Experimental evolution of the fungal pathogen Fusarium oxysporum

Natural selection is a fundamental evolutionary process that acts on changes in a genome and results in the adaptation of an organism. Genome changes range from single nucleotide polymorphism (SNPs), small insertion/deletion, segmental duplication, chromosomal rearrangement, to whole genome duplication. How do these different changes influence the evolutionary processes under different selection pressure? To explore answers to these questions, this study takes an experimental approach to observe evolving processes using a model organism Fusarium oxysporum, a highly adaptive species complex containing the mobile and lineage-specific (LS) chromosomes that are rich for transposons and determines host-specific pathogenicity. The same starting population (F. oxysporum f. sp. lycopersici strain 4287, a tomato pathogenic isolate) was passaged ten times through three distinct serial transfers in: its host, on rich media plates, or on minimal media plates. We have sequenced 5 evolved populations from each serial transfer at the end of the experiment. Comparative genomics revealed the presence of segmental duplications and deletions on parts of LS regions, confirming the highly dynamic nature of the F. oxysporum genome. Interestingly, the populations that evolved in rich media tended to lose parts of or entire LS chromosomes, suggesting the dispensable nature and energy cost associated with these chromosomes when growing on rich medium. We observed few SNPs which can explain most of the phenotypic changes. These results highlight that different evolutionary constraints determine the outcome when populations are adapting to different environments.