DOI: 10.5061/dryad.kh18932b1
title: Intraspecific genome SNP frequencies comparison

description: 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.
description: The assembled nuclear and mitochondrial
 (mt) genome data of Agaricomycetes were downloaded from the National
 Center of Biology Information (NCBI, https://www.ncbi.nlm.nih.gov/genome/?term=) and the Joint Genome Institute (JGI, https://mycocosm.jgi.doe.gov/mycocosm/home) genome database up to August 31, 2022. For each analyzed genome, the sequencing technology used, assembled genome size, sequencing read coverage depth, number of scaffolds and/or contigs, N50 (the minimum scaffold/contig length needed to cover 50% of the genome, L50 (the number of contigs required to reach N50), the mitogenome size and the related references were all retrieved when available. The species containing at least two nuclear or two mt genomes were selected for further analyses. 
description: The genome-wide SNP analyses within
 individual species were determined by the alignment-based program MUMmer
 3.23, with longer assemblies (larger genome and better-assembled
 genomes/fewer scaffolds) in each pairwise comparison serving as the
 reference for each analyzed species. Our alignments used the following
 specific commands: “–mum -p” parameter for aligning each pair of assembled
 genomes and identifying overlapping regions between two profiles
 (maxgap=500, mincluster=100), followed by “delta-filter -1” processing to
 filter out repeated comparisons, then “show-snps -CHITrl” to detect base substitutions.
 Insertions and deletions (InDels) in those overlapping regions were
 excluded from SNP frequency calculations.