Genetics of natural product biosynthesis by symbiotic fungi: Various alkaloids and other metabolites produced by plant-symbiotic fungi protect the host plants from insects and other pests, whereas others can negatively affect livestock and wildlife. Some of these natural products are similar or identical to pharmaceuticals. Agricultural and biotechnological uses of both native and introduced grasses can be facilitated by a thorough understanding of their natural product chemistry and the underlying genetics. Complex pathways are often involved, but the genes tend to occur together in genomic segments called clusters. We have identified and completely sequenced numerous such gene clusters and continue to find and analyze others.

Evolution and population genetics of plant-fungus symbiotic systems: The epichloe endophytes are a group of fungi symbiotic with cool-season grasses, to which they provide biological protection from insects and nematodes, as well as improved growth and drought tolerance. The evolution of these endophytes is especially interesting because they are the clearest example of mutualists that have evolved from pathogens. Patterns of evolution tend to differ for endophytes exhibiting different degrees of mutualism. Population-level genetic analysis by high-throughput DNA sequencing helps identify species, elucidate the timing and mechanisms of speciation, and assess the degree to which host evolution affects symbiont evolution and vice versa.

Genomics and functional genomics of endophytic symbionts of grasses: The epichloe endophytes are remarkable for the intimacy of their associations with grass hosts. They pervade the aerial parts of the plant, transmit into new tillers and stolons, and even transmit via seeds to ensure maintenance of the symbioses through thousands of host generations. All the while, the host plants show little or no negative effects, and in most such symbioses the hosts are greatly benefited. We are interested in learning how host and symbiont communicate, how each benefits the other while minimizing negative effects, and how the endophyte can colonize so many different host tissues and thereby manage to persist for successive host generations. The hunt for genes involved is conducted by high-throughput sequencing of mRNAs expressed during colonization of the various host tissues, and on genome sequencing.