Intraspecific diversity of the ITS region
The ITS region was extracted directly from assembled genomes using the top hit with a BLASTn search (command -outfmt ‘6 sseq’-max_target_seqs 1 ) and aligned with ITS sequences of P. allenii , P. azurescens , P. cyanescens , P. makarorae , P. subaeruginosa , and P. weraroa from GenBank using MAFFT. Sequences of P. cubensis were used as an outgroup, based on its sister group relationship with P. cyanescens(Bradshaw et al., 2022). We searched for the maximum likelihood tree in IQTree v.2 based on an alignment that contained one representative of each ITS sequence type and used a phylogenetic hypothesis to explore whether the ITS region was monophyletic at species rank in P. subaeruginosa and related taxa. We used PopART to visualise the distribution of ITS genotypes across the entire ITS dataset.