Within the framework of the JGI Mycorrhizal Genomics Initiative (MGI), we are sequencing a phylogenetically and ecologically diverse suite of mycorrhizal fungi (Basidiomycota and Ascomycota), which include the major clades of symbiotic species associating with trees and woody shrubs. In addition, we are re-sequencing genomes of Laccaria bicolor to get insight into the historical microevolutionary forces driving the genomic evolution of symbiosis-related genes.

The Laccaria Pan-Genome

Laccaria is a cosmopolitan genus of mushrooms (Agaricales, Hydnangiaceae) collected frequently throughout North America and Eurasia. Its taxa make up a sizeable part of the basidiomycetous ectomycorrhizal (ECM) species and have been reported from every continent except Antarctica. Because of the relative ease with which some species of Laccaria can be manipulated in the laboratory, several taxa including L. bicolor, L. laccata and L. proxima are widely used in applied and basic research on ECM fungi, whereas L. amethystina ecology has been investigated in many ecosystems.

The analysis of the genome sequence of the ectomycorrhizal basidiomycete Laccaria bicolor highlighted gene networks involved in rhizosphere colonization and symbiosis development and functioning (Martin et al., 2010). This 61-megabase genome assembly contains ~23,000 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.

Therefore, evolutionary genomics of Laccaria would have applied implications because of the ecological and potential economic importance of many of its taxa in addition to adding to our basic knowledge of fungi which form symbiosis. To fully apply comparative, evolutionary genomics to symbiotic fungi, intragenus and population genome samples are needed. In the Laccaria pan-genome project, we are investigating the interspecific- and intraspecific genome polymorphisms, focusing on the evolution of symbiosis-related genes.

A large collaborative effort led by PI of this project, Francis Martin (INRA), aims for master publication(s) of the MGI data analysis. Researchers who wish to publish analyses using data from unpublished MGI genomes are respectfully required to contact the PI and JGI to avoid potential conflicts on data use and coordinate other publications with the MGI master paper(s).

JGI Laccaria bicolor S238N portal

JGI Laccaria amethystina portal

Publication: The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature. 2008 Mar 6;452(7183):88-92.