- An increased understanding of secondary metabolism in fungi is important for both biological and societal reasons. The ascomycete genus, Tolypocladium, is an ideal system to explore secondary metabolism characterization, ecology, evolution and regulation. The genus produces and has the genomic potential to produce a wide array of metabolites. Paired with the ecological diversity of the genus, which includes endophytes, entomopathogens, mycoparasites, and endolichenic species, questions can be asked not only about the diversity and regulation of secondary metabolites, but also how this diversity has evolved in the context of speciation and associated ecologies. This dissertation employs a multidisciplinary approach to explore these questions. Chapter two focuses on the distribution and evolution of the simA biosynthetic gene cluster, which produces cyclosporin. Within Tolypocladium, homologs of the core gene of the simA gene cluster, a large multimodular non-ribosomal peptide synthetase, is only found in one well-supported clade which contains the insect pathogen, T. inflatum, as well as several species that were isolated from soil. Within this clade, there is a pattern of loss that
begins with the loss of cyclosporin production (or phenotype) and is followed by loss of genotype which is seen by the degradation and eventual loss of the cluster. In a larger survey of the Hypocreales, a simA homolog was also found in Neocosmospora, with some similarities is cluster composition. Inconsistencies between the species tree and gene three for simA suggest that this disparate distribution of simA is more likely to be a result of horizontal gene transfer than a complex series of loss and gains. Chapter three proposes a method of mass culturing to further characterize the secondary metabolome of T. inflatum and to link secondary metabolite genotype to phenotype. By culturing T. inflatum on an array of media that differ by amino acid composition, we influence the expression of the T. inflatum genome with a greater impact of secondary metabolite genes. Through use of RNAseq and LC-MS/MS, we propose a biosynthetic gene cluster for a lipopeptaibol previously isolated from T. geodes and identify further clusters for future elucidation. Chapter four investigates the function of kmt6, a global epigenetic regulatory gene, and its impact on secondary metabolite expression and production in T. inflatum. There exists a general pattern of genetic upregulation, particularly at the ends of assembled unitigs, which represent near-chromosomal level assemblies, in a kmt6 deletion strain. These patterns however, are condition dependent and are altered as a function of environment. In all conditions, several identified secondary metabolites are downregulated in expression and production. This dissertation will add to our current knowledge of secondary metabolism in Tolypocladium and identify steps for further characterization.