Sequence alignment and variant calling
Genomic sequences were analyzed in parallel using two pipelines: (1) the first pipeline trimmed the data using TrimGalore version 0.3.3, aligned using Bowtie2 (Langmead & Salzberg), and SAMtools (Li et al. 2009) to include only reads that mapped concordantly and only once to remove PCR duplicates. Variants were called for each alignment using HaplotypeCaller, combined into a common variant file with GenotypeGVCFs and further quality filtered with VariantFiltration (QD<2.0||FS>60.0||MQ<40.0||MQRankSum< -12.5||ReadPosRankSum< -8.0) in Genome Analysis Tool Kit (GATK) (McKenna et al. 2010; Van der Auweraet al. 2013). (2) The second pipeline trimmed the sequences using Trimmomatic (Bolger et al. 2014), mapped the reads using BWAmem (Li 2013), filtered using SAMtools, called variants using BCFtools call and filtered with BCFtools view. For both pipelines, the sequence data were mapped to the monokaryotic Serpula lacrymans isolate S7.3, version 2 (Eastwood et al. 2011). Repetitive regions of theS. lacrymans v. 2 genome were annotated using the REPET package v.2.5 (Flutre et al. 2011), following the procedure outlined in (Sipos et al. 2017). Regions annotated as transposable element-derived were filtered from the SNP data set using BEDtools (Quinlan & Hall 2010). A combined data set using only SNPs called by both pipelines resulted in 419,196 high quality SNPs for the 36 isolates included in this analysis.