A total of 166 core genes in the genomes of 10 Pythium insidiosum strains and 5 other Pythium species (Table S1 ) were used for phylogenetic analysis. These genes were selected by scanning through our homologous gene cluster data for genes present in all 15 genomes that did not possess length variations of more than 45% relative to the longest representative gene in each cluster (or each row in the Pythium Gene Table). Nucleotide sequences of each gene from all genomes were aligned using ClustalW version 2 with default parameters [36 (link)]. All ClustalW alignment results were then subjected to gap removal and concatenated to produce a single multiple-sequence alignment file. FastTree2 was then used to create a maximum-likelihood tree [37 (link)]. A bootstrap analysis was carried out to test the reliability of the tree. Finally, the phylogenetic tree was visualized using FigTree v1.4.4 (http://tree.bio.ed.ac.uk/software/figtree/ ; accessed on 4 July 2022).
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