Mitochondrial genomic variation, evolutionary dynamics, and phylogeny of forest-associated Phytophthora species in the Qinling Mountains of China

The genus Phytophthora (Oomycota) comprises highly destructive and widely distributed plant pathogens that threaten global agriculture and forest ecosystems; however, the evolutionary significance of intraspecific and interspecific mitogenomic variation within this genus remains poorly understood. In this study, complete mitochondrial genomes of 11 Phytophthora species, isolated from forest tree rhizospheres in the Qinling Mountains of China, were sequenced, assembled, and annotated to resolve their genetic diversity and evolutionary patterns. All 11 mitogenomes possess typical circular topologies, ranging in size from 37,502 bp ( P. citrophthora ) to 41,542 bp ( P. cryptogea ), with a uniform GC content averaging approximately 21.96%. The gene repertoire was highly conserved across all genomes, containing 34 core protein-coding genes (PCGs), two rRNA genes, 24–25 tRNA genes, and no introns. Selective pressure analysis showed that Ka/Ks ratios for all 34 core PCGs were significantly below 1 (ranging from 0.0096 to 0.1737), demonstrating that purifying selection drives mitochondrial genome evolution in Phytophthora . Combined mitogenomic and multi-locus phylogenomics clarified the phylogenetic placement of these taxa and provided timescale estimates for their divergence. Overall, this work enriches the mitogenomic resources of Phytophthora from pristine natural ecosystems and establishes a critical genomic baseline for accurate species identification, taxonomic revisions, and the study of evolutionary dynamics in oomycetes.