Archive for the ‘Ecosystems’ category

1000 Fungal Genome (1KFG) project: Graduate Student-Postdoc Challenge (2014)

August 6th, 2014

The 1000 Fungal Genome (1KFG) project is a large-scale community sequencing project supported by the Joint Genome Institute (JGI).  The goal of 1KFG is to facilitate the sequencing of fungal genomes across the Kingdom Fungi with the objective to significantly advance genome-enabled mycology.  The sampling guideline is to sequence two species of fungi for every family-level clade of Fungi so that genomic data is representative of phylogenetic diversity of Fungi. In support of this endeavor, 1KFG is pleased to announce the Graduate Student/Postdoc Challenge.  From July 2014-June 30 2015 we will accept nominations to sequence up to 100 species of fungi in support of graduate student and postdoctoral research projects.  Students and postdocs are encouraged to nominate species and submit DNA and RNA samples for genomic sequencing.


Follow the link to find out how to nominate species.


Mycorrhizal Genomics Initiative – Year 3

July 31st, 2014

In 2003, the Poplar Mesocosm Sequencing project was launched to sequence the genome of three Populus-associated fungi, the ectomycorrhizal (EM) basidiomycete Laccaria bicolor, the arbuscular mycorrhizal (AM) glomeromycete Rhizophagus irregularis (formerly Glomus intraradices), and the poplar leaf rust Melampsora larici-populina. The publication of the genome sequence of L. bicolor was a landmark event for the mycorrhizal community. It has been rapidly followed by the release of the genome of the iconic edible EM Tuber melanosporum, the Périgord black truffle and more recently, by the genome of Rhizophagus irregularis. These genomes have provided unprecedented knowledge about the structure and functioning of the mycorrhizal fungal species and their interactions with their host plants. Genome-wide transcript profilings have also led to the identification of master genes with crucial roles in symbiosis formation, such as those coding for Mycorrhiza-induced Small Secreted Proteins (MiSSPs) controling plant immunity and development.

An international effort, referred as to the Mycorrhiza 25 Genomes Project and then the Mycorrhizal Genomics Initiative (MGI), aiming to unearth the evolution and functioning of mycorrhizal symbioses through large-scale genome sequencing has been launched in 2011. As of writing, this initiative targets a set of 35 fungal species that are able to form various types of mycorrhizal symbioses, i.e., EM, arbuscular, ericoid and orchid mycorrhizae (see my previous posts ‘Mycorrhizal Genomics Initiative‘ and ‘Exploring the Mycorrhizal Genomes‘ ). Sequencing is carried out at JGI and Genoscope in the framework of the JGI Community Science Program, the 1000 Fungal Genomes Project and the TuberEvol project. Comparison of these genomes should facilitate the characterization of the genetic mechanisms that underpin the formation and evolution of ecologically-relevant mycorrhizal symbioses and characterization of genes selectively associated with particular symbiotic patterns.

The fungal species sequenced have been selected based on: (1) their phylogenetic position, (2) their ecological relevance, and (3) their ability to establish different types of mycorrhizal symbiosis. As of today, genomic sequences and gene repertoires are publicly available for 28 mycorrhizal fungi, including 24 ectomycorrhizal species, 3 ericoid species, 2 orchid mycorrhizal species and 1 arbuscular mycorrhizal species (see Table below & see the JGI MycoCosm Mycorrhizal Fungi portal.

Genomes of the sequenced mycorrhizal fungi range in size from about 36 Mb, as in the case of Rhizopogon vinicolor, to a 193 Mb, as in Tuber magnatum (Table). Repetitive DNA, mostly in the form of transposable elements (TE), is responsible for the bulk of the variation. A striking feature is the wide variation in repetitive DNA content (from 3.6 % for H. cylindrosporum to 58.3% for T. magnatum). Predicted gene contents range from about 7500 for T. melanosporum to ~28000 genes for Rhizophagus irregularis.

We are drafting a paper summarizing the main conclusions from the analysis of the first series of mycorrhizal genomes. Stay tune!


Species Genome size Gene #
1 Amanita muscaria Koide v1.01 40,699,759 18,153
2 Boletus edulis v1.01 46,637,611 16,933
3 Cenococcum geophilum 1.58 v2.01 177,557,160 14,748
4 Choiromyces venosus 120613-1 v1.01 126,035,033 17,986
5 Cortinarius glaucopus AT 2004 276 v2.01 63,450,306 20,377
6 Gyrodon lividus BX v1.01 43,048,674 11,779
7 Hebeloma cylindrosporum h7 v2.01 38,226,047 15,382
8 Laccaria amethystina LaAM-08-1 v1.01 52,197,432 21,066
9 Laccaria bicolor 81306 v1.01 50,950,722 17,791
10 Laccaria bicolor D101 v1.01 70,029,479 22,538
11 Laccaria bicolor S238N-H70 v1.01 57,049,857 19,903
12 Laccaria bicolor S238N-H82 v1.01 52,023,709 18,706
13 Laccaria bicolor S238N-H82xH70 v1.01 42,115,601 17,045
14 Laccaria bicolor v2.01 60,707,050 23,132
15 Meliniomyces bicolor E v2.03 82,384,847 18,619
16 Meliniomyces variabilis F v1.03 55,857,776 20,389
17 Morchella conica CCBAS932 v1.01 48,213,273 11,600
18 Oidiodendron maius Zn v1.03 46,426,256 16,703
19 Paxillus involutus ATCC 200175 v1.01 58,301,126 17,968
20 Paxillus rubicundulus Ve08.2h10 v1.01 53,011,005 22,065
21 Piloderma croceum F 1598 v1.01 59,326,866 21,583
22 Pisolithus microcarpus 441 v1.01 53,027,657 21,064
23 Pisolithus tinctorius Marx 270 v1.0 71,007,534 22,701
24 Rhizophagus irregularis DAOM 181602 v1.02 91,083,792 30,282
25 Rhizopogon vinicolor AM-OR11-026 v1.01 36,102,320 14,469
26 Scleroderma citrinum Foug A v1.01 56,144,862 21,012
27 Sebacina vermifera MAFF 305830 v1.04 38,094,242 15,312
28 Suillus brevipes v1.01 51,712,595 22,453
29 Suillus luteus UH-Slu-Lm8-n1 v1.01 37,014,302 18,316
30 Terfezia boudieri S1 v1.01 63,234,573 10,200
31 Tricholoma matsutake 945 v3.01 175,759,688 22,885
32 Tuber aestivum1 131,544,163 9,344
33 Tuber magnatum v1.01 192,781,443 9,433
33 Tuber melanosporum v1.01 124,945,702 7,496
34 Tulasnella calospora AL13/4D v1.04 62,392,858 19,659
35 Wilcoxina mikolae CBS 423.85 v1.01 117,288,895 13,093


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).

Fungal Carbon Sequestration

March 29th, 2013


By  K. E. Clemmensen, A. Bahr, O. Ovaskainen, A. Dahlberg, A. Ekblad, H. Wallander, J. Stenlid, R. D. Finlay, D. A. Wardle, B. D. Lindahl


Abstract. Boreal forest soils function as a terrestrial net sink in the global carbon cycle. The prevailing dogma has focused on aboveground plant litter as a principal source of soil organic matter. Using 14 C bomb-carbon modeling, we show that 50 to 70% of stored carbon in a chronosequence of boreal forested islands derives from roots and root-associated microorganisms. Fungal biomarkers indicate impaired degradation and preservation of fungal residues in late successional forests. Furthermore, 454 pyrosequencing of molecular barcodes, in conjunction with stable isotope analyses, highlights root-associated fungi as important regulators of ecosystem carbon dynamics. Our results suggest an alternative mechanism for the accumulation of organic matter in boreal forests during succession in the long-term absence of disturbance]

Read also the linked Commentary by Kathleen K. Treseder and Sandra R. HoldenFungal Carbon Sequestration.

Photo: One of the investigated island situated in the two adjacent lakes Uddjaure and Hornavan in the Northern boreal zone of Sweden (from Björn Lindahl’s home page).


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).

A Cornucopia of Mycorrhizal Genomes

February 23rd, 2013

Mycorrhizal symbioses are nearly universal in terrestrial plants. Based on host plant and characteristic symbiotic structures, several classes of mycorrhizal symbioses are currently recognised, with the two major types being the endocellular arbuscular mycorrhiza (AM) and the intercellular ectomycorrhiza (ECM). Mark Brundrett’s web site provides an excellent introduction to the different types of mycorrhizal symbioses. Briefly,

In AM association, the fungal hyphae penetrates host roots to form intracellular arbuscules and vesicles.

In ECM, colonizing hyphae remain in the intercellular, apoplastic space forming the Hartig net. They do not penetrate the root cells. ECM are mostly form by basidiomycetes (e.g., Amanita, Boletus, Sebacina), but some are formed with ascomycetes (e.g., Tuber, Terfezia).

Additionally, the ericoid mycorrhiza (ERM) has been regarded as the most specific of mycorrhizas because of its limitation to hosts belonging to a restricted number of families of the Ericales and the participation of a small group of ascomycetous fungi (e.g., Helotiales) as mycobionts in the association. Ericoid fungi form hyphal coils in outer cells of the narrow “hair roots” of plants in the family Ericaceae, such as Vaccinium and Calluna.

All orchids are myco-heterotrophic at some stage during their lifecycle and form orchid mycorrhizas with a range of basidiomycete fungi (e.g., Tulasnella). The mycobiont forms coils of hyphae within roots or stems of orchidaceous plants. This type of mycorrhiza is unique because the endophytic fungus supplies the plant with carbon during the heterotrophic seedling stage of orchidaceous plants. The mycorrhizal fungi are often Tulasnellales, a basidiomycetous order that contains plant parasites and saprobes capable of degrading complex carbohydrates, such as cellulose.

Whether these different types of mycorrhizal fungi forming strikingly different anatomical structures and with contrasted biology and ecology differ in their gene repertoires and symbiosis-related gene networks is currently unknown and tackling these major questions is the main impetus of the current Mycorrhizal Genomics Initiative lead by the JGI and INRA (see my previous posts ‘Mycorrhizal Genomics Initiative‘ and ‘Exploring the Mycorrhizal Genomes‘ )

The genome of 30 representatives of these various types of mycorrhizal symbioses are currently sequenced and these tremendous genomic resources are providing new highlights on the biology, genetic and ecology of these symbioses. The findings obtained previously on L. bicolor and T. melanosporum genomes suggested that the ECM condition represents a syndrome of variable traits and that mycorrhizal fungi share fewer functional similarities in their molecular ‘toolboxes’ than anticipated (Plett & Martin, 2011) and this hypothesis is confirmed by the newly available genomes. We see very different symbiosis-upregulated genes in the various mycorrhizal lineages suggesting that these are non-homologous ecologies and that there are many routes to the similar nutritional modes. Several talks and posters at the forthcoming 27th Fungal Genetics Conference in Asilomar will illustrate several breakthroughs obtained by the MGI consortium members.

As of writing, the mycorrhizal species sequenced, assembled and annotated span a wide section of the evolutionary tree of Ascomycota and Basidiomycota, and include ectomycorrhizal, ericoid and orchid symbionts as follows:

Ectomycorrhizal species:

  • Amanita muscaria,
  • Boletus edulis
  • Cenococcum geophilum,
  • Cortinarius glaucopus,
  • Hebeloma cylindrosporum h7  (v2.0),
  • Laccaria amethystina 08-1,
  • Laccaria bicolor (v2.0),
  • Paxillus involutus,
  • Paxillus rubicundulus,
  • Piloderma croceum F 1598,
  • Pisolithus microcarpus 441,
  • Pisolithus tinctorius 270,
  • Scleroderma citrinum FougA,
  • Suillus luteus UH-Slu-Lm8-n1,
  • Terfezia boudieri,
  • Tricholoma matsutake 945.

Orchid mycorrhizal species:

  • Tulasnella calospora AL13/4D
  • Sebacina vermifera MAFF 305830,

Ericoid mycorrhizal species

  • Oidiodendron maius Zn,
  • Meliniomyces bicolor,
  • Meliniomyces variabilis.

As of today, 20 mycorrhizal genomes have been released on the JGI MycoCosm web portal and 10 additional genomes will be publicly released by the end of 2013 (see also our MGI web portal).

In addition to these new genomes/transcriptomes, those of Rhizopogon vinicolor, Gyrodon lividus, Choiromyces venosus, Lactarius quietus, Leccinum scabrum, Thelephora terrestris, Tomentella sublilacina, Tuber aestivum, Tuber magnatum, Rhizoscyphus ericae are expected to be released in 2013.

The genomes of mycorrhizal species released over the last two years, combined with previous studies of the L. bicolor and T. melanosporum genomes, provides a rich foundation for future studies to elucidate the unique features of these ubiquitous plant symbionts. Let’s find the gems in these genetic blueprints!

Photo: Fruiting bodies of the ectomycorrhizal Fly Agaric (Amanita muscaria).

F1000 nominations

December 18th, 2012

Great news!!! A new nomination tool for the 1000 Fungal Genome Project has been released ( to entire research community.  Any JGI registered user can click on MycoCosm tree nodes at (, choose ‘Nominate’ to suggest new fungal species for sequencing and provide DNA/RNA samples to fill the gaps in the Fungal Tree of Life.  The nominations can be made all year around; after review the approved candidates will be added to the list of JGI projects.

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 current nomination will help in selecting the most interesting suggestions from our community.

Photo: Mycena sp. belongs to a large genus of small saprotrophic mushrooms. Mycena galopus will be sequenced within the framework of the Forest Soil Metatranscriptome Project (CSP570) © F Martin

In the limelight …

December 1st, 2012

Forests, Trees, Tree-Microbe Interactions, Symbiosis, Mycorrhizas, Wood Decayers, Carbon Sequestration & Cycling, Global Changes, Genomics … words I have used many times during this amazing week. Starting with an interview by Sophie Bécherel from France Inter on Monday,  followed by a journalist crew’s visiting the lab on Tuesday, then an interview at France Info with Marie-Odile Monchicourt on Wednesday and the INRA Award ceremony on Thursday with the Minister of Higher Education and Research, Geneviève Fioraso, and the Minister of the Agriculture, Stéphane Le Foll. I haven’t fully realized yet that I was awarded the INRA Laurel Wreath for Excellence for my work on tree-microbe interactions and fungal genomics. I hope this award will help in promoting the research on soil microbial ecology, forest ecosystems and symbiotic interactions.

> François Le Tacon, Annegret Kohler, Claude Murat, Alice Vayssières and I describing our on-going research: View the video (in French)


From Left to Right : Frédéric Dardel (President of the INRA Scientific Advisory Board), David Lowe (journaliste), Michel Pellé (Research Support Award), Olivier Hamant (The Young Researcher Award), Mariane Damois (Research Support Award), Hélène Bergès (The Engineer’s Award), François Houllier (INRA CEO), Stéphane Le Foll (Minister for Agriculture) and myself  (The Laurel Wreath for Excellence). © INRA, B. Nicolas

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).

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..




Soil & Civilization

August 3rd, 2012

I’m reading Edward Hyam’s book entitled ‘Soil and Civilization‘. Published in 1952, that’s a provocative classic described as ‘the first of its kind to cover the vast panorama of human history from a strictly ecological point of view‘. Although a bit outdated now, some of its message is still true. This is an account of the relationship between people and soil. Each has shaped the other for millenia. Hyam describes people as “parasites” leeching th goodness from the soil. Several writers have documented the fall of civilizations throughout history in parallel with the destruction of their soil (see Erosion of Civilizations). These stories are stark reminders not to take soil and soil stewardship for granted — soil is not an inexhaustible resource.

Soil and civilization. 1976. Edward Hyams. New York: Harper & Row. (Originally published in 1952).

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



8th JGI Users Meeting

August 2nd, 2012

Aboveground-belowground interactions

August 1st, 2012

The British Ecological Society, the Biochemical Society and the Society for Experimental Biology are organising a meeting entitled ‘Aboveground-belowground interactions: technologies and new approaches’, which is being held on 8-10 Oct 2012 in London.

The aim of the symposium is to promote cross-disciplinary collaboration by bringing together existing technology users and developers (e.g. biochemists, geneticists, bioinformaticists) who are interested in applying their skills to address research questions at the whole organism and ecological scales with above-belowground researchers working at biochemical, ecological, physiological, and molecular scales who have a desire to learn and apply new research technologies.

July 18th, 2012

Plant Science For Future Needs

June 11th, 2012

The Linnean Centre invites plant scientists to Uppsala for a two-day conference October 11th and 12th, 2012. The conference aims to tackle upcoming challenges like climate change and food security by setting a foundation for future collaborations between different sub-disciplines of plant science. Eight scientific sessions with plenary presentations, short talks and posters will highlight prevailing directions and novel findings.

NOTE: Registration deadline 31st of August, 2012.

Confirmed speakers are:

  • Vincent Colot, Ecole Normale Supérieure Paris
  • Thomas Kraft, Syngenta Seeds
  • Cris Kuhlemeier, Bern University
  • Gary Loake, University of Edinburgh
  • Francis Martin, INRA, Nancy
  • John McKay, Colorado State University
  • Kalien A. Mooney, UC Irvine
  • Michele Morgante, University of Udine

More information about the plenary speakers can be found here.


JGI Spring 2012 Primer

May 29th, 2012

The Spring 2012 edition of the DOE Joint Genome Institute (DOE JGI) newsletter The Primer is now available for download:
and features highlights from the DOE JGI Genomics of Energy & Environment Meeting #7.

Videos of the talks from Meeting #7 are posted here:

Be sure to Save the Date for meeting #8 the week of March 25-29, 2013.