Gap-free comparative genomics uncover virulence factors for Fusarium wilt of watermelons

Watermelon (Citrullus lanatus L.) is a globally important fruit crop, yet it is susceptible to devastating diseases such as vascular wilt caused by Fusarium oxysporum f. sp. niveum (Fon), with limited control options. Fon rapidly evolves to overcome host resistance, constantly threatening production through new pathogenic races. High-quality genomic resources are key to understanding the molecular mechanisms underlying Fon virulence evolution for disease management. Here, we de novo assembled and annotated gapless genomes of three isolates affiliated with different physiological races of Fon (race 1, 2, and 3), and dissected the mechanisms behind their distinctive virulence through comparative genomics and transcriptomics. Core and accessory chromosomes in Fon were identified, where each race-affiliated isolate carried a unique set of accessory chromosomes or regions. Comparative transcriptomics of Fon infection revealed distinctive temporal patterns of gene expression even among core gene families, particularly those related to cell wall degradation enzymes. Effectoromic prediction and comparative analysis in three gap-free genomes identified 13 FonR3-specific effectors (FonR3SEs), one (FonR3SE1) of which was a critical virulence factor of FonR3 on watermelon as demonstrated via functional experiments. These gap-free genome assemblies and FonR3SEs provide valuable resources for studying Fon pathobiology and evolution and improving development of disease control strategies.