Genome reshaping by Helitron transposons in Fusarium oxysporum TR4 affects secondary metabolism but not virulence

Transposable elements (TEs) are significant drivers of genome evolution, influencing the genome dynamics of clonal fungal pathogens such as those in the Fusarium oxysporum species complex (FOSC) that cause Fusarium wilt in over 100 plant hosts. Among these, Tropical Race 4 (TR4), a clonal lineage within the FOSC, poses a severe threat to global banana production. However, the contribution of TEs to genome variation and functional traits in TR4 remains poorly understood. Here, we investigated Helitron-associated structural variations in a TR4 strain from Mozambique (M1). This revealed two large deletions in core chromosomes associated with an active FoHeli1 Helitron transposon. One of these (464 kb) disrupted 151 genes, including the entire fusaric acid (FA) biosynthetic gene cluster, consequently abolishing FA production, altering secondary metabolite profiles, and increasing sensitivity to exogenous FA. Despite these metabolic changes, infection assays using wild-type, mutant, knock-out, and complemented strains demonstrated that FA production is dispensable for TR4 virulence in banana. Our study highlights the role of FoHeli1 in modulating the genetic and metabolic landscape of TR4, underscoring the broader impact of TEs on fungal genome evolution and functional diversification, especially in clonal lineages.