8 Chloroplast Genome Diversity in Panax Genus Vo Ngoc Linh Giang, Woojong Jang, Hyun-Seung Park, and Tae-Jin Yang Abstract The chloroplast genome variation between plant species and individuals is especially valuable for studying plant genome diversity. Recently, 45S rDNA and the complete chloro- plast genome sequences from seven Panax and relative species have enhanced our under- standing of the genetic and molecular basis that can exploit genome evolution, diversity and conservation in the Araliaceae family. In this chapter, we characterize the genetic diversity and present the phylogenetic rela- tionship of Panax and relative species. We also show the 60kbp of chloroplast genome segments which transferred into mitochondrial genomes and remained conserved as extra copies in the mitochondrial genomes that can cause false authentication or confusion. The study provides genomic resources for under- standing of evolution in the Panax genus and practical DNA markers suitable for authenti- cation and barcoding of each species. 8.1 Introduction Chloroplast are photosynthesis organelles play- ing vital roles in plant physiology, such as the major synthesis and a plethora of metabolites that required for plant development (e.g., vitamins, fatty acids, amino acids, nucleotides and phyto- hormones) (Bobik and Burch-Smith 2015). They contain independent genomes (chloroplast DNA, cpDNA), which are highly conserved, not subject to Mendelian inheritance and uni-parentally inherited (Birky 1995). In angiosperms, cpDNA occurs in circular form with length ranging from 120 to 160 kb, the cpDNA sequence is arranged in a quadripartite fashion consisting of an 80–90 kb large single copy (LSC), two copies of 20–28 kb inverted repeats (IRs) and a 16–27 kb small single copy (SSC) (Jansen et al. 2005). As technology advances, the next-generation sequencing (NGS) technologies have increased the ability to accomplish chloroplast genetics and genomics astonishingly. Insights gained from the development and application of NGS to chloro- plast genome sequences are improved our sci- entific knowledge for plant genetic structure, genome diversity, phylogenetic and systematic evolutionary analyses (Daniell et al. 2016). Ginseng, Panax species (Araliaceae), is a slow growing perennial herbal medicine plant, containing triterpene glycosides commonly referred to as ginsenosides. Eastern societies widely used ginseng for the treatment or V. N. L. Giang Á W. Jang Á H.-S. Park Á T.-J. Yang (&) Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea e-mail: tjyang@snu.ac.kr © Springer Nature Switzerland AG 2021 J. Xu et al. (eds.), The Ginseng Genome, Compendium of Plant Genomes, https://doi.org/10.1007/978-3-030-30347-1_8 95