Archive for February, 2013

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).