Genome-wide comparisons reveal broad variations in intraspecific SNP frequencies among species in Agaricomycetes, Basidiomycota

Background: Genome sequence analyses can provide crucial information for understanding population history, speciation, and taxonomy. In Class Agaricomycetes where most mushroom-forming fungi belong, species so far have been defined based on morphological, ecological, and/or molecular features. At present, there is little how such features reflect their genome diversity. this study, we investigated genome-wide single nucleotide polymorphism (SNP) frequencies between strains within to understand the patterns of variation. Methods: A total 112 in 72 genera contained nuclear mitochondrial sequences from at least two each public databases. Together, obtained 398 106 available genomes respectively these taxa. Pairwise strain comparisons individual were conducted obtain SNP frequencies. Results: The ranged 0–7.69% while genome, pairwise 0–4.41%. Spearman’s non-parametric rank correlation test showed a weak but statistically significant positive paired frequencies. Overall, observed significantly higher frequency than species. Interestingly, across broad Basidiomycetes, ratios SNPs pairs almost all lower 1, with mean 0.24. Conclusions: Our revealed variations among intraspecific both genomes. However, was consensus examined ratios, suggesting that ratio could potentially serve as an indicator sequence-based identification.