Ecological diversification without genomic reorganization: repeat dynamics and regulatory evolution in Metarhizium robertsii

How can closely related organisms occupy distinct ecological niches without extensive genomic reorganization? We addressed this question by comparing eight strains of the entomopathogenic fungus Metarhizium robertsii that span a shallow phylogenetic gradient yet exhibit striking differences in virulence, plant associations, and metabolic capabilities. Despite nucleotide identity exceeding 98.5% and extensive macrosynteny, these strains showed pronounced variation in repeat-rich genomic regions: synteny gaps were twofold enriched near chromosome ends, transposable element loads varied from less than 3% to over 13% across strains diverging within ∼0.3 million years, and repeat-induced point mutation signatures tracked TE activity rather than phylogenetic distance. Notably, repeat expansion occurs through diverse spatial mechanisms rather than being uniformly concentrated in chromosome-terminal regions. In contrast, core functional repertoires, proteases, carbohydrate-active enzymes, developmental regulators, and most secondary metabolite biosynthetic genes, were highly conserved, with phenotypic differences in virulence and secondary metabolism arising primarily from regulatory divergence and local structural variation rather than gene presence or absence. Metabolic specialization similarly reflected functional repurposing within a conserved enzymatic framework: loss of processive cellulases alongside enrichment of oxidative auxiliary activity enzymes produced a profile convergent with brown-rot fungi but adapted for insect-associated and rhizosphere niches. These results support a hierarchical model of ecological diversification in which diverse repeat expansion mechanisms, TE dynamics, and regulatory innovation operate as coupled axes of localized genomic change within an otherwise constrained genomic framework, reconciling rapid niche differentiation with strong structural conservation and suggesting a general mechanism for intraspecific adaptation in complex eukaryotic microbes.