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Transposons and accessory genes drive adaptation in a clonally evolving fungal pathogen

Summary

Researchers studied how a fungal plant pathogen called Fusarium oxysporum rapidly adapts to new environments by analyzing genetic changes during repeated passages through tomato plants and laboratory media. They discovered that jumping genes (transposons) were responsible for most mutations driving adaptation, and surprisingly found that genes located in specialized ‘accessory’ regions of the fungus’s genome controlled important functions like growth and virulence. This research reveals how fungal pathogens can evolve quickly to become better competitors or invaders.

Background

Fungal pathogens with compartmentalized genomes containing conserved core regions and lineage-specific accessory regions (ARs) display remarkable adaptive plasticity. Transposable elements (TEs) and ARs are theoretically thought to promote pathogen adaptation, but direct experimental evidence supporting this role has been limited.

Objective

To investigate the mechanisms underlying rapid adaptation in the clonally evolving fungal pathogen Fusarium oxysporum using experimental evolution and genome resequencing to determine the relative roles of transposons and accessory genes in environmental adaptation.

Results

Transposon insertions accounted for over 70% of mutations in evolved lines, with a single non-autonomous MITE (Hormin) responsible for 63% of all detected mutations. TE insertions preferentially targeted accessory regions marked by H3K27me3 histone modifications. Adaptive mutations in accessory genes substantially impacted core fungal functions including growth, development, quorum sensing, and virulence.

Conclusion

Transposons and accessory regions serve as primary drivers of rapid adaptation in clonally evolving F. oxysporum. The study demonstrates that accessory genes, previously thought to function mainly in host-specific interactions, play unexpected roles in conserved fungal processes, revealing a two-speed genome mechanism for evolutionary adaptation.
  • Published in:Nature Communications,
  • Study Type:Experimental Evolution Study,
  • Source: 10.1038/s41467-025-62213-y, PMID: 40739135
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