Studies of selection, divergence, and diversity at mating compatibility loci
Alleles at mating compatibility loci identified by McTaggart et al. (2023) were searched in gene annotations with BLASTp. STE3.2genes and HD genes (HD1 and HD2 ) at pheromone/receptor (PR) and homeodomain (HD) loci, were aligned with MAFFT, concatenated, and the most likely tree was searched in IQTree v.2 (Minh et al., 2020) with a model test (command -m TEST), 10,000 ultrafast bootstraps and 10,000 approximate likelihood ratio tests (Minh, Nguyen, & von Haeseler, 2013).
We called SNPs with kSNP across the longest contigs that contained mating compatibility loci (HD locus: BRIP75299; PR locus: POZ38-3). A lower kmer cutoff was used (kmer cutoff 21) to increase the number of SNPs called across these shorter genomic regions. vcftools (Danecek et al., 2011) was used to determine FST, nucleotide diversity (pi), and Tajima’s D across contigs and using populations defined by DAPC analyses. FST, pi, and Tajima’s D were plotted across HD and PR contigs with 10,000 and 3,500 base pair windows using ggplot2 in R.
Mating compatibility was tested based on clades recovered in phylogenetic relationships of the PR locus. Pieces of culture, 1×1 cm, were placed adjacently on rice water agar (333 g rice, 20 g sucrose, 15 g agar, 1L distilled water) and left for three weeks. Presence or absence of clamp connections, as an indication of mate compatibility, was determined from hyphae sampled at the interaction zone under a light microscope at ×1000 magnification.