Objective  Characteristics and phylogeny of chloroplast genomes of the medicinally and economically valuable species in Panax genus were studied.

  Methods  Using bioinformatics software, the properties, repeats, structural variation, evolution, and phylogeny of the genomes of chloroplasts from 14 ginseng species were analyzed.

  Results   The genomes consisted of typical quadripartite structure with 114 unique genes. The long repeats in them were mainly of palindromic and forward types with a length between 30 bp and 39 bp. The simple sequence repeats were largely A/T type and most abundantly mononucleotides. No gene rearrangement occurred in the genomes was observed. The boundary between the inverted repeat region and the single copy region was highly conserved. Of the 12 regions with highly variable nucleotides, 7 were in the large and 5 in the small single copy region. Indicated by the dN/dS ratios, the positive selection could occur on clpP, ycf1, and ycf2 with unknown functions. The phylogenetic analysis showed that P. stipulenatus and P. trifolius were in the basal lineage, the tetraploid P. ginseng and P. quinquefolius separated from other diploid species, while P. notoginseng, P. japonicus, and P. vietnamensis closely related.

  Conclusion  The chloroplasts of the ginseng species examined were basically same in number and order of genomes, conservative in structure, but divert in number and type of repeats. The nucleotide polymorphism of the chloroplasts was higher in single copy region than inverted repeat regions. The positive selection genes identified in the study might result from the ecological adaptation of these Panax species.