Panax L. (the ginseng genus) is a shade-demanding group within the family Araliaceae and all of its species are of crucial significance in traditio nal Chinese medicine. Phylogenetic and biogeographic analyses demonstrated tha t two rounds of whole genome duplications accompanying with geographic and ecol ogical isolations promoted the diversification of Panax species. However, contributions of the cytoplasmic genome s to the adaptive evolution of Panax species remained largely uninvestigated. In this study, we sequenced the chloroplast and mitochondrial geno mes of 11 accessions belonging to seven Panax species. Our results show that heterogeneity in nucleotide substitution rate is abundant in both of the two cytoplasmic genomes, with the mitochondrial genome possessing more variants at the total level but the chloroplast showing higher sequence polymorphisms at the genic regions . Genome-wide scanning of positive selection identified five and 12 genes from the chl oroplast and mitochondrial genomes, respectively. Functional analyses further revea led that these selected genes play important roles in plant development, cellular metabo lism and adaptation. We therefore conclude that positive selection might be one of t he potential evolutionary forces that shaped nucleotide variation pattern of these Panax species. In particular, the mitochondrial genes evolved under stronger selective p ressure compared to the chloroplast genes.
