Comparative Genomics of Pythium Species

We compared gene contents across multiple genomes to investigate their genomic variability. All genes found in the genome of 10 P. insidiosum strains, together with the genome of 5 other Pythium species (Table 1), were subjected to a sequence-similarity-based gene-grouping process using our previously published protocol [35 (link)]. We used the following thresholds for each sequence comparison to group genes into the same cluster: BLAST E-value of 10⁻⁶, pairwise sequence identity of at least 30%, and pairwise sequence alignment coverage for both query and subject of at least 50%. These lenient criteria allowed the grouping of distant homologs and helped to minimize false positives in identifying group- or genome-specific genes (only present in a subset of genomes). With such criteria, if a particular gene is still not found in a genome, it is very likely that the gene is truly absent as opposed to present but may be significantly diverged from its corresponding orthologous genes found in other genomes. The final homologous gene cluster result is presented in table format, namely the Pythium Gene Table, where each row represents a gene and columns represent the 15 Pythium genomes used in this study. Each cell in the table contains information regarding homologous genes or genomic regions found in the corresponding genome.