Cultivation of the medicinal herb Panax ginseng Meyer began by domesticating wild mountain ginsengs several hundred years ago in Korea. Elucidating the diversity of the maternally inherited plastid genome (plastome) in diverse ginseng collections including wild ginsengs would provide valuable information on ginseng breeding and cultivation history. We sequenced and compared the plastomes of 44 ginseng accessions collected from various Northeast Asian countries. The plastomes revealed 18 polymorphic sites, including 11 SNPs and 7 InDels, which portrayed less diversity than in the most closely related species, P. quinquefolius. We developed 10 kompetitive allele-specific PCR (KASP) markers and utilized them along with four previously developed InDel markers to characterize the genotypes of 203 ginseng accessions. Digital genotyping based on the developed KASP markers classified the accessions into 10 main and 2 branching haplotypes. Four InDel markers derived from different copy numbers of tandem repeats showed dynamic subgrouping within the haplotypes due to the occurrence of multi-alleles and reversible mutations. The digital haplotype genotyping (haplotyping) revealed that haplotype A, representing 60.1% of the accessions, might be the original plastome form without any SNP occurrence. Accumulation patterns of the variations suggest that nine main haplotypes (B-J) diverged independently by new SNP occurrences from the original plastome, and branching haplotypes may have derived from the first mutant lineage by additional SNP deposition. The digital haplotyping system based on plastome diversity deepens understanding of ginseng evolution and serves as a useful molecular breeding tool.

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• PCR-Based Molecular Authentication Method for Sources of Agrimoniae Herba via Comparative Analyses of Complete Chloroplast Genomes
  Woojong Jang, Sae Hyun Lee, Wook Jin Kim, Sungyu Yang, Byeong Cheol Moon
  International Journal of Molecular Sciences.2025; 26(22): 11189.     CrossRef
• Development and authentication of Panax ginseng cv. Sunhong with high yield and multiple tolerance to heat damage, rusty roots and lodging
  Jiho Seo, Joon-Soo Lee, Sung-Lye Shim, Jun-Gyo In, Chol-Soo Park, Yong-Jae Lee, Hee-Jun Ahn
  Horticulture, Environment, and Biotechnology.2023; 64(5): 753.     CrossRef
• The current research progress of ginseng species: The cultivation and application
  Kaimei Zhang, Shengai Zhang, Atsushi Ebihara, Xiaoqi Zhou, Likun Fan, Pengfei Li, Zhuqi Zhang, Yuyan Wang, Yu Shen
  Cogent Food & Agriculture.2023;[Epub]     CrossRef
• In Vitro Cultivation and Ginsenosides Accumulation in Panax ginseng: A Review
  Fengjiao Xu, Anjali Kariyarath Valappil, Ramya Mathiyalagan, Thi Ngoc Anh Tran, Zelika Mega Ramadhania, Muhammad Awais, Deok Chun Yang
  Plants.2023; 12(17): 3165.     CrossRef

Although genomics provides useful tools for crops, most wild resource plants still lack molecular data. To retrieve useful genomic data and thus provide fundamental information for a resource plant, we established a multi-directional approach using two low coverage whole-genome shotgun sequence (WGS) data of Euonymus hamiltonianus, which is a wild resource plant with potential as a medicinal and ornamental plant. We assembled complete chloroplast genome and nuclear ribosomal DNA (nrDNA) sequences and analyzed polymorphic simple sequence repeats (pSSRs) in the nuclear genome based on the comparison of WGS data between two different phenotypes. We developed a bioinformatics pipeline to identify pSSR motifs by systematic comparison of two WGS datasets. The pipeline is composed of multiple steps including end-joining of paired reads, isolation of joined reads harboring SSR motifs derived from unique non-repetitive regions, identification of pSSR via in silico comparison with counterpart WGS reads, design of pSSR primer sets, and validation. The pipeline was applied to WGS data of E. hamiltonianus and identified 161 contigs with pSSR motifs between the two different phenotypes. Based on the pSSR motifs, 20 primer pairs were designed, of which seven were successfully validated as real pSSR markers. We expect this information to be applicable to genomic resources of E. hamiltonianus.

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• A First Approach for the In Vitro Cultivation, Storage, and DNA Barcoding of the Endangered Endemic Species Euonymus koopmannii
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• High-throughput discovery of plastid genes causing albino phenotypes in ornamental chimeric plants
  Hyun-Seung Park, Jae-Hyeon Jeon, Woohyeon Cho, Yeonjeong Lee, Jee Young Park, Jiseok Kim, Young Sang Park, Hyun Jo Koo, Jung Hwa Kang, Taek Joo Lee, Sang Hoon Kim, Jin-Baek Kim, Hae-Yun Kwon, Suk-Hwan Kim, Nam-Chon Paek, Geupil Jang, Jeong-Yong Suh, Tae-J
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• Analysis of the complete plastomes and nuclear ribosomal DNAs from Euonymus hamiltonianus and its relatives sheds light on their diversity and evolution
  Young Sang Park, Jong-Soo Kang, Jee Young Park, Hyeonah Shim, Hyun Ok Yang, Jung Hwa Kang, Tae-Jin Yang, Sudhindra R. Gadagkar
  PLOS ONE.2022; 17(10): e0275590.     CrossRef
• Comparative Analyses of Euonymus Chloroplast Genomes: Genetic Structure, Screening for Loci With Suitable Polymorphism, Positive Selection Genes, and Phylogenetic Relationships Within Celastrineae
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• De Novo Assembly and Species-Specific Marker Development as a Useful Tool for the Identification of Scutellaria L. Species
  Hakjoon Choi, Wan Seok Kang, Jin Seok Kim, Chang-Su Na, Sunoh Kim
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Eclipta prostrata and E. alba are annual herbal medicinal plants and have been used as Chinese medicinal tonics. Both species are widely distributed in tropical and subtropical regions as well as in Korea. Both species have similar morphological features but E. alba has smoother leaf blade margins compared with E. prostrata. Although both species are utilized as oriental medicines, E. prostrata is more widely used than E. alba. Morphological semblances have confounded identification of either species. Here, we report the complete chloroplast genomes of both species to provide an authentication system between the two species and understand their diversity. Both chloroplast genomes were 151,733–151,757 bp long and composed of a large single copy (83,285–83,300 bp), a small single copy (18,283–18,346 bp), and a pair of inverted repeats (25,075–25,063 bp). Gene annotation revealed 80 protein coding genes, 30 tRNA genes and four rRNA genes. A phylogenetic analysis revealed that the genus Eclipta is grouped with Heliantheae tribe species in the Asteraceae family. A comparative analysis verified 29 InDels and 58 SNPs between chloroplast genomes of E. prostrata and E. alba. The low chloroplast genome sequence diversity indicates that both species are really close to each other and are not completely diverged yet. We developed six DNA markers that distinguish E. prostrata and E. alba based on the polymorphisms of chloroplast genomes between E. prostrata and E. alba. The chloroplast genome sequences and the molecular markers generated in this study will be useful for further research of Eclipta species and accurate classification of medicinal herbs.

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• A review on the phytochemicals of Eclipta prostrata and Eclipta alba: Antioxidants and antidiabetic activities
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  Pharmacological Research - Natural Products.2026; 10: 100483.     CrossRef
• Construction of a Single File Reference Transcriptome Database for Deodeok (Codonopsis lanceolata) and Sseumbagwi (Ixeridium dentata)
  Tae-Ho Lee, Yun-Ho Oh, Ji-Nam Kang, Si-Myung Lee
  Korean Journal of Breeding Science.2023; 55(4): 321.     CrossRef
• Unraveling the secrets of Eclipta alba (L.) Hassk.: a comprehensive study of morpho-anatomy and DNA barcoding
  D. K. Wahyuni, B. F. Yoku, S. R. Mukarromah, P. R. Purnama, M. Ilham, G. A. Rakashiwi, D. T. Indriati, Junairiah, S. Wacharasindhu, S. Prasongsuk, S. Subramaniam, H. Purnobasuki
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• Comparative Chloroplast Genome Analyses of Species in Gentiana section Cruciata (Gentianaceae) and the Development of Authentication Markers
  Tao Zhou, Jian Wang, Yun Jia, Wenli Li, Fusheng Xu, Xumei Wang
  International Journal of Molecular Sciences.2018; 19(7): 1962.     CrossRef

Rhus chinensis is a shrub widely distributed in Asia. It has been used for traditional medicine and ecological restoration. Here, we report the complete chloroplast genome sequence of two R. chinensis genotypes collected from China and Korea. The assembled chloroplast genome of Chinese R. chinensis is 149,094 bp long, consisting of a large single copy (97,246 bp), a small single copy (18,644 bp) and a pair of inverted repeats (16,602 bp). Gene annotation revealed 77 protein coding genes, 30 tRNA genes, and 4 rRNA genes. A phylogenomic analysis of the chloroplast genomes with 11 known complete chloroplast genomes clarified the relationship of R. chinensis with the other plant species in the Sapindales order. A comparative chloroplast genome analysis identified 170 SNPs and 85 InDels at intra-species level of R. chinensis between Chinese and Korean collections. Based on the sequence diversity between Korea and Chinese R. chinensis plants, we developed three DNA markers useful for genetic diversity and authentication system. The chloroplast genome information obtained in this study will contribute to enriching genetic resources and conservation of endemic Rhus species.

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• Complete plastid and 45S rDNA sequences allow authentication of Liriope platyphylla and Ophiopogon japonicus
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• Variation among the Complete Chloroplast Genomes of the Sumac Species Rhus chinensis: Reannotation and Comparative Analysis
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• Phytochemical, Antioxidant, Anti-Microbial, and Pharmaceutical Properties of Sumac (Rhus coriaria L.) and Its Genetic Diversity
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• Authentication of Rubus coreanus and Related Species via DNA Barcoding and HPLC Approaches
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  Korean Journal of Medicinal Crop Science.2021; 29(6): 425.     CrossRef
• Plastid genomes of the North American Rhus integrifolia-ovata complex and phylogenomic implications of inverted repeat structural evolution in Rhus L.
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  PeerJ.2020; 8: e9315.     CrossRef

Korean ginseng (Panax ginseng) is a well-known valuable medicinal plant with excellent therapeutic effects, however its complex genome structure has not been elucidated yet. To understand its genome structure, we obtained ten ginseng bacterial artificial chromosome (BAC) clone sequences by single-molecule real-time (SMRT) sequencing platform using a pooled DNA of the BAC clones. Out of the ten BAC clones, nine were completely assembled without any gap and one remained a single gap. The total length of BAC clone sequences was 1,163,364 bp. Sophisticated sequence analysis revealed that the 89.7% of the sequences are high copy repeat regions and the remaining 10.3% are non-repeat regions. Eleven protein-coding genes were identified in the non-repeat regions. Most of the repeat regions show more than 1,000 copies and complex structure of various repetitive elements. Ty3/Gypsy family long terminal repeat retrotransposons (LTR-RTs) are predominant repeats occupying 46.9% of the 1,163-kbp sequence. We identified six novel LTR-RTs and their insertion time. Fluorescence in situ hybridization (FISH) analysis demonstrated that PgDel2 and PgDel5 elements had a subgenome-biased distribution. Collectively, our analysis reveals that ginseng genome has very complex genome structure with abundant repetitive elements and rare gene frequency.

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• High-resolution genetic map and SNP chip for molecular breeding in Panax ginseng, a tetraploid medicinal plant
  Woohyeon Cho, Woojong Jang, Hyeonah Shim, Jiseok Kim, Youngju Oh, Jee Young Park, Young Chang Kim, Jung-Woo Lee, Ick-Hyun Jo, Misun Lee, Jinsu Gil, Martin Mascher, Murukarthick Jayakodi, Xuejiao Liao, Jiang Xu, Deqiang Dou, Yi Lee, Tae-Jin Yang
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• Construction of a Single File Reference Transcriptome Database for Deodeok (Codonopsis lanceolata) and Sseumbagwi (Ixeridium dentata)
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• Complete Mitochondrial Genome and a Set of 10 Novel Kompetitive Allele-Specific PCR Markers in Ginseng (Panax ginseng C. A. Mey.)
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Most ginseng cultivars bear red berry and only one cultivar ‘Gumpoong’ (GU) bears golden berry. GU is an elite cultivar bred by pedigree selection from a golden berry landrace (a mixed population) ‘Hwangsook’ (HS). We developed three unique polymorphic markers from complete chloroplast genome sequences of GU and HS. A population of GU showed uniform band amplicon against three chloroplast markers whereas HS population displayed mixed genotypes for both GU and HS. Using the characteristics of mixed genotypes in HS population, we developed a convenient method to differentiate GU and HS population by application of pooled DNA template for PCR analysis (pooling method). The pooling method revealed that the GU pool was identical with GU genotype while the HS pool showed both GU and HS genotype. The pooling method is a cost and time effective method for accurate authentication of both golden berry ginseng cultivars. The method is useful to protect GU products from its tentative counterfeits from seeds to mature plant stages as well as processed root products.

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