Abstract
Panax L. (the ginseng genus) is a shade-demanding group within the family Araliaceae and all of its species are of crucial significance in traditional Chinese medicine. Phylogenetic and biogeographic analyses demonstrated that two rounds of whole genome duplications accompanying with geographic and ecological isolations promoted the diversification of Panax species. However, contributions of the cytoplasmic genomes to the adaptive evolution of Panax species remained largely uninvestigated. In this study, we sequenced the chloroplast and mitochondrial genomes 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 chloroplast and mitochondrial genomes, respectively. Functional analyses further revealed that these selected genes play important roles in plant development, cellular metabolism and adaptation. We therefore conclude that positive selection might be one of the potential evolutionary forces that shaped nucleotide variation pattern of these Panax species. In particular, the mitochondrial genes evolved under stronger selective pressure compared to the chloroplast genes.
Highlights
Flowering plants contain three genomes in distinct compartments, namely nuclear, mitochondrion and plastid, with each possessing different evolutionary trajectories and relatively independent genetic systems (Smith and Keeling, 2015)
Sequence polymorphisms maintained in the cytoplasmic genomes have long been regarded as selectively neutral (Bock et al, 2014)
Genetic analyses based on 113 grass chloroplast genomes revealed that both locusspecific and lineage effects have contributed to the heterogeneity of sequence polymorphism (Piot et al, 2017)
Summary
Flowering plants contain three genomes in distinct compartments, namely nuclear, mitochondrion and plastid, with each possessing different evolutionary trajectories and relatively independent genetic systems (Smith and Keeling, 2015). This tripartite distribution of nuclear and cytoplasmic genomes has profound impacts on the evolution and diversification of flowering plants (Roux et al, 2016; Sharbrough et al, 2017). In addition to the photosynthesis that converts solar energy to carbohydrates and oxygen, chloroplast genome plays crucial roles in plant growth and development, including nitrate and sulfate assimilation, amino acids, chlorophyll and carotenoids biosynthesis (Jensen and Leister, 2014; Daniell et al, 2016)
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