Comparative Genomic Analysis of Fusarium oxysporum f. sp. cubense Tropical Race 4 Strains From South America

ABSTRACT

Fusarium wilt, caused by Fusarium oxysporum f. sp. cubense (Foc) Tropical Race 4 (TR4), represents a significant threat to global banana production. This study investigates the genetic diversity and phylogenetic relationships of Foc TR4 populations in South America, crucial for developing effective region‐specific containment and management strategies. We report a genomic analysis that combines sequencing of new Venezuelan isolates with previously sequenced Colombian and Peruvian isolates. A high‐resolution genome‐wide SNP‐based phylogenetic analysis was conducted using 32 Foc genomes. The results show that the Venezuelan isolate VNZ_F3 and Colombian isolates were grouped in the same monophyletic clade with 100% bootstrap support, suggesting they have a shared introduction source or a direct transmission event. This study also confirms at least two distinct incursions of Foc TR4 into South America, with Peruvian isolates forming a separate, genetically distinct clade. Interestingly, Venezuelan isolates VNZ_F29 and VNZ_F32 showed a separated lineage indicating rapid evolutionary divergence within Venezuela. Comparative genomic analysis, visualized in a Circos plot, revealed changes consistent with the SNP‐based phylogeny. Gapped regions, representing missing DNA sequences, were observed, supporting a closer genetic relationship between Colombian and most Venezuelan isolates. This study highlights the usefulness of genomic surveillance to identify genetic changes as Foc TR4 evolves and spreads, helping in the development of targeted quarantine measures.