Posts Tagged ‘mycorrhiza␁Ľ

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 ‚Äėtoolboxes‚Äô 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).

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 onhttp://storify.com/KamounLab/30th-new-phytologist-symposium-immunomodulation-by). Read more …

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).

Biocomplexity of Plant-Fungal Interactions

February 7th, 2012

The book ‘Biocomplexity of Plant-Fungal Interactions‘ edited by Darlene Southworth (Southern Oregon University)¬†has been published. The target audience is botanists who may not have¬†considered¬†the roles that close contacts with fungi play in the life of plants‚ÄĒat¬†the level of the individual or the community. The chapters¬†promote ideas that tell¬†the reader the nature of the interactions and their significance. It includes chapters on endophytes, arbuscular and ectomycorrhizal symbioses, leaf-interacting fungi, ‘sex, diseases and deception’ and soil fungal networks. It looks great (I could be biased as Jonathan and I wrote a chapter on molecular interactions in mycorrhizal development).

You can buy the book on Amazon.com.

Mycorrhizal Genomics Initiative: an Update

January 18th, 2012

I am writing to touch base about our JGI Mycorrhizal Genomics Initiative. As of today, the genome annotations publicly released are those of:

The genome of Piloderma croceum and Tulasnella calospora are in the JGI annotation pipeline and should (hopefully) be available in the coming weeks. Those of Cenococcum geophilum, Sebacina vermifera, and Pisolithus tinctorius are in the final phase of sequencing, but Cenococcum and Pisolithus are difficult (large and polymorphic) genomes and JGI cannot give an estimated date of release.

The transcriptome of free-living mycelium of C. geophilum, H. cylindrosporum, O. maius, P. involutus, P. croceum, P. microcarpus, P. tinctorius, Scleroderma citrinum, Sebacina vermifera and T. calospora are sequenced (RNA-Seq) and a series of dedicated databases are under construction.

Finally, Igor Grigoriev, Joey Spatafora and I would like to invite you to Walnut Creek in mid-March 2012 to participate in several important JGI meetings:

  • Fungal Jamboree (March 19, 2011 8am-8pm) to discuss progress and coordination of large scale initiatives in fungal genomics: (1) Genomic Encyclopedia of Fungi, (2) 1000 fungal genomes, and (3) Fungal model systems and metagenomes (including our Mycorrhizal Genome Initiative).
  • JGI User Meeting (March 20-22, 2012:¬†http://www.jgi.doe.gov/meetings/usermeeting/) and workshops including MycoCosm Tutorial (March 20, afternoon)

You could access our recently opened MycorWeb portal dedicated to this project, Mycorrhizal Genomics Initiative, for links and updates.

A Sweet Deal: Mycoheterotrophy

March 23rd, 2011

neottieIn her latest blog post, ‘Stygian Orchids Sucking on the Broom Bush Roots ‚ÄĒ And Shedding Chloroplast Genes‘, Jennifer Frazer discussed mycoheterotrophy, one of the most fascinating plant-fungus interactions, a ‘m√©nage √† trois’ between a beautiful orchid (here the Western Underground Orchid, Rhizanthella gardneri), its associated mycorrhizal mycelium and their sugar tree provider. In this case, Melaleuca uncinata, the broom bush. The majority of mycoheterotrophic plants studied thus far cheat one of the most widespread mutualisms on earth ‚Äď the mycorrhizal symbiosis. Mycoheterotrophic plants obtain all of their carbon needs through symbiotic associations with fungi, and, while achlorophyllous, they are not directly parasitic on other plants. Mycoheterotrophic orchids use the sugar from associated mycorrhizal fungi, and thus the carbon from nearby autotrophic plants. These ‘intimate’ associations are not only botanical curiosities, but topical biological systems scrutinized¬†by scientists aiming to understand evolution of plants and fungi (Selosse & Cameron, 2010).

Read more … ¬†Virtual Special New Phytologist Issue on Mycoheterotrophy

Photo: The¬†Bird’s-nest Orchid,¬†Neottia nidus-avis (Chantelouve, Vallon de la Malsanne, Oisans) ¬© F Martin

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