Towards a Phylogenomic Framework for the Fusarium oxysporum Species Complex

The Fusarium oxysporum species complex (FOSC) is a genetically diverse and globally distributed group of fungi that includes both pathogenic and non-pathogenic lineages with broad host ranges and major agricultural importance. To provide a higher-resolution view of its diversity and evolutionary history, we assembled and quality-filtered genomes, generating a curated dataset of 336 high-quality assemblies complemented by seven NCBI reference genomes (total 343). Orthology inference recovered 4286 conserved single-copy coding sequences, which resolved evolutionary relationships across the complex with high confidence. This framework recognizes three major clades, resolves several taxonomic inconsistencies, and delineates phylogenomic boundaries among distinct lineages. Despite overall nucleotide identities exceeding 96%, whole-genome comparisons consistently supported the existence of distinct species lineages. Within Clade 2, we identified two previously unrecognized lineages: the Fusarium “afroindicum” clade, distributed across Africa and Asia, and the Fusarium “europaeum” clade, restricted to Europe. Both lineages are genetically coherent, ecologically distinct, and strongly supported by phylogenomic evidence. Finally, a global metadata survey revealed that Fusarium fabacearum—rather than F. oxysporum sensu stricto—is the most widespread and host-diverse member of the complex. Collectively, this large-scale assembly effort and comprehensive phylogenomic framework provide the most robust evolutionary context to date for the FOSC and shed light on its global diversity and ecological breadth.