Exploring the Genome Diversity of Mycorrhizal Fungi to Unearth Symbiosis Evolution
By 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).
Ascomycotina: Meliniomyces 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).
Ascomycotina: Meliniomyces 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.
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.