Complete Sequencing of Chloroplast Genomes of Two Panax ginseng Cultivars Reveals Unique Intra Species Variation

Abstract

Plant chloroplast genome sequence is an important target to study phylogenetic relationships in plants because sequence variations show concrete inter-species polymorphism and very less intra-species variation. In addition, polymorphic sites in chloroplast genomes sequence are very useful targets for barcode-based authentication of medicinal plants. Next generation sequencing (NGS) technology provides a high throughput method to generate complete chloroplast genome sequence with low cost and time. Here, I assembled complete chloroplast sequences of two elite Korea ginseng cultivars, Chunpoong and Yunpoong using Illumina genome sequence reads of low-depth. Chloroplast genome sequences of Chunpoong and Yunpoong are 156,248 bp and 156,355 bp in length, respectively. By comparative analysis of the complete chloroplast genomes of both cultivars, I identified three polymorphic sites including two Indels and one SNP and then developed DNA markers based on these polymorphic sites. The DNA markers showed unique polymorphism among cultivars of Panax ginseng, and even among Panax species such as P. ginseng, P. quinquefolius, and P. notoginseng. These markers will be valuable and important resources for authentication and protection of Panax ginseng cultivars.