Comparative genomics of Sympodiorosea identifies genome evolution mediated through selective pressure on the metabolic gene repertoire

Abstract Biological interactions involving host-associated fungi are driven by chemistry shaped over evolutionary time. For antagonistic fungi, specialization often involves acquiring genes for novel secretions—including proteins and specialized metabolites—that mediate nutrient acquisition and host defense interactions. Here, we conducted a phylogenomic investigation of Sympodiorosea, ascomycetes commonly found in basal fungus-growing ant gardens. While Sympodiorosea and related genera (Escovopsis, Luteomyces, Manidigitorum, Escovopsioides) are canonically viewed as virulent mycoparasites, non-virulent species may also emerge within these attine-associated fungi. We explored genomic variation in Sympodiorosea to assess potential alternative lifestyles, focusing on the diversity and evolution of metabolic genes. Our study revealed a constrained selective landscape across the Sympodiorosea genome. However, outcomes of in vitro host interactions were diverse and predictable based on the antagonist's ant-species-of-origin, suggesting functional diversification. Phylogenomics indicated that gene gain/loss events in carbohydrate-active enzymes and specialized metabolism drive this diversification. Although selection acts intensely on metabolism-related genes overall, specific metabolic genes experience diversifying selection, indicating their critical role in host associations. Furthermore, Sympodiorosea exhibits protease gene expansions and contractions discordant with a strictly mycoparasitic lifestyle, suggesting either an alternative lifestyle within ant gardens or recent evolution from other niches. These results provide novel insights into fungal genome evolution and the chemistry of the fungus-growing ant symbiosis.