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Gymnopus earleae
Gymnopus earleae Murrill. Photograph by R. E. Halling, © 1997, at New York Botanical Garden

Within the framework of the CSP 'Metatranscriptomics of Forest Soil Ecosystems' and the 1000 Fungal Genomes (1KFG) project, we are aiming to explore the interaction of forest trees with communities of soil fungi, including saprotrophic soil fungi impacting carbon sequestration in forests and ectomycorrhizal symbionts that dramatically affect tree growth. We are sequencing the genomes of the most abundant fungal species harvested on studied long-term experimental sites to provide sufficient taxonomic coverage of fungal genomes to identify and analyze DNA and RNA samples sequenced from environmental samples.

Gymnopus earleae is a spring mushroom that is common in North America. The species is a decayer (saprotroph) that grows in clumps on soil. Thus, G. earleae navigates a heterogeneous environment including wood and other plant tissues, as well as diverse organisms dwelling in soil and leaf litter. Gymnopus is a gilled mushroom (an “agaric”) that is classified in Omphalotaceae (Agaricales). Other Omphalotaceae genomes hosted in MycoCosm include Gymnopus androsaceus, Gymnopus luxurians, Rhodocollybia butyracea and Omphalotus olearius. The shiitake mushroom, Lentinula edodes, is also in Omphalotaceae. Members of this family are all saprotrophs but they vary in their substrates, including leaf litter, pine needles, and wood. By comparing the genomes of species in Omphalotaceae, it will be possible to understand the mechanistic bases of adaptations of closely related saprotrophic fungi to diverse substrates, including the complex, heterogeneous soil and litter layers of the forest floor.

Researchers who wish to publish analyses using data from unpublished CSP genomes are respectfully required to contact the PI (Dr. Francis Martin) and JGI to avoid potential conflicts on data use and coordinate other publications with the CSP master paper(s).


Halling, R. E. 1983. The genus Collybia (Agaricales) in the Northeastern United States and adjacent Canada," Mycologia Memoirs 8: 1-148.

Halling, R. E. 1997-2009. A revision of Collybia s.l. in the northeastern United States and adjacent Canada. http://www.nybg.org/bsci/res/col/colintro.html

Matheny, P. B., J. M. Curtis, V. Hofstetter, M. C. Aime, J.-M. Moncalvo, Z. W. Ge, Z. L. Yang, J. C. Slot, J. F. Ammirati, T. J. Baroni, N. L. Bougher, K. W. Hughes, D. J. Lodge, R. W. Kerrigan, M. T. Seidl, D. K. Aanen, M. DeNitis, G. M. Daniele, D. E. Desjardin, B. R. Kropp, L. L. Norvell, A. Parker, E. C. Vellinga, R. Vilgalys. and D. S. Hibbett. 2006. Major clades of Agaricales: a multi-locus phylogenetic overview. Mycologia 98: 982-995.

Wilson, A. W., and D. E. Desjardins. 2005. Phylogenetic relationships in the gymnopoid and marasmioid fungi (Basidiomycetes, euagarics clade). Mycologia 97:667-679.