Research Overview
Research in our lab uses genome-scale data and computational biology to address questions in fungal evolutionary biology. Current and research projects in our lab include:
Basidiobolus – an enigmatic fungus of the reptile and amphibian (herptile) gut microbiome. Basidiobolus is a zygomycetous fungus with a complex life cycle that includes the the herptile gut microbiome, free-living in soil and leaf litter, and an insect dispersal stage. Evolutionary genomic analyses have demonstrated that it has a complex genome comprising 100s of chromosome, complex ploidy and numerous genes that were horizontally transferred from bacteria and that function in secondary metabolism. Community analyses have shown that the genus is a common and dominant fungal component of the herptile gut microbiome and is co-structured with the bacterial gut microbiome community. Our research aims to understand the evolutionary patterns and processes that lead to this ubiquitous, yet enigmatic lineage, and its functional role in the herptile gut microbiome and fungal-bacterial interactions.
1000 Fungal Genomes Project. The 1000 Fungal Genomes (1KFG) project, is supported by the Joint Genome Institute of the Department of Energy. The goal of 1KFG is to facilitate the genomic sampling of species from every family-level clade of fungi. We are interested in numerous questions including primary metabolism of non-Dikarya Fungi and transitions between major fungal ecologies and nutritional modes (e.g., terrestrial vs. marine, saprobe vs. symbiont, etc.). Visit 1000 Fungal Genomes to learn more.
Phylogenomics and secondary metabolism of Cordyceps and Hypocreales. For the better part of 30 years, our lab has worked on systematics of Cordyceps (Hypocreales, Ascomycota) and related insect pathogenic fungi. While we continue to be interested in basic systematics of the group, much of our recent focus is on phylogenomics and secondary metabolism of Cordyceps and Hypocreales and the evolution of ecologies and nutritional modes. These fungi are unique in that they include plant pathogens, symbionts and saprobes, insect pathogens and symbionts, and mycoparasites. We are seeking to understand patterns and processes of genomic evolution and secondary metabolism diversification that function in these ecologies.
Systematics and Population Biology/Ecology of Rhizopogon. Rhizopogon (Boletales) is genus of basidiomycete truffles that are ectomycorrhizal with trees of Pinaceae. Species of the genus are common and ecologically important in the forests of the Pacific Northwest (PNW) and wherever species of Pinaceae grow. Our lab is interested in phylogenetics, community ecology, and population biology of the genus.
Basidiobolus – an enigmatic fungus of the reptile and amphibian (herptile) gut microbiome. Basidiobolus is a zygomycetous fungus with a complex life cycle that includes the the herptile gut microbiome, free-living in soil and leaf litter, and an insect dispersal stage. Evolutionary genomic analyses have demonstrated that it has a complex genome comprising 100s of chromosome, complex ploidy and numerous genes that were horizontally transferred from bacteria and that function in secondary metabolism. Community analyses have shown that the genus is a common and dominant fungal component of the herptile gut microbiome and is co-structured with the bacterial gut microbiome community. Our research aims to understand the evolutionary patterns and processes that lead to this ubiquitous, yet enigmatic lineage, and its functional role in the herptile gut microbiome and fungal-bacterial interactions.
1000 Fungal Genomes Project. The 1000 Fungal Genomes (1KFG) project, is supported by the Joint Genome Institute of the Department of Energy. The goal of 1KFG is to facilitate the genomic sampling of species from every family-level clade of fungi. We are interested in numerous questions including primary metabolism of non-Dikarya Fungi and transitions between major fungal ecologies and nutritional modes (e.g., terrestrial vs. marine, saprobe vs. symbiont, etc.). Visit 1000 Fungal Genomes to learn more.
Phylogenomics and secondary metabolism of Cordyceps and Hypocreales. For the better part of 30 years, our lab has worked on systematics of Cordyceps (Hypocreales, Ascomycota) and related insect pathogenic fungi. While we continue to be interested in basic systematics of the group, much of our recent focus is on phylogenomics and secondary metabolism of Cordyceps and Hypocreales and the evolution of ecologies and nutritional modes. These fungi are unique in that they include plant pathogens, symbionts and saprobes, insect pathogens and symbionts, and mycoparasites. We are seeking to understand patterns and processes of genomic evolution and secondary metabolism diversification that function in these ecologies.
Systematics and Population Biology/Ecology of Rhizopogon. Rhizopogon (Boletales) is genus of basidiomycete truffles that are ectomycorrhizal with trees of Pinaceae. Species of the genus are common and ecologically important in the forests of the Pacific Northwest (PNW) and wherever species of Pinaceae grow. Our lab is interested in phylogenetics, community ecology, and population biology of the genus.
