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In order to clarify the phylogenetic relationship between the chloroplast genome characteristics of three medicinal plants, Panax japonicus var. major, P. japonicus var. bipinnatifidus, P. pseudoginseng var. elegantior in Qinba Mountains, we analysed the chloroplast genome characteristics and codon usage preferences by using bioinformatics techniques. The results were as follows: (1) The chloroplast genomes of three species of Panax were typical tetrad structure, the genome full size was between 156 071 to 156 104 bp, and the total GC-content was 38.10% with a high degree of genome size similarity. (2) A total of 133 coding genes were annotated, including 88 protein coding genes (PCGs), 37 tRNA genes, and 8 rRNA genes with a high degree of genome size similarity. (3) The chloroplast codon usage preferences of the three medicinal plants were comparable, with the third base of codon predominantly ending in A/U. Despite being affected by mutations, the codon usage patterns of the three medicinal plants were found to be mainly influenced by natural selection. (4) The phylogenetic results showed that the three Panax species were closely related, and P. pseudoginseng var. elegantior was more closely related to P. japonicus var. bipinnatifidus. In conclusion, this study presents a significant relationship between P. pseudoginseng var. elegantior and the original pharmacopeial plants of P. japonicus var. major. This finding has great importance for the development, utilization, and molecular identification of traditional Chinese medicinal material resources from P. japonicus var. major, and provides an important basis for further studies on the classification, phylogeny and evolutionary mechanisms of Panax species. |
