Accumulation of the spontaneous and random mutations is causative of fungal culture degeneration

Filamentous fungi frequently degenerate during subculturing, which manifests as the reduction or loss of conidiation, sexuality, secondary metabolite production, and/or virulence against hosts. The underlying mechanism of spontaneous fungal degeneration is still elusive. In this study, the fluffy mycelium-type sector variants formed by three ascomycete fungi were transferred and found to show the typical features of culture degeneration. The variant cells were evidenced with the accumulation of reactive oxygen species (ROS), and the ROS-associated formation of hyphal coils. Genome resequencing of these sector cultures identified substantial random mutation sites in each variant in a trend associated with fungal reproduction style. The high bias towards transversions over transitions was similarly detected in degenerate genomes. Otherwise, a higher number of mutations were accumulated in the intergenic regions of the Metarhizium robertsii and Cordyceps militaris sector genomes, whereas the exonic regions of the Aspergillus nidulans variant genes were detected with a higher mutation rate. Unexpectedly, none of those mutated genes had orthologous relationships among the three sectors, while only a few of them were shared between two fungi. A few transcription factor genes with frameshift mutations in sectors were selected for deletions in parental strains, and the null mutants demonstrated the varied degrees of degenerate phenotypes. In addition to reasoning the causal mechanism of fungal degeneration, our data provide insights to better maintain and monitor fungal culture stability.