Fruiting body of the ectomycorrhizal basidiomycete Laccaria bicolor S238N interacting with Douglas fir seedlings (© INRA)

Mycorrhizal symbioses—the union of roots and soil fungi—are universal in terrestrial ecosystems and may have been fundamental to land colonization by plants. Boreal, temperate and montane forests all depend on ectomycorrhizae, a mutualistic interaction between a group of soil basidiomycetes and ascomycetes and tree roots. Identification of the primary factors that regulate development and metabolic activity of the symbiosis will therefore open the door to understanding the role of fungal symbioses in plant biology and ecology, allowing the full environmental significance of this symbiosis to be explored.

Laccaria is a cosmopolitan genus of mushrooms (Agaricales) collected frequently throughout North America and Eurasia.  Its taxa make up a sizeable part of the basidiomycetous ectomycorrhizal species and have been reported from every continent. The analysis of the genome sequence of the ectomycorrhizal basidiomycete Laccaria bicolor (Maire) P.D. Orton (common name: bicoloured deceiver) highlighted gene networks involved in rhizosphere colonization and symbiosis development and functioning. This 65-megabase genome assembly contains ~20,000 predicted protein-encoding genes and a very large number of transposons and repeated sequences. Upon ectomycorrhizae development, L. bicolor expresses effector-type small secreted proteins with unknown function, which probably have a decisive role in the establishment of the symbiosis. Symbiosis induces an increased expression of carbohydrate, oligopeptide and amino acid transporters, suggesting increased fluxes of metabolites at the symbiotic interface. The unexpected observation that the genome of L. bicolor lacks carbohydrate-active enzymes involved in degradation of plant cell walls, but maintains the ability to degrade non-plant cell wall polysaccharides, revealed the dual saprotrophic and biotrophic lifestyle of the mycorrhizal fungus that enables it to grow within both soil and living plant roots.

The predicted gene inventory of the L. bicolor genome, therefore, points to previously unknown mechanisms of symbiosis operating in biotrophic mycorrhizal fungi. The availability of this genome provides an unparalleled opportunity to develop a deeper understanding of the processes by which symbionts interact with plants within their ecosystem to perform vital functions in the carbon and nitrogen cycles that are fundamental to sustainable forest productivity. This project is relevant to the DOE mission with regard to plant health.

To fully apply comparative, evolutionary genomics to this symbiotic clade, JGI is currently resequencing the genome of several Laccaria species (L. laccata, L. proxima, L. tortilis) and geographic strains of L. bicolor and L. amethystina.  These sequences will be mapped to the present reference L. bicolor genome.