Analysis of the chloroplast genome characteristics of three medicinal plants of Panax in the Qinba mountains postprint

Abstract: Based on three medicinal plants of Panax in the Qinba Mountain area, this study analyses the chloroplast genome characteristics and codon usage preferences by using bioinformatics techniques to clarify the phylogenetic relationship between the chloroplast genome characteristics of three medicinal plants, P. japonicus var. major, P. japonicus var. bipinnatifidus, P. pseudoginseng var. elegantior, and to provide a basis for molecular identification of Panacis majoris rhizom. The results were as follows: (1) The chloroplast genomes of three species of Panax were typical tetrad structure, the genome 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) 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 codon 3 bases 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 are closely related, and P. pseudoginseng var. elegantior. is closely related to P. japonicus var. bipinnatifidus. This study presents a significant relationship between P. pseudoginseng var. elegantior and two original pharmacopeial plants of Panacis majoris rhizom. This finding has great importance for the development and utilization of resources from Panacis majoris rhizom, and provides an important basis for further studies on the classification, phylogeny and evolutionary mechanisms of Panax species.