Archive for the ‘Plant Biology’ category


March 11th, 2014

Back home

June 22nd, 2013

We welcome Dr. Jessy Labbé, a former lab Ph.D. student, who joins us from the Biosciences Division at Oak Ridge National Laboratory (TE, USA). Within the framework of the DOE Plant-Microbe Interfaces project, Jessy is working with François Le Tacon and myself on the QTL for mycorrhiza formation in poplar. He is funded by the LabeX ARBRE.

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.

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).


March 13th, 2013

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).

myTree of the Month

January 27th, 2013

Philip Greenwood

Snow Night (1974)

Phil Greenwood was born in 1943 in Dolgellau North Wales. Phil is an artist whose work whether in print or paint is inspired by landscape.

Other paintings … ‘Phil Greenwood Prints at CCA Galleries



Effector Wisdom

January 20th, 2013

30th New Phytologist Symposium: Immunomodulation by Plant-associated Organisms

Meeting Report by Amy Huei-Yi Lee, Benjamin Petre, David L. Joly

Many organisms such as bacteria, fungi, oomycetes, nematodes and insects grow, feed and/or reproduce in close association with plant hosts. To establish such intimate interactions, symbionts (either mutualistic or parasitic) secrete effectors into host tissues, which are molecules that modulate plant cell structures and processes (Win et al., 2012a). This last decade, advances in genomics have revealed that symbionts possess dozens to hundreds of effectors. Currently, the field is moving rapidly from effector identification towards effector characterization, which provides a better understanding of how these effectors promote the establishment of a successful relationship with host plants. The 30th New Phytologist Symposium clearly illustrated this theme, as an international panel of c. 150 scientists was brought together to discuss current efforts to decipher effector functions within a wide range of biological systems. The remote location of the meeting in the Sierra Nevada mountains of California, USA, promoted lively discussions between participants during and after the sessions, but also via social networks (the whole conference was covered by a twitter feed, #30NPS tag, available on Read more …

On the Air

December 6th, 2012


La vie symbiotique dans les sous-sols forestiers : la chronique de Marie-Odile Monchicourt

Les Lauriers de l’INRA : la Remise du Laurier de la Recherche agronomique

Photo: the Laurel Wreath for Excellence Award, a Sculpture by Karen Finkelstein © C Slagmulder, Inra.

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

myTree of the Month

November 2nd, 2012

In the ground of the Chaumont-sur-Loire castle, Rainer Gross has created sculptures in blackened wood. They are inspired by the roofs of the Chaumont-sur-Loire castle. One of these sculptures lies under a few centuries-old cedar and can be seen from the Loire river, which in turn can be viewed through an opening in the sculpture. These works seem to take root in the very landscape from which their materials were sourced. Rainer Gross “depicts the ambiguity of Man within Nature and the paradox of being both a product of Nature and yet independent from it“.

Mycorrhizal Genomes Medley

November 1st, 2012

In less than two weeks, mycorrhizasts will gather at the INRA in Nancy, to enjoy an exciting workshop on the mycorrhizal genomes. So much novel and unexpected information is emerging from these genome and transcriptome exploration. That’s like exploring a Terra Incognita.

Below is the agenda;

2nd Mycorrhizal Genomics Initiative (MGI) Workshop

INRA-Nancy, November 13 & 14, 2012

Tuesday 13 November

  • 9:00 – 9:15     Opening remarks
  • 9:15 – 9:40     Exploring the genome diversity of mycorrhizal fungi. Project status. By F Martin
  • 9:40 – 10:00   The MycoCosm database & Fungal Genomics at JGI. By I Grigoriev
  • 10:00 – 10:30 Annotation and analysis of ECM genomes. By A Kuo
  • 11:00 – 11:20 Identifying transposable elements and other repeated elements in mycorrhizal genomes. By C Murat
  • 11:20 – 11:40 A new approach to infer protein function based on whole genomes and phylogenetic information. By L.G. Nagy
  • 11:40 – 12:00 Analysis of multigene families and duplications in mycorrhizal genomes. By E Morin
  • 12:00 – 12:20 CAZYmes and FOLymes in mycorrhizal genomes. By B Henrissat
  • 12:20 – 12:40 The secretome in mycorrhizal genomes. By C Fourrey
  • 14:00 – 14:20 The MGI transcriptome databases. By E Tisserant
  • 14:20 – 14:40 Identifying symbiosis-regulated genes by RNA-Seq. By A Kohler

14:40 – 15:30 Genome descriptions by species

  • Paxillus involutus & P. rubicundulus By A Tunlid & M Gardes
  • Hebeloma cylindrosporum By G Gay & J Doré
  • Amanita muscaria & A. thiersii By A. Pringle/J Hess

16:00 – 18:00 Genome descriptions by species

  • Laccaria amethystina By F Martin
  • Piloderma croceum By  M Tarkka et al.
  • Suillus luteus By J Colpaert et al.
  • Scleroderma citrinum By A Deveau
  • Pisolithus tinctorius & P. microcarpus By A Kohler
  • Sebacina vermifera By A Zuccaro
  • Tulasnella calospora By M Girlanda

18:00 – End

Wednesday 14 November

9:00 – 11:00   Genome descriptions by species

  • Cenococcum geophilum By M Peter
  • Oidiodendron maius By S Perotto et al.
  • Meliniomyces bicolor, M. variabilis By G Grelet
  • Tuber species By C Murat & R Ballestrini et al.
  • Terfezia boudierii By Y Sitrit

11:00 – 11:30 New Mycorrhizal Genomes Projects

CSP2012 #570 – Metatranscriptomics of Forest Soil Ecosystems: C Murat, M Buée, F Martin

CSP2013 #978 – MGI: Exploring the Symbiotic Transcriptomes: A Kohler, F Buscot, A Tunlid, F Martin

11:30 – 12:30 Discussions: MGI: Papers & Future activities

Photo: One of the sequenced ectomycorrhizal basidiomycete, the Amethyst Deceiver (Laccaria amethystina) (© F Martin)

A Putative Strigolactone Receptor

September 12th, 2012

Strigolactones are carotenoid-derived lactones involved in root development, arbuscular mycorrhizal symbiosis, branching and leaf senescence. These plant hormones are synthesized in the roots and transported acropetally to modulate axillary bud outgrowth (i.e., branching). In Current Biology Online NowCyril Hamiaux et al. have identified the DAD2 gene from petunia and present evidence for its roles in strigolactone perception and signaling. Their main findings are as follows:

  • DAD2 gene, identified by transposon tagging, encodes an α/β hydrolase fold protein,
  • DAD2 acts in the shoot; mutants are insensitive to strigolactones,
  • DAD2 crystal structure shows an internal cavity capable of binding strigolactones,
  • DAD2 can hydrolyze the strigolactone GR24.
  • These observations suggest that DAD2 acts to bind the mobile strigolactone signal and then interacts with PhMAX2A during catalysis to initiate an SCF-mediated signal transduction pathway.

    Figure: © Current Biology.

    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).

    myTree of the Month

    August 15th, 2012

    From Pop Entosa’s site. Pep’s work is focused on an exploration of the medium itself–deconstructing and reconstructing photographic images to create new visual experiences. I like the series dedicated to trees. Multiple shots of each tree were taken while walking in a circle around it, then blended together and reworked to discover what became of the orbit – the tree and its environment.

    Morning Glory

    August 12th, 2012

    Full sun exposure …


    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