Intraspecific genome SNP frequencies comparison

Genome sequence analyses can provide crucial for understanding the origin
and spread of infectious diseases, population history, speciation, and
taxonomy. In Class Agaricomycete where most mushroom-forming fungi belong,
most species so far have been defined based on morphological, ecological,
and/or molecular features, but there is no defined threshold for any type
of features that can be applied across multiple genera, families, and
orders. In this study, we investigated genome-wide single nucleotide
polymorphism (SNP) frequencies within species to understand the patterns
of variation within both the nuclear and mitochondrial genomes of the
current whole-genome sequenced species. In total, our analyses included
398 and 106 published available nuclear and mitochondrial genomes of
Agaricomycetes, respectively. The SNP frequencies among nuclear genomes
within individual species ranged 0.00~7.69% while for the mitochondrial
genome comparison, the intraspecific SNP frequencies ranged 0.00~4.41%.
The Spearman’s non-parametric rank correlation test showed a weak but
statistically significant positive correlation between the paired nuclear
and mitochondrial genome datasets. Overall, we observed a significantly
higher SNP frequency in the nuclear genome than in the mitochondrial
genomes between strains within most species. Interestingly, across the
broad Basidiomycetes, the ratios of mitochondrial genome SNPs and nuclear
genome SNPs between pairs of strains within each species were highly
similar, with a mean of 0.24. We discuss the implications of these results
for Agaricomycetes systematics and the implementation of genome
sequence-based species delimitation in fungi.