Next generation sequencing (NGS) approaches can also be useful tool for characterization of organelle genomes. We generated chloroplast (CP) genome sequences of two Korean ginseng cultivars, Chunpoong and Yunpoong, based on reference-guided assembly using whole genome NGS data. We used 0.5x of P. ginseng genome NGS reads to assemble CP genome. Of the NGS reads used, about 6% were mapped to the reference CP genome with mean coverage of 94x due to high copy number of CP genome in plant cell. CP genomes of the two cultivars were predicted to be 156,248 bp and 156,355 bp in length and showed about 0.1% differences at nucleotide level, compared to reference CP genome sequenced from P. ginseng (Acc.no. NC_006290), whereas difference between CP genomes of the two cultivars is very rare. In this study, we developed the molecular marker to perform taxon identification and also to elucidate phylogenetic relationship among Korean ginseng cultivars. Now, we are analyzing the CP genomes of other P. ginseng cultivars together with other Panax species including American ginseng and Panax related species.

Genetic map provides basic and important informations for breeding. Therefore, genetic map construction is a essential process in plant research. Panax ginseng is one of the most famous medical plant in the world. However, genetic informations of this medical plant for breeding are not enough. Because of little informations, genetic map construction of panax ginseng provides very useful information for breeding. Using Solexa next generation sequencing (NGS) technology, we have been produced a lot of expressed sequence tags (ESTs) and whole genome sequences from Chunpoong (368 Gb) and Yunpoong (6 Gb) cultivar. To develop large amount of DNA markers and thus construct high resolution genetic map, we inspect large scale of SSR motif and putative SNP sites which can be used as dCAPs markers using produced ginseng’s sequence data. As a result, we can find a number of DNA markers that have polymorphism between Yunpoong and Chunpoong cultivar. These developed DNA markers were analyzed for F2 population of Yunpoong x Chunpoong to find markers showing Mendelian segregation ratio 1:2:1.