Sheng, HuiyuMetarhizium fungi are a keystone genus of soil-inhabiting ascomycetes providing essential ecosystem services as saprotrophs, plant symbionts and insect pathogens, among other roles. Recent studies have looked at how Metarhizium niches have evolved and shaped genome evolution over large time scales within the Metarhizium genus. This dissertation uses Metarhizium robertsii (M. robertsii) as a model to explore the evolution of its dual roles as an entomopathogen and endophyte by examining phenotypic and genomic differences among eight closely related strains. The study found that early diverged strains, characterized by slow germination on insect cuticles, low virulence, and extensive sporulation, exhibit a biotrophic lifestyle, systemically colonizing living hosts. In contrast, recently diverged strains exhibited rapid germination, high virulence, and reduced sporulation, indicating a shift towards a necrotrophic lifestyle. The study highlighted the influence of host immune responses in shaping M. robertsii-insect interactions, and showed that strong insect virulence correlated with better colonization of plant roots. Comparative genomics revealed that recently diverged strains expanded a small number of gene families related to gene expression as well as carbohydrate-degrading enzymes and proteases enhancing metabolic capabilities, insect virulence, and endophytic potential. Some early diverged strains exhibited high Repeat-Induced Point mutation activity, suggesting cryptic sexual reproduction in their evolutionary past. Overall, M. robertsii strains maintained a conserved genome with similar protein family sizes, with differences in gene expression patterns driving their varied lifestyles. This research provides new insights into M. robertsii’s recent co-evolution with plants and insects, highlighting the importance of understanding the ecological and evolutionary dynamics of these interactions for optimizing its use in sustainable agriculture.enDissertationEntomologyMicrobiologyBioinformaticscomparative genomicsevolutionhost-pathogen interactionsMetarhiziumplant endophytes