field. The course runs from August 1-17, 2012.

**Students accepted to the course often receive GENEROUS scholarships towards tuition and travel. **

The course website and on-line application can be found at:

The application deadline is April 11, 2012.


Deb Hogan and Andy Alspaugh

MBL Molecular Mycology Course co-Directors

Mycorrhizal Genomics Initiative: an Update

January 18th, 2012

I am writing to touch base about our JGI Mycorrhizal Genomics Initiative. As of today, the genome annotations publicly released are those of:

The genome of Piloderma croceum and Tulasnella calospora are in the JGI annotation pipeline and should (hopefully) be available in the coming weeks. Those of Cenococcum geophilum, Sebacina vermifera, and Pisolithus tinctorius are in the final phase of sequencing, but Cenococcum and Pisolithus are difficult (large and polymorphic) genomes and JGI cannot give an estimated date of release.

The transcriptome of free-living mycelium of C. geophilum, H. cylindrosporum, O. maius, P. involutus, P. croceum, P. microcarpus, P. tinctorius, Scleroderma citrinum, Sebacina vermifera and T. calospora are sequenced (RNA-Seq) and a series of dedicated databases are under construction.

Finally, Igor Grigoriev, Joey Spatafora and I would like to invite you to Walnut Creek in mid-March 2012 to participate in several important JGI meetings:

  • Fungal Jamboree (March 19, 2011 8am-8pm) to discuss progress and coordination of large scale initiatives in fungal genomics: (1) Genomic Encyclopedia of Fungi, (2) 1000 fungal genomes, and (3) Fungal model systems and metagenomes (including our Mycorrhizal Genome Initiative).
  • JGI User Meeting (March 20-22, 2012: and workshops including MycoCosm Tutorial (March 20, afternoon)

You could access our recently opened MycorWeb portal dedicated to this project, Mycorrhizal Genomics Initiative, for links and updates.

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).

Genomic Impact of Eukaryotic Transposable Elements

June 24th, 2011

For details, see the conference website:

Basidiomycete Genome Meeting

December 19th, 2010

FomitopsisIgor Grigoriev, David Hibbett and I are organizing a one-day workshop on March 21, 2011 at the JGI in Walnut Creek to cover comparative genome analysis of basidiomycetes. This jamboree will take place between the Fungal Genetics Conference in Asilomar (Mar 15-20) and the JGI User Meeting (Mar 22-24). The workshop will  include sessions on wood decayers, symbionts and soil fungal metagenomics.

The various sessions will include an update on current genome sequencing projects running at the JGI, including the Wood Decayers and Mycorrhizal Symbionts projects, and cross-all-basidio comparisons.

People willing to make a contribution can contact Igor, David or myself.

Photo: Early stages of Fomitopsis fruiting body development. Spruce forest near Pierre Percée in the Vosges range. © F Martin

26th Fungal Genetics Conference

September 22nd, 2010


The preliminary program for the  Twenty Sixth Fungal Genetics Conference (FGC) is now online. The conference will be held on March 15- 20, 2011, at the Asilomar Conference Center in Pacific Grove, California. It will include four plenary sessions, twenty-four concurrent sessions and extensive poster viewing time. I am glad to chair the ‘Symbiosis‘ plenary session.

Several jamborees and workshops dealing with the on-going fungal genome sequencing projects  will take place during the conference. Igor Grigoriev and I would like to organize a workshop aiming to bridge fungal genomics and soil metagenomics between the FGC and the 6th JGI Users meeting (March 22 – 24, 2011, at Walnut Creek, California). I would like to hear your ideas about the best way to run this workshop.

The FGC Website is here:

JGI Basidiomycete Genome Jamboree

February 24th, 2010

CoprinA Basidiomycete Genomes Jamboree will take place on March 24 – 26, 2010 at the Marriott in Walnut Creek, California, as a satellite meeting of the Annual JGI User Meeting. This jamboree will include brief updates on individual on-going basidiomycete genome projects (Agaricus, Ceriporiopsis, Coprinopsis, Heterobasidion, Melampsora, Pleurotus, Rhodosporidium, Serpula, Tremella) and discussion of comparative genomics of basidiomycete gene families (CAZy, transposable elements, secondary metabolism, pheromones, secretome, transporters).

Progress of the on-going Genome Encyclopedia of Fungi programme will also be discussed.

We will be there to discuss the progress of our own projects.

Photo: Coprinus comatus (the shaggy mane) (© F Martin).