Genomic evolution and diversity in Botryosphaeriales: insights from pan-genomic and population genetic analyses of representative species

The fungal order Botryosphaeriales includes numerous ecologically and economically important plant-associated taxa, yet its genomic diversity and evolutionary mechanisms remain poorly understood. Here, we present high-quality de novo genome assemblies for three representative species—Botryosphaeria dothidea, Neofusicoccum parvum, and Phyllosticta capitalensis—and perform integrative analyses using comparative genomics, population genetics, and pan-genome frameworks. Pathogenic species (B. dothidea and N. parvum) exhibit significant expansions in gene families related to membrane transport and metabolism, suggesting enhanced adaptability and virulence potential. Selective sweep analyses highlight population-level divergence in metabolic and stress-response pathways, reflecting natural selection in host and environmental adaptation. Cross-species pan-genome comparisons of six Phyllosticta species reveal a conserved core genome, dynamic gene family turnover, and extensive horizontal gene transfer from bacterial, and archaeal sources—potentially driving ecological diversification. Furthermore, effector proteins display striking domain variation across genera, particularly in regions associated with host cell wall targeting, indicating convergent strategies for host adaptation. Together, these findings provide comprehensive insights into the genomic evolution, adaptation, and virulence mechanisms of Botryosphaeriales fungi, laying a foundation for future studies on plant–fungal interactions.