Comparative Genomics Reveals Ancient and Unique Pathogenicity Features in Australian <i>Fusarium oxysporum</i> f. sp. <i>vasinfectum</i>
2025
Angel David Popa-Baez | Linda J. Smith | Warwick N. Stiller | Melanie Soliveres | Gunjan Pandey | Christopher A. Saski | Don C. Jones | Iain W. Wilson
<i>Fusarium oxysporum</i> f. sp. <i>vasinfectum</i> (<i>Fov</i>) is a devastating cotton pathogen. Australian <i>Fov</i> strains are distinguished by their ability to infect plants without nematode interaction and are genetically distinct from global <i>Fov</i>, classified into two vegetative compatibility groups (VCG-01111 and VCG-01112). Here, we present chromosome-level genome assemblies of a historical isolate for each Australian <i>Fov</i> VCG. The end-to-end gapless genome assemblies demonstrate high contiguity and completeness, with 97.7% BUSCO completeness for both isolates. Phylogenetic analysis indicates that the Australian <i>Fov</i> lineages diverged from other known <i>Fov</i> genomes over 3.6 million years ago, while VCG-01111 and VCG-01112 separated approximately 1.1 million years ago. Comparative genomics analysis identified four accessory chromosomes unique to the Australian isolates. Functional annotations revealed 14,495 and 15,342 genes in VCG-01111 and VCG-01112, respectively, with accessory chromosomes containing significantly fewer genes than core chromosomes. Ortholog analysis uncovered unique gene clusters enriched in key metabolic pathways, pathogenicity, and cell division processes. Additionally, we identified several novel lineage-specific peptides unique to each Australian isolate. This comprehensive genomic characterization provides the first insights into the unique evolutionary history of Australian <i>Fov</i>, distinguishing them from global <i>Fov</i> races. Our findings lay the foundation for understanding the genetic factors underlying their exceptional virulence, which makes Australian <i>Fov</i> among the most aggressive cotton pathogens worldwide.
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