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.