Phylogenetic Analysis of Korean Domestic and Foreign White-Rot Fungi

In addition to the 81 ITS sequences obtained from the CCM of Incheon National University, 137 ITS sequences of S. commune published in the NCBI were also included for systematic analysis. The list of S. commune strains in NCBI is shown in Table S2. Multiple sequence alignment analysis was performed using a Muscle sequence aligner (ver. 3.8.31). The aligned sequences were trimmed by using the trimAL program (ver. 1.4. rev15) on the Linux server (Ubuntu 16.04.5 LTS). At this time, the gap threshold option (-gt) was set as 0.75, which removes all positions in the alignment with gaps in 25% (1-0.75) or more of the sequence. RAxML (ver. 8.2.12) was used to draw the maximum-likelihood tree. The options for the CAT model of rate heterogeneity (‘-m GTRCAT’) and for automatic bootstrapping (‘-N autoMRE’) were used to select the most suitable analytical model. For visualization, the ape and ggtree packages in R were used. To analyze the nucleotide and haplotype diversity, the pegas package in R was used.