Posts Tagged ‘Fungal Biology’

Genomics of Fungal Drug Producers

March 2nd, 2013

In a breakthrough paper, Schardl’s group and collaborators have published 15 genomes of diverse species of Clavicipitaceae plant endophytes and parasites in the last issue of PloS Genetics. The Clavicipitaceae (PezizomycotinaSordariomycetes, Hypocreales) includes “ergot” fungi that parasitize ears of cereals and produce  the toxic ergoline derivatives; ergot fungi have historically caused epidemics of gangrenous poisonings, the ergotism, also known as the Saint Anthony’s Fire. The ascomycetous family also includes plant endophytic symbionts that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. They synthesize alkaloids with chemical similarities to biogenic amines that deter insects, livestock, and wildlife from feeding on the fungus or plant. Thanks to this chemical warfare, Epichloae protect their hosts from cattle grazing. The lysergic acid diethylamide (LSD), a semisynthetic ergot alkaloid originally developed as an antidepressant, is the most potent known hallucinogen.

In this study, they sequenced the genomes of 10 epichloae, three ergot fungi (Claviceps species), a morning-glory symbiont (Periglandula ipomoeae), and the bamboo witch’s broom pathogen (Aciculosporium take), profiled the alkaloids in these species and compared the gene clusters for four classes of alkaloids. The genomes were primarily sequenced by shotgun 454 pyrosequencing, but paired-end and mate-pair reads were used to scaffold several assemblies. Size of the assembled genome among the sequenced strains varied 2-fold from 29.2 to 58.7 Mb, with wide ranges even within the genera Claviceps (31–52.3 Mb) and Epichloë (29.2–49.3 Mb). This genome size variation is mainly resulting from the abundance of repeated elements, which ranged from 4.7 to 56.9%. Annotated genome sequences have been posted at

In the epichloae, the clusters of genes coding for enzymes of alkaloid biosynthesis contain very large blocks of repetitive elements which promote gene losses, mutations, and even the evolution of new genes. Two striking features emerged from the detailed analysis of alkaloid biosynthesis gene clusters. Firstly, in most alkaloid loci in most species, the periphery of each cluster was enriched in genes that by virtue of their presence, absence, or sequence variations determined the diversity of alkaloids within the respective chemical class. Second, alkaloid gene loci of the epichloae had extraordinarily large and pervasive blocks of AT- rich repeats derived from retroelements, DNA transposons, and MITEs. This finding suggests that these plant-interacting fungi are under selection for alkaloid diversification.

In their conclusions, the authors suggest that this selection of chemotypes is related to the variable life histories of the epichloae, their protective roles as symbionts, and their associations with the ecologically diverse cool-season grasses.

Schardl CL, Young CA, Hesse U, Amyotte SG, Andreeva K, et al. (2013) Plant-Symbiotic Fungi as Chemical Engineers: Multi-Genome Analysis of the Clavicipitaceae Reveals Dynamics of Alkaloid Loci. PLoS Genet 9(2): e1003323. doi:10.1371/journal.pgen.1003323

Image: Claviceps purpurea -Franz Eugen Köhler, Köhler’s Medizinal-Pflanzen (Wikimedia Commons).

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).


August 9th, 2012

This Summer, I’m devoting my free time to write a book on Fungi/Mushrooms (Champignons in french) for the Editions Quae: “200 Clès pour comprendre les champignons” (Mushrooms Facts: 200 Questions & Answers). Mushrooms possess considerable mystique and they have been the subject of numerous papers, accounts and books, and I’m browsing the web to search for documents on these fascinating organisms … and they are great gems, including superbe paintings as follows:

Image from Meyers Blitz-Lexikon ‘Die Schnellauskunft für jedermann in Wort und Bild‘ © Wikimedia Commons

Fungal Fruiting Bodies and Fanatics

August 8th, 2012

In her review of  two recent books, Mushroom (by Nicholas Money) and Mycophilia (by Eugenia Bone) devoted to the standing of mushrooms in nature and in human culture, Linnaea Ostroff wrote a short, but vibrant, description of fungal fruiting bodies and sex in these exciting organisms:

[“Mushrooms are the sex organs of fungi. They are ballistics experts that emerge when the fungus is ready to reproduce, launch spores by the billion, and vanish. Or rather, they puff up and deflate. The sudden appearance of mushroom on a lawn or under a log, like many illusions, is achieved with extensive advance setup and hydraulics. After a spore germinates, it sends filaments out underground in all directions in search of food and other fungi. When two fungal colonies—or three or more, as fungi are substantially less constrained than animals—of the same species meet, their cells merge and their DNA combines in the mushroom version of mating. New spores are produced, and the cells of the future mushroom are organized around them. This process occurs at the tips of the filaments, accounting for mushrooms’ quirk of appearing in rings. When the conditions are right, water rushes in and pressurizes the assembly, swelling the cells and inflating the mushroom. In many species, that takes only a few hours, the spores are soon released, and the mushroom shrivels by sundown. Others survive a week or more, and some tougher forms may last for months.” ]. Read more

‘Mushroom’ by Nicholas P. Money, Oxford University Press, New York, 2011. 221 pp.

Mycophilia. Revelations from the Weird World of Mushrooms by Eugenia Bone, Rodale, New York, 2011. 368 pp..




Genome sequence of the insect pathogenic fungus Cordyceps militaris

March 4th, 2012

Species in the ascomycete fungal genus Cordyceps have been proposed to be the teleomorphs of Metarhizium species. The latter have been widely used as insect biocontrol agents. Cordyceps species are highly prized for use in traditional Chinese medicines, but the genes responsible for biosynthesis of bioactive components, insect pathogenicity and the control of sexuality and fruiting have not been determined.

Chengshu Wang’s group from the Shanghai Institutes for Biological Sciences report the genome sequence of the type species Cordyceps militaries in the last issue of Genome Biology. Phylogenomic analysis suggests that different species in the Cordyceps/Metarhizium genera have evolved into insect pathogens independently of each other, and that their similar large secretomes and gene family expansions are due to convergent evolution. However, relative to other fungi, including Metarhizium spp., many protein families are reduced in C. militaris, which suggests a more restricted ecology. Consistent with its long track record of safe usage as a medicine, the Cordyceps genome does not contain genes for known human mycotoxins. This study shows that C. militaris is sexually heterothallic but, very unusually, fruiting can occur without an opposite mating-type partner. Transcriptional profiling indicates that fruiting involves induction of the Zn2Cys6-type transcription factors and MAPK pathway; unlike other fungi, however, the PKA pathway is not activated.

The data offer a better understanding of Cordyceps biology and will facilitate the exploitation of medicinal compounds produced by the fungus.

Zheng et al. (2011) Genome Biology 12: R116

Photo: Chinese Tussah silkmoth pupae colonized by C. militaris (© Zheng et al.)

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

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).

Metatranscriptomics of Forest Soil Ecosystems

October 29th, 2011


Forest soils (including litter, humus and coarse woody debris) host diverse microbial communities that impact tree health and productivity, and which play pivotal roles in terrestrial carbon sequestration, and biogeochemical cycles. Among these microbial communities, fungi are undoubtly major players. Traditionally, they have been divided into discrete ecological guilds, such as leaf litter-decomposers, humus saprobes, white- and brown-rot wood decayers, parasites and mycorrhizal symbionts. However, the actual functional properties of individual species, and the synergistic effects among them, are often obscure. Moreover, the basic biodiversity of the vast majority of soil systems (e.g., boreal forests and subartic taiga) remains unexplored using high-throughput DNA barcoding approaches.

We hypothesize that firm distinctions between fungi commonly labeled mycorrhizal, wood decomposer, humus and litter saprobes are, in some instances, unwarranted, and that crucial ecosystem processes, such as carbon sequestration, wood and litter decay and trophic mutualism, can only be understood in the context of interactions among multiple species representing a functional continuum. The number of available fungal genomes has expanded dramatically in recent months, and this provides unprecedented opportunities to study the functional (and taxonomic) diversity of soil communities.

Within the framework of the DOE Joint Genome Institute Community Sequencing Program, we have therefore embarked in a challenging large-scale metatranscriptomics project to explore the interaction of forest trees with communities of soil fungi, including ectomycorrhizal symbionts that dramatically affect tree growth, and saprotrophic soil fungi impacting carbon sequestration in forests. We are going to sequence the metatranscriptome of soil fungi (i.e., wood decayers, litter and humus saprotrophs, and ectomycorrhizal symbionts) in woody debris, litter/humus, rhizosphere and ectomycorrhizal roots of ecosystems representative of major Earth biomes, the boreal, temperate and mediterranean forests.

Metatranscriptome samples. A range of forest ecosystems has been selected on the basis of their ecological importance and the availability of metadata linked to these forest sites. In contrast to agricultural soils, forest soils, in particular those of boreal forests with low pH values, are characterised by strong vertical stratification due to the resulting absence of fauna causing mixing. This provides a spatial structure for evaluation of hypotheses concerning functional attributes of taxa occupying spatially distinct horizons.

Sampling will be conducted on selected stands in long-term observatories (LTOs) or national survey sites:

  • Boreal forests: Bonanza Creek (Alaska) and Siljansfors (Sweden).
  • Temperate forests: DOE long term studies at Duke Forest, the post-fire stands at the Bitterroot National Forest and Michigan maple N-deposition sites (USA), a forest-woodland-grassland transect in Rollainville (France), and the Breuil-Chenue plantation (France).
  • Mediterranean forests at Puéchabon near Montpellier (France) and at Aspurz south-western Pyrenees (Spain).

For these soil samples, we will run: (1) Tag-encoded FLX-titanium amplicon pyrosequencing (TEFAP) of the fungal rDNA ITS to survey the existing communities and (2) RNA-Seq of soil samples. For this cDNA profiling, we will sequence ~110Gbp per site for a total of 1 terabase using Illumina HiSeq PE chemistry. Reads produced by RNA-Seq will be used to reconstruct de novo the different fungal metatranscriptomes (best case scenario). In addition, we will use Illumina fragment recruitment, a process of aligning sequencing reads to reference genomes. Metatranscriptomic reads will thus be aligned to the >100 genomes of soil fungi available in the JGI MycoCosm. To improve this crucial step, we also propose the gDNA sequencing and RNA-Seq of the 25 most abundant fungal species harvested on the studied sites to serve as the foundation for a reference database for metagenomics of fungi and for a comprehensive survey of the potential soil fungal metabolome. We will annotate the fungal genomes/transcriptomes and soil fungal metagenomes with all these characteristics and will compare the different metagenomes in terms of these characteristics.

These experimental datasets will provide a mechanistic insight into the fungal communities’ structural organization and functioning in forests. In addition, the present metagenomic data will give a comprehensive picture of the organization of the tree-associated microbiome in terms of metabolic pathways, subsystems, molecular functions and biological processes.

Sequencing of new fungal species will be performed in concert with existing large-scale genome studies (e.g., the 1000 Fungal Genomes project), so as to minimize unnecessary redundancies. As such we recognize that this project represents a large effort and great challenge in defining the microbiome of important forest ecosystems and a group of micro-organisms, the soil fungi.


Image (top): Denali Ntl Park, Alaska (© F Martin)

JGI Fall 2011 Primer

October 24th, 2011

The Fall edition of the U.S Department of Energy (DOE) Joint Genome Institute (JGI) newsletter The Primer is now available for download:

…featuring articles and images:

  • Tagging enzymes that can take the heat
  • Carbon fixation in the dark ocean
  • Linking fungi to boreal forests
  • Notable publications & more…


Reviews on Effectors

September 24th, 2011

Two new reviews on oomycete and fungal effectors:

both in Cellular Microbiology.

Image: Fig. 1C from Kale & Tyler: Assays for detecting pathogen-independent entry of effectors.

A Sneak Preview: ‘Effectors in Plant-Microbe Interactions’ book

September 17th, 2011

The book ‘Effectors in Plant-Microbe Interactions’

Edited by Sophien Kamoun and I, will be released by Wiley-Blackwell on January 2012:

A sneak preview …

Effectors are defined as molecules produced by bio-aggressors/pathogens/symbionts to manipulate their host plants, thereby facilitating infection (virulence or symbiotic factors, toxins, inhibitors) and/or triggering defense responses (avirulence factors, elicitors). This dual (and conflicting) activity of effectors has been broadly reported in many plant–microbial interactions. This research topic is actively investigated using a combination of approaches (genetics, molecular biology, biochemistry, physiology and developmental biology) and benefits from the recent advances in plant and microbial functional genomics and genome-wide evolutionary analyses. Tremendous progress has been made in recent years but many questions remain unanswered. The book aims to act as a catalyst for future research by bringing together a collection of contributions on plant–microbe interactions across a range of organisms (viruses, bacteria, fungi and nematodes) to identify and focus on these important questions. A book on this topic will be timely. It combines chapters by researchers involved in a diversity of plant-microbe systems that use biochemical, physiological, and developmental approaches as well as comparative genomics. Such a broad-ranging approach is providing a unique insight and a better understanding of the functions of this new class of proteins. Authors have been encouraged to discuss far reaching extensions of their current or past work and to propose cross-cutting research questions whenever possible.

Image: A great, arty photo from Sebastian Schornack (TSL) showing red fluorescent Phytophthora infestans colonizing its host. The central necrotrophic zone (in black) is surrounded by the biotrophic area (in fluo green).  The biotropic zone was caused by the action of effectors that suppressed the host responses.


Fungal Bioremediation

February 18th, 2011

large_cover201103Magic mushrooms‘ by Philip Patenall. I like this painting of fruiting bodies from the fly agaric (Amanita muscaria). It has been inspired by the review  ‘Untapped potential: exploiting fungi in bioremediation of hazardous chemicals‘ by Hauke Harms, Dietmar Schlosser & Lukas Wick in Nature Reviews Microbiology 9, 177-192 (March 2011).

[Fungi possess the biochemical and ecological capacity to degrade environmental organic chemicals and to decrease the risk associated with metals, metalloids and radionuclides, either by chemical modification or by influencing chemical bioavailability. Furthermore, the ability of these fungi to form extended mycelial networks, the low specificity of their catabolic enzymes and their independence from using pollutants as a growth substrate make these fungi well suited for bioremediation processes. However, despite dominating the living biomass in soil and being abundant in aqueous systems, fungi have not been exploited for the bioremediation of such environments.] To read more see Nature Reviews Microbiology.

Painting: © Philip Patenall.

Blurred Boundaries

December 4th, 2010

PoplarLaccariaECMOur review paper on the genomes of ectomycorrhizal fungi is available online at the Trends in Genetics site.

Plett JM & Martin F. 2010. Blurred boundaries: lifestyle lessons from ectomycorrhizal fungal genomes. Trends in Genetics. doi:10.1016/j.tig.2010.10.005

Abstract. “Soils contain a multitude of fungi with vastly divergent lifestyles ranging from saprotrophic to mutualistic and pathogenic. The recent release of many fungal genomes has led to comparative studies that consider the extent to which these lifestyles are encoded in the genome. The genomes of the symbiotic fungi Laccaria bicolor and Tuber melanosporum are proving especially useful in characterizing the genetic foundation of mutualistic symbiosis. New insights gleaned from these genomes, as compared to their saprotrophic and pathogenic cousins, have helped to redefine and shape our understanding of the nature of the symbiotic lifestyle. Here we detail the current state of research into this complex relationship and discuss avenues for future exploration.”

Photo: section of Populus/Laccaria ectomycorrhizal root – JM Plett © INRA.

What is the most abundant deposited fungal genus in GenBank?

October 30th, 2010


Jason Stajich wrote a few Perl and BioPerl scripts to analyze the distribution of fungal species with ribosomal DNA internal transcribed spacer ( ITS) sequences in NCBI GenBank. The whole spreadsheet of the data is public and available here and Jason’s comments are available on his blog post. According to this analysis, soil  Fusarium is the most abundant deposited genus. As stressed by Jason, the analyzed sequences are mainly from Sanger-based studies. The recent released of 454 seq’ing based fungal surveys will certainly change this current picture.

Histoire de Fourmis … suite: Ant Genomes

August 29th, 2010


Symbioses between plants and fungi, fungi and ants, and ants and plants all play important roles in ecosystems. For those interested by ant ecology and biology, and their interaction with plants, I would recommend reading the paper from Defossez et al. on Ant‐plants and fungi: a new threeway symbiosis‘ published on March 11, 2009 in the New Phytologist. For further ant reading go to the comparative genomics paper published by Bonasio et al. in the 27 August 2010 issue of Science. A collaborative research consortium involving scientists from the US and China report that they have sequenced the genomes of two ant species: Harpegnathos saltator, known as Jerdon’s jumping ant, and the Florida carpenter ant, Camponotus floridanus.

By comparing the genome structure and gene repertoire of the two ant species, and analyzing their transcriptome profiling in different castes, the team obtained clues about gene regulation and epigenetic processes underlying diverse physical and behavioral features in these ant species. They identified up-regulation of telomerase and sirtuin deacetylases in longer-lived H. saltator reproductives, caste-specific expression of microRNAs and SMYD histone methyltransferases, and differential regulation of genes implicated in neuronal function and chemical communication. Their findings provide clues on the molecular differences between castes in ants paving the way for further investigations on everything from brain function and behavior to aging.

Photo: Florida Carpenter Ant (by Alex Wild)

Emerging Fungal Diseases

February 17th, 2010

Roscoff-Port-ClocherConference – ‘New and Emerging Fungal Diseases of Animals and Plants: evolutionary aspects in the context of global changes? in Brittany, 17th – 21st April 2010.

From the site: “The world is changing rapidly as environments are modified by human activity. Superimposed upon this background of environmental change are signatures of ‘Globalisation’ as species are introduced into non-native, ecosystems. Many of these species are invasive, often pathogenic, organisms, and this conference Jacques Monod focuses on a Kingdom that is increasingly being recognised as having a widening impact on ecosystem, agricultural and human health, the Fungi.”

IMC9: The Biology of Fungi

December 24th, 2009


With the surge of fungal genome release, studying the biology of the Mycota has never been as exciting as it is today. The International Mycological Congress represents one of the largest scientific forum to provide an up-to-date perspective of mycology in all its guises. The 9th International Mycological Congress (IMC9: the Biology of Fungi) will be held in August 2010 in Edinburgh, Scotland. The conference themes will include:

  • Cell biology, biochemistry and physiology
  • Environment, ecology and interactions
  • Evolution, biodiversity and systematics
  • Fungal pathogenesis and disease control
  • Genomics, genetics and molecular biology

Register at:

The Genome Encyclopedia of Fungi

October 18th, 2009

jgiBecause of the importance of fungi to Department of Energy (DOE) mission areas such bioenergy production, bioremediation and carbon cycling, the Joint Genome Institute has decided to develop a formal Fungal Genomics Program. In bioenergy projects alone, for example, fungal genome data have been used not only to ensure the health of crops that serve as biomass feedstocks (e.g., Poplar/Melampsora interaction) but also provide enzymes that can break down the biomass. Currently, the vast majority of fungi whose genomes have been sequenced are ascomycetes and basidiomycetes. The result of this bias is that we don’t have a grasp of the enzymatic and metabolic diversity found in the fungal kingdom. The JGI has thus developed a Fungal Genomics Program headed by Igor Grigoriev. The program’s first project, launched October 1, is the Genome Encyclopedia of Fungi (GEF). The program aims to explore fungi’s ecological diversity and breadth across the Tree of Life. One thrust area will be devoted to basidiomycetes. Another thrust area of this program will aim to sequence genomes across the fungal tree of life.  Additional thrust areas will be aimed at in depth sequencing of other fungal groups that are key to DOE mission areas, such as the Dothideomycetes.

hc2Years 2009 and 2010 will be devoted to building and piloting a fungal genome sequencing pipeline that scales – from DNA sample preparation to automated annotation to comparative genomics tools. Five genomes will initially sequenced per month. Within the candidate basidiomycetes for sequencing there are several soil fungi involved in wood degradation and ectomycorrhizal symbiosis, including Gloeophyllum trabeum (brown-rot), Fomitiporia mediterranea (white-rot), and Hebeloma cylindrosporum (symbiont). These multiple genomes will allow a thorough comparative analysis of the genome traits underlying the fungal lifestyles.

August 28th, 2009

hongosThe Xth International Fungal Biology Conference will be held in Ensenada, Baja California, Mexico on December 6 – 10, 2009. The International Fungal Biology Conferences are a prestigious series of conferences held at 3-4 year intervals at different locations around the world.

Several talks and symposia will be dedicated to genomics and postgenomics of fungi.

Please visit the website for details on the scientific programme, registration, hotel accommodations, transportation etc.

August 24th, 2009


The 22nd New Phytologist Symposium entitled ‘Effectors in plant–microbe interactions’ will be held at INRA Versailles Research Centre, Paris, France from 13 to 16 September 2009. For full details about the meeting, see The New Phytologist web site.

“Effectors are defined as molecules produced by bio-aggressors/pathogens/symbionts to manipulate their host plants, thereby facilitating infection (virulence or symbiotic factors, toxins, inhibitors) and/or triggering defense responses (avirulence factors, elicitors). This dual (and conflicting) activity of effectors has been broadly reported in many plant–microbial interactions. This research topic is actively investigated using a combination of approaches and benefits from the recent advances in plant and microbial functional genomics and genome-wide evolutionary analyses. The 22nd New Phytologist Symposium aims to bring together scientists working on plant–microbe interactions across a range of organisms (viruses, bacteria, fungi and nematodes) to identify and focus on these important questions.” from H. Slater.