Posts Tagged ‘Symbiosis’

Alisha owenby lands an NSF DDIG

May 23rd, 2013

From Joey Spatafora Lab blog

[Alisha Owensby, PhD candidate in the lab, was recently awarded an NSF Doctoral Dissertation Improvement Grant (DDIG) for her proposal, “Evolutionary Genomics of Inter-Kingdom Host-Jumping in the Fungal Genus Elaphocordyceps“.  Way to go!  If you follow our blog, you know that Alisha is currently in Nancy, France working in the laboratory of Francis Martin at INRA.  She is working on the genome of Elaphomyces, one of the hosts of Elaphocordyceps.  This is a particularly challenging project as Elaphomyces does not culture and thus the genomic libraries are prepared from DNA and RNA extracted directly from sporocarps and are metagenomic in nature.  The photo is of Alisha working in Francis’ lab doing an RNA extraction.  Just a few more weeks and she’ll be back.  Bring wine and cheese!!]

Photo: Alisha and Nicolas extracting Elaphomyces RNA for RNA-Seq

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).

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 Earth’s Vast Symbiosphere

December 11th, 2011

Effectors in Plant-Microbe Interactions

November 17th, 2011

Just got a copy of our book on Effectors in Plant-Microbe Interactions by Sophien Kamoun and I. It looks georgious … although the photo on the cover page is reminiscent of ‘The Eye of Sauron‘ as portrayed in Peter Jackson’s Lord of the Ringsmovie  trilogy.

Search inside this book at


Unraveling the secrets of the mother of plant root endosymbioses

November 17th, 2011

Glomus intraradices, alias G. irregulare, is a widespread arbuscular mycorrhizal fungus (AMF) (Glomeromycota) found in different ecosystems throughout the world, including temperate and tropical locations. As a symbiont G. intraradices is highly effective in mobilizing, taking up and transferring mineral nutrients from soils to plants, and it readily colonizes many plant species including agriculturally important species such as wheat, alfalfa, rice, and key model plants such as Medicago truncatula, Lotus japonicum, and Populus trichocarpa. For these reasons G. intraradices is among the most studied AMF and is the prime ingredient in several commercially available inocula. G. intraradices can also be grown in vitro in dual culture with transformed carrot roots. G. intraradices is also the only species whose spores are available commercially in pure form in large quantities.

From an evolutionary standpoint, the AMF are unique obligate symbionts with coenocytic hyphae (lacking cellular structure) that transport organelles and nutrients over long distances. The concept of an individual does not apply, raising substantial questions about natural selection and population genetics of these highly unusual organisms.

To provide long-awaited insights into the molecular basis of symbiosis-associated traits, the Glomus Genome Consortium investigated the transcriptome from G. intraradices (strain DAOM 197198). From >437,000 ESTs, we generated a set of 25,906 nonredundant virtual transcripts (NRVTs) transcribed in germinated spores, extraradical mycelium and symbiotic roots using Sanger and 454 sequencing. These NRVTs were then used to construct an oligoarray for investigating gene expression.

Take-home points:

  • We identified transcripts coding for the meiotic recombination machinery, as well as meiosis-specific proteins, suggesting that the lack of a known sexual cycle in G. intraradices is not a result of major deletions of genes essential for sexual reproduction and meiosis.
  • Induced expression of genes encoding membrane transporters, such as ammonium and phosphate transporters, and small secreted proteins in intraradical mycelium, together with the lack of expression of hydrolytic enzymes acting on plant cell wall polysaccharides (e.g. cellulases, pectin lyases), are all features of G. intraradices that are shared with ectomycorrhizal symbionts and obligate biotrophic pathogens.

Our results illuminate the genetic basis of symbiosis-related traits of the most ancient lineage of plant biotrophs, hopefully advancing future research on these agriculturally and ecologically important symbionts.

Next challenge: Assembling the highly polymorphic genome sequence of G. intraradices.

Read more …

Parniske M (2008) Arbuscular mycorrhiza: the mother of plant root endosymbioses. Nature Reviews Microbiology 6, 763-775.

Bonfante P, Genre A (2010) Mechanisms underlying beneficial plant-fungus interactions in mycorrhizal symbiosis. Nature Communications 1: 4

Photo: The most beautiful photo of G. intraradices arbuscules, branching profusingly in its host plant cell (Thanks to Yves Piché, Laval University).

DOE JGI 2012 Community Sequencing Program Portfolio

November 4th, 2011

Trillions Served: Massive, Complex Projects Dominate DOE JGI 2012 Community Sequencing Program Portfolio.

‘The 2012 Community Sequencing Program (CSP) call invited researchers to submit proposals for projects that advance capabilities in fields such as plant-microbe interactions, microbes involved in carbon capture and greenhouse gas emission, and metagenomics—the characterization of complex collections of microbes from particular environmental niches. The total allocation for the coming year’s CSP portfolio will exceed 30 trillion bases (terabases or Tb), a 100-fold increase compared with just two years ago, when just a third of a terabase was allocated to more than 70 projects. This amounts to the equivalent of at least 10,000 human genomes in data …’ Read more


Photo:  The boreal forest, one of the ecosystem investigated by the CSP 2012 program. Denali Natl Park, Alaska  (© F Martin)

A lovely fungus

October 12th, 2011

Annegret and Yohann took this photo of our favorite ectomycorrhizal fungus Laccaria bicolor (strain S238N) fruiting near its poplar host. Its whithish mycelium is seen growing on ectomycorrhizal roots.

Image: Fruiting body of Laccaria bicolor S238N (© INRA: A Kohler & Y Daguerre).


September 22nd, 2011


First Mutualist Effector, the Laccaria MiSSP7

July 14th, 2011

Great day!!! Our paper on the first secreted effector from a symbiotic ectomycorrhizal fungus, Laccaria bicolor is available online at Current Biology New Articles.

As you know, tree roots form a nutrient-acquiring, ectomycorrhizal mutualistic symbiosis with soilborne fungi.  Symbiosis development requires a cross-talk involving signals and unknown proteins.  In this paper, we present MiSSP7, a symbiosis-upregulated gene from the ectomycorrhizal fungus L. bicolor that is indispensable for development of symbiosis.  MiSSP7 is secreted by the fungus, imported into the plant cell via endocytosis due to an RXLR-like motif that binds plant PI-3-P, targeted to plant nuclei of compatible host root cells where it alters the transcriptomic fate of the plant cell.  L. bicolor transformants with severely reduced expression of MiSSP7 do not enter into symbioses with poplar roots.  We conclude that MiSSP7 is a genuine symbiotic effector protein and this provides unparalleled opportunities to determine how ectomycorrhizal fungi manipulate their hosts to establish symbioses.

Coincidentally, Natalia Requena and her colleagues from the Karlsruhe Institute of Technology (KIT) also publish in Current Biology New Articles the first report of an arbuscular mycorrhizal fungal effector, SP7. The symbiont Glomus intraradices also secretes a protein that interacts with the pathogenesis-related transcription factor ERF19 in the plant nucleus, contributing to develop the biotrophic status of arbuscular mycorrhizal fungi in roots by counteracting the plant immune program.

These very cool findings call into question the very nature of the mycorrhizal mutualistic relationships; perhaps it is very similar to some pathogenic interactions. They use effectors to live in ‘‘pretend harmony’’ with their host.

Our work on MiSSP7 benefited tremendously from a very efficient collaboration with Brett Tyler and Shiv Kale at Virginia Tech and Ale Pardo and Minna Kemppainen at Quilmes University in Argentina.

Kloppholz S, Kuhn H, Requena N (2011) A Secreted Fungal Effector of Glomus intraradices Promotes Symbiotic Biotrophy. Current Biology, 10.1016/j.cub.2011.06.044.
Plett JM, Kemppainen M, Kale SD, Kohler A, Legué V, Brun A, Tyler BM, Pardo AG, Martin F (2011) A Secreted Effector Protein of Laccaria bicolor Is Required for Symbiosis Development. Current Biology, 10.1016/j.cub.2011.05.033.

Photo: MiSSP7 immunolocalisation in poplar ectomycorrhiza. © JM Plett – INRA.



Surviving the Ant Gut

March 12th, 2011

leaf-cutting-ant-1403Leaf-cutting ants of the genera Acromyrmex and Atta (Family Formicidae: Subfamily Myrmicinae: Tribe Attini) live in mutualistic symbiosis with the basidiomycete Leucocoprinus gongylophorus (Agaricaceae). The ants cultivate the mycobiont mycelium in ‘fungal gardens’ where they brought freshly cut and chew leaves. They apply fecal droplets to the leaf pulp before depositing this mixed substrate to the top of the garden. The fecal fluid contains a large range of hydrolytic enzymes (proteases, pectinases, carbohydrate degrading enzymes) able to efficiently degrade the plant cell wall and cell material. Released carbohydrates serve as a primary source of nutrient for the fungus which then differenciate clusters of a unique tissular structure so-called the ‘gongylidia‘. This massive hyphal swelling are the main food source of the farming leaf-cutting ants. In ant agriculture,the attine ants actively propagate, nurture and defend the basidiomycete cultivar. This mutualistic symbiosis is thought to have originated in the basin of the Amazon rainforest some 50–65 million years ago. The molecular mechanisms driving this ant-fungus mutualism are poorly know.

In their study published in BMC Biology, Schiøtt et al. showed that the pectinolytic enzymes present in the ant fecal droplets are produced by the fungus. The genes encoding the hydrolytic enzymes are  induced in the gongylidia mycelium, ingested by the feeding ants, transported throughout the ant gut before being released in fecal fluids on the top of the fungal garden. It is suggested by the authors that the fungal enzymes evolved to survive the harsh conditions of the ant gut. The on-going sequencing of the genome of Leucocoprinus gongylophorus will undoubtly provide novel insights on the evolution from saprotrophism to this unique mutualistic symbiosis.


Figure by Schiøtt et al. BMC Biology 2010 8:156   doi:10.1186/1741-7007-8-156

Schiøtt et al. (2010 Leaf-cutting ant fungi produce cell wall degrading pectinase complexes reminiscent of phytopathogenic fungi. BMC Biology 2010, 8:156

Recommended reading: Fungus-Ant mutualism

Photo: ©,59,AN.html

MPMI 2011 in Kyoto

February 20th, 2011

mpmiThe XV International Congress on Molecular Plant-Microbe Interactions will take place in Kyoto (Japan) from August 2 to 6, 2011.

The MPMPI meeting is recognized as one of the most important international meetings for those working on plant-microbe interactions. Through plenary lectures, concurrent sessions, special workshops and various events, attendees experience innovative plant-microbe interactions research.

Plenary Sessions (speakers and topics) are now Online.

Abstract submission is open.

Early Registration is also open.

Sighting the Past Symbiosis

December 4th, 2010

428px-Haeckel_Hepaticae“Early plant life attempting to colonize land from marine environments would have encountered a very hostile environment. Heat and high levels of atmospheric carbon dioxide and a substrate poor in bio-available nutrients, would have been huge stresses upon organisms adapted to aqueous environments. Some fungi colonizing land at the same time developed the ability to form symbiotic relationships with early plant protostele/roots.  As with their modern day representatives, fungi grew in the thin soil substrate as spreading colonies of filamentous hyphae prospecting for nutrients, minerals and water.  If fungal symbiosis worked then as it does today, it is assumed that early plants gained nutrients and water from their fungal partner for growth in return for photosynthetically derived carbon.

The most ancient evidence of such a symbiosis, with fungal hyphae resembling the Glomus genus, has been dated to 460 million years ago (Mya) from Ordovician rocks in Wisconsin and in the Rhynie Chert flora.  This fossil record continues through the Carboniferous period in the roots of gymnosperms through to the Triassic period in Antarctica fossil beds.  The presumed symbiotic structures, where the fungal hyphae and the plant roots form a common tissue, have been classified roots infected with arbuscular mycorrhizal (AM) fungi.  It is likely that this plant-fungal symbiosis would have been key in the establishment of plants on land.”*

One way to confirm this paleobotanical speculation is to study the interactions between AMF and actual lower plants. In the 2 November online issue of Nature Communications, Humphreys et al. published a study of mutualistic mycorrhiza-like symbiosis in the most ancient extant clade of land plants, the thalloid liverwort (Marchantiophyta). They showed that colonization of this lower plant with AMF significantly promotes photosynthetic carbon uptake, growth and asexual reproduction. The host plant fitness increased thanks to AMF-enhanced uptake of phosphorus and nitrogen from soil. A simulated CO2-rich atmosphere, similar to that of the Palaeozoic when land plants originated, significantly amplified the net benefits of the symbiosis and likely selection pressures for establishment of the symbiosis. This study is providing the needed functional evidence supporting AMF symbionts as drivers of plant terrestrialisation in early Palaeozoic land ecosystems.

Claire P. Humphreys, Peter J. Franks, Mark Rees, Martin I. Bidartondo, Jonathan R. Leake & David J. Beerling (2010) Mutualistic mycorrhiza-like symbiosis in the most ancient group of land plants. Nature Communications 1, 103 doi:10.1038/ncomms1105.

* from: Plett JM & Martin F. Molecular Interactions in Mycorrhizal Development. In Plant-fungal interactions (Southworth D, ed.), Wiley Blackwell, in press.

Image: Haeckel Hepaticae © Wikimedia Commons.

100 Rhizobium Genomes

November 28th, 2010


A joint venture has been established between the Centre for Rhizobium Studies (CRS) led by Dr Wayne Reeve at Murdoch University (Australia) and the Joint Genome Institute (JGI, USA) led by the Head of the Microbial Program Dr Nikos Kyrpides to completely decipher the genetic code for 100 geographically distinct root nodule rhizobial strains.’

Wayne Reeve will coordinate the activities of this GEBA-RNB (Genome Encyclopedia of Bacteria and Archaea-Root Nodule Bacteria) project consisting of an international consortium of 32 scientists from 15 different countries.

Mycorrhiza 25 Genomes project approved

September 22nd, 2010

IMG_7095I am glad to report that our proposals ‘ Exploring the Genome Diversity of Mycorrhizal Fungi to Understand the Evolution and Functioning of Symbiosis in Woody Shrubs and Trees ‘ and ‘Community proposal to sequence a diverse assemblage of saprotrophic Basidiomycota (Agaricomycotina) ‘ to JGI’s Community Sequencing Program was approved for sequencing this cycle. This is extremely exciting, because it means that sometime between this Fall and next Summer we will have a large set of new mycorrhizal and  saprotrophic Agaricomycotina genomes, followed later in 2011-12 by another set of genomes. By the end of 2011, we should be able to mine and compare 50 novel symbiotic and saprotrophic  genomes.

As of this writing, JGI 454 and Illumina machines are busily churning out DNA from Hebeloma cylindrosporum, Piloderma croceum, Cenococcum geophilum, Pisolithus tinctorius and P. microcarpus.  Amanita muscaria, Boletus edulis, Laccaria amethystina, Lactarius quietus, Paxillus rubicundulus, Suillus luteus, and Sebacina vermifera will soon be queuing for sequencing.

Photo: The Fly Agaric, Amanita muscaria © F Martin

Living Stones

August 29th, 2010

Villaron - pierre colorée de lichens

Together with the mycorrhizal symbiosis, the lichen symbiosis has fascinated biologists for decades.

Lichens are composite organisms consisting of a fungus (the mycobiont) interacting with a photosynthetic partner (the photobiont), an algae or a cyanobacterium, to form a mutualistic interaction. These chimeric organisms are found in most ecosystems, including in some of the most extreme environments — deserts, rocky coasts, mountains, artic tundra, … . They are also abundant as epiphytes on trees, on bare rocks, such as walls, benches and tombstones. The morphology and physiology of lichens are very different from those of the free-living fungi and algae, but very little is known on the signals, genes and proteins involved in the complex symbiotic interactions.

The genomes of two ectomycorrhizal symbionts, the basidiomycete Laccaria bicolor and the ascomycete Tuber melanosporum, are now available to study the evolution of fungal symbiosis. No lichen genome was available to date to investigate how this other major fungal symbiosis evolved. This is thus great to see that the 36-Mb genome of the lichen Cladonia grayi has been sequenced (by 454 and Illumina). C. grayi is a member of the Cladoniaceae, a well-studied world-wide family of stalked-cup lichens classified within the Lecanoromycetes, a class that includes more than 70% of the lichen-forming fungal diversity. The 60 Mb genome of the Asterochloris photobiont associated with C. grayi has also been sequenced. Asterochloris sp. a single celled member of the largest family of lichen-forming green algae, the Trebouxiaceae.

We are excited to be part of the Cladonia Genome Consortium leaded by Daniele Armaleo and François Lutzoni (Duke University).

Photo: A lichen community on a stone wall in the Villaron hamlet (Haute-Maurienne, France). © F Martin

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)

A Virus in a Fungus in a Plant

August 8th, 2010

YNPFor those interested by plant endophytes (see previous post on poplar endophytes), get back to Márquez’s paper published in Science in 2007. The authors showed that mutualistic association between the fungal endophyte Curvularia protuberata and its host plant, the tropical panic grass from geothermal soils Dichanthelium lanuginosum allows both organisms to grow at high soil temperatures (65°C) in Yellowstone National Park. This stress tolerance requires the presence of a dsRNA  virus colonizing the fungal endophyte. Fungal isolates cured of the virus are unable to confer heat tolerance, but heat tolerance is restored after the virus is reintroduced. The virus-infected fungus confers heat tolerance not only to its native monocot host but also to a eudicot host, which suggests that the underlying mechanism involves pathways conserved between these two groups of plants.

Recently, complex tripartite symbioses have also been found among arthropods, bacteria, and mutualistic bacteriophages.

Márquez LM, Redman RS, Rodriguez RJ, Roossinck MJ (2007) A Virus in a Fungus in a Plant: Three-Way Symbiosis Required for Thermal Tolerance. Science 315, 513 – 515.

Photo: ©

25 Mycorrhiza Genomes

May 13th, 2010

Exploring the Genome Diversity of Mycorrhizal Fungi to Unearth Symbiosis Evolution

TintinBy the end of May, we will submit a proposal to the JGI Community Sequencing Program 2011 for whole-genome shotgun sequencing and deep transcriptomics of 25 symbiotic mycorrhizal fungi aiming to develop a phylogeny-driven genomic encyclopedia of symbiotic fungi. This project will be developed under the umbrella of the JGI Fungal Genomics Program initiated in October 2009.

The analysis of the Laccaria bicolor and Tuber melanosporum genomes emphasized the importance of having sequence data for more than one representative of each phylum of ECM fungi. As today, only a few ECM species were targeted for genome sequencing because of an interest in a specific characteristic of the organism. The model species nominated by the ECM symbiosis community are Paxillus involutus (CSP 2008), Rhizopogon salebrosus (CSP 2009), and Pisolithus tinctorius and P. microcarpus (CSP 2010). They belong to the Boletales, a large phylum of symbiotic basidiomycetes. None of the sequence has been released yet.

In addition to the on-going sequencing of Pisolithus species, we now propose a two-year project to sequence the 23 following reference genomes for basidiomycetous and ascomycetous mycorrhizal fungi. These species have been selected based on their ecological and phylogenetic importance, ability to establish different types of mycorrhizal symbiosis, and the avalaibility of HMW DNA:

JGI Fungal Genome Programme (MycoCosm): The ascomycetous Cenococcum geophilum (Dothideomycetes) and basidiomycetous Hebeloma cylindrosporum (Agaricales, Cortinariaceae) ectomycorrhizal fungi have been selected within the JGI Fungal Genome Programme in October 2009. As of this writing, DNA has been extracted and shipped to JGI for sequencing.

Tier 1 [11 species]

Basidiomycotina: Amanita muscaria (Agaricales; Amanitaceae), Laccaria amethystina (Agaricales; Hydnangiaceae), Lactarius quietus (Russulales, oak-specific symbiont), Paxillus rubicundulus (Boletales, Paxilineae, alder-specific), Piloderma croceum (Atheliales), Suillus luteus (Boletales, Suillineae), Scleroderma citrinum (Boletales, Sclerodermataceae), Thelephora terrestris (Thelephorales), Sebacina vermifera (Sebacinales).

AscomycotinaMeliniomyces bicolor (Helotiales, forms both ericoid mycorrhizas and ectomycorrhizas), Rhizoscyphus ericeae (Helotiales, ericoid mycorrhizal fungus), Terfezia boudieri (Pezizales, Pezizaceae; forms both endo- and ectomycorrhizas).

Tier 2 [10 species]

Basidiomycotina: Boletus edulis (Boletales, Boletineae), Cantharellus cibarius (Cantharellales), Corticia cinnamomea (Hymenochaetales), Cortinarius glaucopus (Agaricales; Cortinariaceae), Gymnomyces xanthosporus (Russulales), Ramaria formosa (Gomphales), Tomentella sublilacina (Thelephorales), Tricholoma matsutake (Agaricales; Tricholomataceae), Tulasnella calospora (Cantharellales; Tulasnellaceae).

AscomycotinaMeliniomyces variabilis (Helotiales, root endophyte)

The Tier 1 taxa are proposed for sequencing in 2010. If sequencing capacity exists, Tier 2 taxa could be sequenced in 2011.

The proposed taxa include representatives of the major clades (orders or subclasses) of culturable Mycotina that contain mycorrhizal taxa. This phylogenetically based sample of the genomes that we propose would propel the field forward and allow us to answer fundamental questions about the evolution of this mutualism and the variation in function and interaction across the phylogenetic depth occupied by these organisms. The fact that mycorrhizal fungi appear to be independently derived from multiple saprobic lineages means that genomic data will provide independent assessments of what is required to become ectomycorrhizal. This initiative would be complementary to the project aiming to sequence the genome of the lignocellulose-degrading basidiomycetes submitted by Hibbett, Cullen, Eastwood and Martin to CSP2011.

Community Interest

The proposed genome sequences will be of great interest to diverse scientists with interests in 1) development and evolution of the mycorrhizal symbiosis; 2) carbon cycling and carbon sequestration in terrestrial ecosystems; 3) diverse aspects of fungal molecular biology; 4) molecular ecology of communities of mycorrhizal fungi; 5) plant health and domesticated bioenergy trees; 6) fungal phylogenetics; and 7) evolution of terrestrial ecosystems.

If you are interested by joining this exciting project and/or willing to provide a letter of support for this proposal, contact me.