Nucleotide substitutions have played an important role in molecular evolution, and understanding their dynamics would contribute to genetic studies. Related research with defined DNA sequences lasted for decades until whole-genome sequencing arose. UV radiation (UVR) can generate base changes and other genetic variations in a short period of time, so it would be more meaningful to explore mutations caused by UVR from a genomic perspective. The monokaryon enoki strain WT583 was selected as the experimental material in this study because it can spontaneously produce large amounts of oidia on PDA plates, and the monokaryons originating from oidia have the same genotype as their mother monokaryon. After exposure to UV radiation, 100 randomly selected mutants, with WT583 as the reference genome, were sent for genome sequencing. BWA, samtools, and GATK software were employed for SNP calling, and the R package CMplot was used to visualize the distribution of the SNPs on the contigs of the reference genome. Furthermore, a k-mer-based method was used to detect DNA fragment deletion. Moreover, the non-synonymous genes were functionally annotated. A total of 3707 single-base substitutions and 228 tandem mutations were analyzed. The immediate adjacent bases showed different effects on the mutation frequencies of adenine and cytosine. For adenine, the overall effects of the immediate 5′-side and 3′-side bases were T > A > C > G and A > T > G > C, respectively; for cytosine, the overall effects of the immediate 5′-side and 3′-side bases were T > C > A > G and C > T > A > G, respectively. Regarding tandem mutations, the mutation frequencies of double-transition, double-transversion, 3′-side transition, and 5′-side transition were 131, 8, 72, and 17, respectively. Transitions at the 3′-side with a high mutation frequency shared a common feature, where they held transversions at the 5′-side of A→T or T→A without covalent bond changes, suggesting that the sequence context of tandem motifs might be related to their mutation frequency. In total, 3707 mutation sites were non-randomly distributed on the contigs of the reference genome. In addition, pyrimidines at the 3′-side of adenine promoted its transversion frequency, and UVR generated DNA fragment deletions over 200 bp with a low frequency in the enoki genome. The functional annotation of the genes with non-synonymous mutation indicated that UVR could produce abundant mutations in a short period of time.

Fungal hydrophobins reduce the surface tension of hyphae so that hyphae can grow into the air. Reduced expression of hydrophobin genes results in abnormal morphogenesis of both hyphae and the fruiting body of Flammulina filiformis. Previous studies showed that filamentous-growth MAPK signaling pathway directly modulates pseudohyphae formation in budding yeast, so we hypothesized that the specific transcription factor in this pathway may also directly regulate the expression of hydrophobin genes in F. filiformis. Downstream of the G protein, the cAMP/PKA signaling pathway is parallel with the filamentous-growth MAPK signaling pathway in regulating the filamentous growth of fungi. Thus, the cAMP addition test was carried out to exclude the involvement of the PKA/cAMP signaling pathway in aerial-hyphae deficiency of the three mutants used in our previous study. Transcriptomic analysis showed common changes in the MAPK signaling pathway of the three mutants, including 6 downregulated and 3 upregulated genes in common. Transcription factor Tec1 was one of the upregulated genes, and it is a pathway-specific transcription factor for filamentous growth. Motif prediction showed that putative binding sites of Tec1 and Ste12 existed in the promoter region of the three chosen hydrophobin genes mentioned in our previous study, and DAP-seq analysis suggested that putative binding sites of Tec1 and Ste12 were located in 10 hydrophobin genes, respectively, and there were 8 in common for both the transcription factors. These results gave suggestive evidence supporting our hypothesis. We have identified a potential regulatory connection between the filamentous-growth MAPK signaling pathway and hydrophobin genes through Tec1 and Ste12. However, functional validation is required to confirm direct regulation between both the transcription factors and the downstream genes.