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.