Evolution of fruiting body forms in the mushroom-forming Fungi (Agaricomycetes): a comparative phylogenetic, phylogenomic, and developmental approach

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Fungi represent a major group of organisms that have profound economic and ecological impacts as decayers, pathogens (of plants and animals, including humans), and mutualists. Fungi are important sources of industrial bioproducts (antibiotics and enzymes) and they are critical to the fermentation industry, including biofuel production. However, much of the basic biology of fungi remains unknown, including knowledge on how fungi develop. This project will address the historical patterns and genetic mechanisms of developmental and morphological evolution in Agaricomycetes, which is a large group of fungi that includes gilled mushrooms, polypores, puffballs, and other complex forms. The results of this research will provide baseline information on the mechanisms of fungal development, as well as gene regulation and other processes of general significance for basic and applied fungal biology. This project will provide training for a PhD student, a Postdoctoral Fellow, and undergraduates. Education and outreach activities will make connections between art and science. Undergraduates with interests in art and science will engage in joint classes that develop observational skills and raise awareness about fungal biodiversity. The project will also create educational posters appropriate for high school students that illustrate fungal biology and general evolutionary principles. Posters and associated lesson plans will be made available for free download on a project web site and will be distributed through workshops at professional conferences for science educators.Gene sequences for thousands of Agaricomycetes are available and complete genomes are available for over 90 species and increasing. However, these data have not been combined and queried to understand processes of fungal developmental evolution. The proposed research includes (1) macroevolutionary analyses, (2) phylogenomic analyses, and (3) developmental analyses. Macroevolutionary analyses will employ large-scale phylogenies (up to ca. 4000 terminals), drawing on publicly available data. Comparative methods will be used to perform ancestral state reconstruction, address directional trends, and test key innovation hypotheses. Phylogenomic analyses will identify shifts in copy number in gene families, such as transcription factors, hydrophobins, lectins and cell wall biogenesis enzymes, that may be correlated with evolution of complex forms. Developmental analyses will focus on Lentinus tigrinus, typically a gilled mushroom, but there is also a puffball-like "secotioid" form that is conferred by a recessive allele at a single locus (Sec). Two genome sequencs of L. tigrinus are available, one carrying the Sec+ allele and the other with the recessive sec allele. Bulk segregant analysis will be used to determine the identity of the secotioid locus. Pileus induction in L. tigrinus requires light and transcriptomic analyses will be used to compare gene expression patterns in vegetative mycelium and fruiting bodies produced in light or in darkness.