Archive for the ‘Genome paper’ category


March 6th, 2014

JGI User Meeting, Genomics of Energy and the Environment

February 19th, 2014

The JGI User Meeting, Genomics of Energy and the Environment, will be held March 18-20 in Walnut Creek, CA.

This year looks like a particularly exciting meeting, with great speakers and a diversity of interesting topics.  The agenda and other details for this meeting can be found at

myTree of the Month

February 15th, 2014

Understanding the Polyporales Evolution

December 15th, 2013

The Saprotrophic Agaricomycetes Sequencing Consortium, lead by David Hibbett (Clark University) analyzed 10 currently available whole genomes of Polyporales, comparing them to known gene datasets. In a special issue of Mycologia, the consortium reported the phylogenomic and phylogenetic analyses of this ecologically-important group of wood-rotters. They also analyzed several single-copy genes to assess them for their potential as markers of relationships between members of this group.

This analysis yielded new details about the evolutionary relationships between species, which they detailed in several phylogenetic trees of several clades (residual polyporoid clade, plebioid clade, antrodia clade and core polyporoid clade).

December 12th, 2013

Labex ARBRE Annual Meeting

October 16th, 2013

The Annual Meeting 2013 of the Lab of Excellence ARBRE will be held at INRA-Nancy on Monday 21st October, 2013.

The primary objective of this meeting will be to present the projects awarded funding by the Labex call for proposals in 2012.  It will aim to highlight and discuss the most noteworthy achievements during the first year of Labex ARBRE, specific to research units and those in each thematic area (Research, Valuation, Training-Dissemination).  Projects selected for funding from the 2013 call for proposals will also be presented.  The day will end with a strategy discussion moderated by project leaders from each thematic area who will focus on how to strengthen relationships between thematic actions and areas of research.

For the detailed meeting agenda please click here – Agenda


Jacques Monod Conference on Bacterial-Fungal Interactions

August 27th, 2013
The deadline for application to the first Jacques Monod Conference on Bacterial-Fungal Interactions entitled :
Bacterial-fungal interactions: a federative field for fundamental and applied microbiology“, is September 15, 2013.
The conference will take place at Roscoff in Britanny (France) from December 8 to 11, 2013.

The Passion Principle

August 15th, 2013

Wilson EO (2013) Letters to a Young Scientist.

New York: Liveright (W.W. Norton). 245 p. ISBN 978-0871403773 (hardcover). US$21.95.


Read the book review by:  Simberloff D (2013) The Passion Principle. PLoS Biol 11(8): e1001629. doi:10.1371/journal.pbio.1001629



First Global Biodiversity Conference

June 26th, 2013

Loosing its claws …

June 26th, 2013

Must read …

The Transition from a Phytopathogenic Smut Ancestor to an Anamorphic Biocontrol Agent Deciphered by Comparative Whole-Genome Analysis
[Abstract. Pseudozyma flocculosa is related to the model plant pathogen Ustilago maydis yet is not a phytopathogen but rather a biocontrol agent of powdery mildews; this relationship makes it unique for the study of the evolution of plant pathogenicity factors. The P. flocculosa genome of ~23 Mb includes 6877 predicted protein coding genes. Genome features, including hallmarks of pathogenicity, are very similar in P. flocculosa and U. maydis, Sporisorium reilianum, and Ustilago hordei. Furthermore, P. flocculosa, a strict anamorph, revealed conserved and seemingly intact mating-type and meiosis loci typical of Ustilaginales. By contrast, we observed the loss of a specific subset of candidate secreted effector proteins reported to influence virulence in U. maydis as the singular divergence that could explain its nonpathogenic nature. These results suggest that P. flocculosa could have once been a virulent smut fungus that lost the specific effectors necessary for host compatibility. Interestingly, the biocontrol agent appears to have acquired genes encoding secreted proteins not found in the compared Ustilaginales, including necrosis-inducing-Phytophthora-protein- and Lysin-motif- containing proteins believed to have direct relevance to its lifestyle. The genome sequence should contribute to new insights into the subtle genetic differences that can lead to drastic changes in fungal pathogen lifestyles.]



Genome of the Honey Mushroom Unearthed

May 23rd, 2013

Collins C, Keane TM, Turner DJ, O’Keeffe G, Fitzpatrick DA, Doyle S (2013) Genomic and Proteomic Dissection of the Ubiquitous Plant Pathogen, Armillaria mellea: Towards a New Infection Model System. J Proteome Research, DOI: 10.1021/pr301131t


Armillaria mellea is a major plant pathogen. Yet, no large-scale ‘-omic’ data are available to enable new studies, and limited experimental models are available to investigate basidiomycete pathogenicity. Here we reveal that the A. mellea genome comprises 58.35 Mb, contains 14,473 gene models, of average length 1575 bp (4.72 introns/gene). Tandem mass spectrometry identified 921 mycelial (n = 629 unique) and secreted (n = 183 unique) proteins. Almost 100 mycelial proteins were either species-specific or previously unidentified at the protein level. A number of proteins (n = 111) were detected in both mycelia and culture supernatant extracts. Signal sequence occurrence was fourfold greater for secreted (50.2%) compared to mycelial (12%) proteins. Analyses revealed a rich reservoir of carbohydrate degrading enzymes, laccases and lignin peroxidases in the A. mellea proteome, reminiscent of both basidiomycete and ascomycete glycodegradative arsenals. We discovered that A. mellea exhibits a specific killing effect against Candida albicans, during co-culture. Proteomic investigation of this interaction revealed the unique expression of defensive and potentially offensive A. mellea proteins (n = 30). Overall, our data reveal new insights into the origin of basidiomycete virulence and we present a new model system for further studies aimed at deciphering fungal pathogenic mechanisms.]

Photo: Fruiting body of Armillaria mellea © F Martin

5th European Plant Science Retreat

April 2nd, 2013

This summer, Ghent university and the VIB will be the host of the annual 5th European Plant Science Retreat (23-27 July). This is a conference and networking event organized by and held for PhD’s in plant research from 11 of the best plant-research institutes around Europe.

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).

JGI Fall 2012 Primer

November 11th, 2012

The Fall 2012 edition of the DOE JGI newsletter, The Primer is now posted:

Highlights include:

Photo: Maze-like pore surface of the polypore Trametes versicolor. Wood-decayers in the Polyporales are primary target for sequencing within the framework of the MycoCosm program. © F Martin.

The Pizza Mushroom Genome

October 9th, 2012

The publication describing the genome from the Button Mushroom (Agaricus bisporus) was published online today  in the early Edition of the journal, the Proceedings of the National Academy of Sciences (PNAS). This paper represents a culmination of five years of work by many people from multiple institutions in France, U.S.A., U.K., The Netherlands, Finland and Germany. This was truly an amazing team effort between the JGI teams and the international consortium. Let’s see if the news coverage of this genome study is as good as the one received for the Black Truffle genome. After all, the Portobello mushroom is one of the most commonly and widely consumed mushrooms in the world.

Below is the abstract of our PNAS paper:

[Abstract. Agaricus bisporus is the model fungus for the adaptation,persistence, and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important component of the human diet for over 200 y and worldwide cultivation of the “button mushroom” forms a multibillion dollar industry. We present two A. bisporus genomes, their gene repertoires and transcript profiles on compost and during mushroom formation. The genomes encode a full repertoire of polysaccharide-degrading enzymes similar to that of wood-decayers. Comparative transcriptomics of mycelium grown on defined medium, casing-soil, and compost revealed genes encoding enzymes involved in xylan, cellulose, pectin, and protein degradation are more highly expressed in compost. The striking expansion of heme-thiolate peroxidases and β-etherases is distinctive from Agaricomycotina wood-decayers and suggests a broad attack on decaying lignin and related metabolites found in humic acid-rich environment. Similarly, up-regulation of these genes together with a lignolytic manganese peroxidase, multiple copper radical oxidases, and cytochrome P450s is consistent with challenges posed by complex humic-rich substrates. The gene repertoire and expression of hydrolytic enzymes in A. bisporus is substantially different from the taxonomically related ectomycorrhizal symbiont Laccaria bicolor. A common promoter motif was also identified in genes very highly expressed in humic-rich substrates. These observations reveal genetic and enzymatic mechanisms governing adaptation to the humic-rich ecological niche formed during plant degradation, further defining the critical role such fungi contribute to soil structure and carbon sequestration in terrestrial ecosystems. Genome sequence will expedite mushroom breeding for improved agronomic characteristics.]

Read: Morin et al. (2012) Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche. Proceedings of the National Academy of Sciences, Early Edition.

Press releases:

JGI: Adaptable Button Mushroom Serves Up Biomass-Degrading Genes Critical to Managing the Planet’s Carbon Stores

INRA: Le génome du champignon de Paris décrypté

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).

Back to the Future

August 24th, 2012

I’ve tried to keep this blog reasonably up to date, but I am falling behind. I have said yes to too many things. I’ve tons of news on our projects in fungal genomics that may be of interest to you. I’ll do my best to cope with my backlog over the next few weeks. Let’s start with one of our consortium paper recently published investigating the evolution of the wood decay machinery in forest fungi. An exciting blend of comparative genomics and paleomycology.

The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes by Floudas et al. (2012) Science 336: 1715-1719

This is the first paper arising from the JGI Saprotrophic Agaricomycotina Project (SAP). It was published in Science on July 29, 2012. Together with the JGI Mycorrhizal Genome project, the SAP project is aiming to reconstruct the evolution of two major lifestyles, saprotrophism and mutualism, in Fungi. This paper is the first account of a large-scale JGI project, lead by David Hibbett (Clark University), reporting twelve new genomes and involving 71 authors from 13 countries. As mentioned by one of the referee: “this manuscript epitomizes the modern publishing era where a one-hundred page supplement presents most of the information in a dry and matter-of-fact tone, while an extremely well-written and exciting summary functions primarily to advertise its findings to a broad audience“. It truly represents an integrative effort ably deploying the methodologies from multiple disciplines to draw exciting conclusions in fungal evolution.

The Wood Decay Machinery. Plant lignin and (hemi)cellulose are the most abundant biopolymers in terrestrial ecosystems. Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. Fungal-mediated degradation of wood lignocellulose is thus a critical link in the environmental carbon cycle, and is of great economic interest for its potential applications in lignocellulose bioconversion, biofuel production and feedstock improvement. Saprotrophic Agaricomycotina are active and abundant degraders of this lignocellulosic biomass. Two principal modes of decay occur in the Agaricomycotina, termed white rot and brown rot. White rot fungi are capable of efficiently degrading all components of plant cell walls, including the highly recalcitrant lignin fraction. Brown rot fungi modify but do not appreciably remove the lignin, which remains as a polymeric residue following removal of cellulose and hemicellulose. Brown rot residues are highly resistant to further decay and contribute to the fixed carbon pool in humic soils, particularly in cool-temperate and boreal, conifer-dominated ecosystems. Brown rot fungi thus play a significant role in terrestrial carbon sequestration.

Some historical background. In March 2010, we proposed the SAP to the JGI community-based sequencing program for whole-genome sequencing of a suite of wood decayers in the subphylum Agaricomycotina. The principal criteria for target selection included: phylogenetic diversity, functional diversity, ecological importance, availability of (homokaryotic) mycelial cultures and community interest. We proposed a suite of 30 species divided into three Tiers of ten species each. As of today, the genome sequences of >20 species have been released and are used in comparative studies that illustrate the diversity and evolution of wood decay strategies. Comparisons of these multiple genomes enables determination of the essential components of white- and brown-rot decay mechanisms reported in the Science paper. Amazingly enough, JGI teams have been able to sequence and annotate all these genomes in about two years … and the Consortium has been able to mine this massive dataset to generate the paper findings in less than one year thanks to David and Igor’s efficient coordination.

The Major Findings. Comparative analyses of 31 fungal genomes suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species. Molecular clock analyses suggest that the evolution of the lignin degrading white rot fungi took place at the end of the Carboniferous (Paleozoic era). During the Carboniferous, vast swathes of forest covered the land, which would eventually be laid down and become the coal beds characteristic of the Carboniferous system. This phylogenomic reconstruction implies that this evolution may have caused the end of the Carboniferous as it ended the large coal deposits characteristic of that period. Well, I agree that this contention is highly speculative. Only a Time Machine would allow us to get back to the dinosaur era and check if this speculation stands true!!!

As in my previous genomics endeavours, I have personally learned a great deal in the course of this work, and I have enjoyed collaborating with so many expert colleagues.

Other commentaries:

Perspective: Chris Todd Hittinger. Endless Rots Most Beautiful. Science 336: 1649-1650. 2012.

Hibbett’s blog: SAP paper published in Science

Tracking the Remnants of the Carbon Cycle: How an Ancestral Fungus May Have Influenced Coal Formation

INRA: Évolution : un champignon préhistorique serait à l’origine de l’arrêt de la formation du charbon

Scientific America: White Rot Fungi Slowed Coal Formation



Photo: Fomitopsis pinicola (Red Banded Polypore) is one of the most conspicuous and widely distributed polypores in coniferous forest regions of the northern hemisphere. F. pinicola is one of the sequenced fungus (see its JGI Portal) (© F Martin).

Les champignons au charbon

August 22nd, 2012

Évolution : un champignon préhistorique serait à l’origine de l’arrêt de la formation du charbon

Voici le communiqué de presse de l’INRA sur notre article dans Science sur l’évolution des mécanismes de dégradation de la lignocellulose chez les champignons du groupe des Agaricomycotina: [“L’apparition, il y a environ 300 millions d’années, d’un champignon capable de détruire efficacement le bois pourrait en partie expliquer l’arrêt de la formation de charbon à base de débris végétaux à cette même période. C’est l’une des conclusions d’une étude menée par des chercheurs de l’Inra, du CNRS et des universités de Lorraine et d’Aix-Marseille dans le cadre d’un consortium international. L’étude a permis également de comprendre le processus de dégradation du bois par les champignons contemporains, ce qui devrait fortement intéresser le secteur des bioénergies.] … en savoir plus

Floudas et al. (2012) The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science 336: 1715-1719.


Photo: Young fruiting body of  Fomitopsis pinicola (Red Banded Polypore) (© F Martin).

JGI Summer 2012 Primer

August 2nd, 2012

The summer 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:

Features include:

  • A summary of the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting
  • Comparative Genomics of White Rot Fungi Providing Insight into Selective Ligninolysis
  • The Omics Response to the Deepwater Oil Spill
  • Assembling the Switchgrass Genome
  • Single-cell Genomics @ the DOE JGI
  • Save the Date for the 8th Annual Genomics of Energy & Environment Meeting MARCH 25-29, 2013 in WALNUT CREEK, CA
  • Other Publication Highlights



Rust in the limelight

April 20th, 2012

Image by Benjamin Petre and Stephane Hacquard on the cover of the March 2012 issue of Molecular Plant Microbe Interactions. Congrats to Steph, David, Seb and coauthors for their paper: ‘A Comprehensive Analysis of Genes Encoding Small Secreted Proteins Identifies Candidate Effectors in Melampsora larici-populina (Poplar Leaf Rust)‘.

Uredinia formed by the rust fungus Melampsora larici-populina 7 days after inoculation on susceptible poplar leaves (severe and weak infection are pictured above and below the midrib, respectively). The panels below show immunofluorescence localization of small secreted proteins at the periphery of distinct infection structures in poplar leaves.