Milk thistle (Silybum marianum Gaertn.) is a well-known medicinal plant which has been used for more than 2,000 years around the world. It produces silymarin, which cures the liver from hepatitis and toxin damages. In this study, a selfed and purified breeding line of the milk thistle from the Korean environment was used as a source of chloroplast genome construction. It showed high concentration of silybin B (3.50 mg/g) in its dried seeds. The complete chloroplast genome of S. marianum acc. ‘912036’ is 152,556 bp in length and G+C content is 37.69%. A total of 87 protein coding genes with 104 exons were annotated. Chloroplast genomes of five accessions from different countries were compared with that of ‘912036’, and no sequence polymorphism among them was identified. Thus, the chloroplast genome from this study can be used to develop S. marianum-specific DNA markers when compared with other diverse S. marianum accessions and Asteraceae species.

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• The genetics and genomics of milk thistle: unlocking its therapeutic potential through modern breeding and biotechnological innovations
  Priskila Tolangi, Jeehyoung Shim, Raña Mae Sumabat, Sunghan Kim, Hyun-Seung Park, Kyung Do Kim, Hyun Uk Kim, Sanghyun Lee, Joong Hyoun Chin
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• Analysis of silybin A and silybin B in different accessions of Silybum marianum seeds
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• A Genomic Evaluation of Six Selected Inbred Lines of the Naturalized Plants of Milk Thistle (Silybum marianum L. Gaertn.) in Korea
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• Assembly and Comparative Analysis of Complete Mitogenome of Silybum marianum (L.) Gaertner
  Jeongwoo Lee, Yedomon Ange Bovys Zoclanclounon, Hwajin Jung, Taeho Lee, Jeonggu Kim, Guhwang Park, Keunpyo Lee, Kwanghoon An, Jeehyoung Shim, Joonghyoun Chin, Suyoung Hong
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Chloroplasts are essential plant organelles that play important roles in photosynthesis and are involved in many fundamental metabolic pathways. Plastid ribosomal proteins are essential components of protein synthesis machinery and have diverse roles in plant growth and development during chloroplast differentiation. In this study, we isolated and characterized T-DNA-tagged rice mutant (prpl13), which exhibited albino seedling lethality. PRPL13 is a nuclear gene encoding the 50S ribosomal protein L13, which is localized in chloroplasts. Transmission electronic microscopy analysis showed abnormal plastid development in the thylakoids of the chloroplasts of the prpl13 mutant seedlings. Chlorophyll and carotenoid contents were also significantly reduced in the leaves of the mutants. Quantitative reverse transcription-PCR analysis revealed that the prpl13 mutations altered the expression levels of genes involved in photosynthesis and chloroplast development. Thus, our data indicate that nuclear-encoded PRPL13 plays an important role in chloroplast development in rice.

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• Characterization and Transcriptomic Analysis of Antarctic Planococcus sp. Mutant with Enhanced Carotenoid Content
  Hee-Sun Park, Jong-il Choi
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  Zhaoqing Li, Jiawei Liu, Irfan Ali Sabir, Yonghua Qin
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  Dariusz Stępiński
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  Eliana Valencia-Lozano, Lisset Herrera-Isidrón, Jorge Abraham Flores-López, Osiel Salvador Recoder-Meléndez, Braulio Uribe-López, Aarón Barraza, José Luis Cabrera-Ponce
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• Solanum tuberosum Microtuber Development under Darkness Unveiled through RNAseq Transcriptomic Analysis
  Eliana Valencia-Lozano, Lisset Herrera-Isidrón, Jorge Abraham Flores-López, Osiel Salvador Recoder-Meléndez, Aarón Barraza, José Luis Cabrera-Ponce
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• OsbHLH073 Negatively Regulates Internode Elongation and Plant Height by Modulating GA Homeostasis in Rice
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  Federico Martinez-Seidel, Olga Beine-Golovchuk, Yin-Chen Hsieh, Joachim Kopka
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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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• 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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Perilla species belong to the Lamiaceae family of flowering plants and are widely grown in East Asia, for use in a traditional herbal medicine or functional food. To identify single nucleotide polymorphisms (SNPs) in Perilla species and conduct a phylogenomic analysis, we determined the complete sequences of the chloroplast (cp) genome and 45S nuclear ribosomal DNA (45S nrDNA) of six cultivated and three wild Perilla species. The complete cp genome ranged in size from 152,588 bp to 152,656 bp and the length variation in cp genomes was 68 bp. The length of the 45S nrDNA ranged from 6,235 bp to 8,303 bp and the main variation of length differences was in the intergenic spacer (IGS) region. Comparative analysis of the cp genome sequences of nine Perilla species showed low genetic diversity at the intra- and inter-species level. Using SNP analysis, we detected 42 synonymous SNPs (sySNPs) from 27 genes and 37 non-synonymous SNPs (nsSNPs) from 15 genes. A comparison of the 45S nrDNA sequences revealed two SNPs in the 18S rRNA, five SNPs in the 26S rRNA, three SNPs and two InDels in the internal transcribed spacer (ITS) 1 region, and six SNPs in the ITS 2 region. Our phylogenomic analysis suggests that the tetraploidization of Perilla cultivars may have arisen from the P. citriodora genome. The genotyping data from this study may be used to develop molecular markers associated with useful traits for use in Perilla breeding.

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• Construction of a core collection of tomato (Solanum lycopersicum) germplasm based on phenotypic traits and SNP markers
  Xiang Chen, Yi-Yang Liu, Fu-Shun Zheng, Guo-Xin Cheng, Meng Guo, Jian-She Li, Xiao-Min Wang
  Scientia Horticulturae.2025; 339: 113855.     CrossRef
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  Juho Lee, Woo-Hyun Jeong, Seon-Kyeong Lee, Kyeong-Ryeol Lee, Sichul Lee, Beom-Gi Kim
  Korean Journal of Breeding Science.2025; 57(4): 359.     CrossRef
• Plastome sequences fail to resolve shallow level relationships within the rapidly radiated genus Isodon (Lamiaceae)
  Ya-Ping Chen, Fei Zhao, Alan J. Paton, Purayidathkandy Sunojkumar, Lian-Ming Gao, Chun-Lei Xiang
  Frontiers in Plant Science.2022;[Epub]     CrossRef
• Foliose Ulva Species Show Considerable Inter‐Specific Genetic Diversity, Low Intra‐Specific Genetic Variation, and the Rare Occurrence of Inter‐Specific Hybrids in the Wild
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  Journal of Phycology.2021; 57(1): 219.     CrossRef
• Heterogeneous Genetic Diversity Estimation of a Promising Domestication Medicinal Motherwort Leonurus Cardiaca Based on Chloroplast Genome Resources
  Jiahui Sun, Yiheng Wang, Thomas Avery Garran, Ping Qiao, Mengli Wang, Qingjun Yuan, Lanping Guo, Luqi Huang
  Frontiers in Genetics.2021;[Epub]     CrossRef

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
  Nur Nahar Sohe, John Sushma Nannepaga, Wan Amir Nizam Wan Ahmad, Norizah Mhd. Sarbon, Mannur Ismail Shaik
  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
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  Brazilian Journal of Biology.2023;[Epub]     CrossRef
• Inheritance of chloroplast and mitochondrial genomes in cucumber revealed by four reciprocal F1 hybrid combinations
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  Scientific Reports.2021;[Epub]     CrossRef
• Comparative Chloroplast Genome Analyses of Species in Gentiana section Cruciata (Gentianaceae) and the Development of Authentication Markers
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  International Journal of Molecular Sciences.2018; 19(7): 1962.     CrossRef

Capsicum chinense is one of the five domesticated pepper species belonging to the Solanaceae family. Capsicum sp. have been used as model systems in comparative and evolutionary genomics because their superior availability of chloroplast genome in the solanaceae family. Similarly, molecular markers derived from the complete chloroplast genome can provide effective tools for species identification and phylogenetic resolution. So far however, only partial taxonomic and phylogenetic analyses have been carried out for the genus. Thus, the complete chloroplast genome sequence of a cultivated pepper (C. chinense) has been reported here. The total length of the chloroplast genome is 156,936 bp, with 37.7% overall GC content. A pair of inverted repeats (IRs) of 25,847 bp was separated by a small single copy (SSC) region of 17,912 bp and a large single copy (LSC) region of 87,330 bp. The chloroplast genome harbors 113 known genes, including 79 protein-coding genes, four ribosomal RNA genes, and 30 transfer RNA (tRNA) genes. In all, 21 of these genes are duplicated in the inverted repeat regions, 15 genes and six tRNA genes contain a single intron, while two genes have two introns. Analysis revealed 117 simple sequence repeat (SSR) loci, which are mostly located in the intergenic regions. The complete chloroplast genome reported here enriches our knowledge of the genetic complement of C. chinense, and contributes to our understanding of the genetic relationships within the genus Capsicum.

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• Characterization of the complete chloroplast genome of the rare medicinal plant: Mandragora caulescens (Solanaceae)
  Heqin Ma, Erdong Zhang, Yajing An, Yuqing Wei, Lei Zhang
  Mitochondrial DNA Part B.2024; 9(6): 812.     CrossRef
• Chloroplast genome characteristic, comparative and phylogenetic analyses in Capsicum (Solanaceae)
  Shuilian He, Yinqi Siman, Gengyun Li, Junheng Lv, Kai Zhao, Minghua Deng
  BMC Genomics.2024;[Epub]     CrossRef
• Monograph of wild and cultivated chili peppers (Capsicum L., Solanaceae)
  Gloria E. Barboza, Carolina Carrizo García, Luciano de Bem Bianchetti, María V. Romero, Marisel Scaldaferro
  PhytoKeys.2022; 200: 1.     CrossRef
• Pan-plastome approach empowers the assessment of genetic variation in cultivated Capsicum species
  Mahmoud Magdy, Lijun Ou, Huiyang Yu, Rong Chen, Yuhong Zhou, Heba Hassan, Bihong Feng, Nathan Taitano, Esther van der Knaap, Xuexiao Zou, Feng Li, Bo Ouyang
  Horticulture Research.2019;[Epub]     CrossRef
• Development of the ovule and seed of Habanero chili pepper (Capsicum chinense Jacq.): Anatomical characterization and immunocytochemical patterns of pectin methyl-esterification
  Jacobo Pérez-Pastrana, Ignacio Islas-Flores, Ivett Bárány, Dulce Álvarez-López, Adriana Canto-Flick, Blondy Canto-Canché, Laura Peña-Yam, Liliana Muñoz-Ramírez, Susana Avilés-Viñas, Pilar S. Testillano, Nancy Santana-Buzzy
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• The Complete Plastome Sequences of Eleven Capsicum Genotypes: Insights into DNA Variation and Molecular Evolution
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  Genes.2018; 9(10): 503.     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
  Yeonjeong Lee, Hyun-Seung Park, Jae-Hyeon Jeon, Jee Young Park, Seung Hyun Kim, Jungmoo Huh, Sunmin Woo, Do-Won Jeong, Tae-Jin Yang
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• Variation among the Complete Chloroplast Genomes of the Sumac Species Rhus chinensis: Reannotation and Comparative Analysis
  Yujie Xu, Jun Wen, Xu Su, Zhumei Ren
  Genes.2022; 13(11): 1936.     CrossRef
• 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
  Young Sang Park, Young Jun Kim, Tae Jin Yang, Ji Yeon Kim
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• Plastid genomes of the North American Rhus integrifolia-ovata complex and phylogenomic implications of inverted repeat structural evolution in Rhus L.
  Craig F. Barrett
  PeerJ.2020; 8: e9315.     CrossRef

Chloroplast genome sequencing has served as valuable source for developing DNA markers, including the authentication of plant material used for health supplement from its fraudulent materials. We sequenced and analyzed the chloroplast genome of Allium victorialis, a medicinal plant, to discover potential marker regions for the authentication from Veratrum patulum, an inedible toxic plant. Although we examined conventional barcode marker loci in chloroplast, matK and rbcL, there was a difficulty in aligning coding regions and determining PCR primer sequences in these two loci between A. victorialis and V. patulum, possibly due to the distant evolutionary relationship. Instead, we identified potential DNA markers that carry Insertion/Deletion (InDels) that are able to discriminate these two species around clpP, petB, petD, rpl22, and ycf2 loci. In this analysis, we demonstrated the possibility of developing potential DNA markers in the chloroplast genome other than conventional barcode markers, such as matK and rbcL. The potential DNA markers identified in this analysis will serve as useful tools for future authentication of Allium and Veratrum species.

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• Complete plastome sequence of Narcissus pseudonarcissus L., one of the most iconic European plants
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• Authentication of Allium ulleungense, A. microdictyon and A. ochotense based on super-barcoding of plastid genome and 45S nrDNA
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• Comparative Analysis of the Complete Chloroplast Genomes in Allium Section Bromatorrhiza Species (Amaryllidaceae): Phylogenetic Relationship and Adaptive Evolution
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• A Review of Genetic Understanding and Amelioration of EdibleAlliumSpecies
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• Gene Loss, Pseudogenization in Plastomes of Genus Allium (Amaryllidaceae), and Putative Selection for Adaptation to Environmental Conditions
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• Complete plastome sequencing of Allium paradoxum reveals unusual rearrangements and the loss of the ndh genes as compared to Allium ursinum and other onions
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• Insights into phylogeny, age and evolution of Allium (Amaryllidaceae) based on the whole plastome sequences
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• Comparative Analysis of the Complete Chloroplast Genomes in Allium Subgenus Cyathophora (Amaryllidaceae): Phylogenetic Relationship and Adaptive Evolution
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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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• Molecular authentication of Paeonia species for paeonia radix production using plastid and nuclear DNA markers
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• Pan-chloroplast genomes for accession-specific marker development in Hibiscus syriacus
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• High-throughput discovery of plastid genes causing albino phenotypes in ornamental chimeric plants
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• High-Throughput Digital Genotyping Tools for Panax ginseng Based on Diversity among 44 Complete Plastid Genomes
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Chloroplast DNA sequences are a versatile tool for species identification and phylogenetic reconstruction of land plants. Different chloroplast loci have been utilized for phylogenetic classification of plant species. However, there is no report for a short DNA sequence that can distinguish all plant species from each other. Molecular markers derived from the complete chloroplast genome can provide effective tools for species identification and phylogenetic resolution. Thus, the complete chloroplast genome sequence of Korean landrace “Subicho” pepper (Capsicum annuum var. annuum) has been determined here. The total length of the chloroplast genome is 156,878 bp, with 37.7% overall GC content. A pair of IRs (inverted repeats) of 25,801 bp was separated by a small single copy (SSC) region of 17,929 bp and a large single copy (LSC) region of 87,347 bp. The chloroplast genome harbors 132 known genes, including 87 protein-coding genes, 8 ribosomal RNA genes, and 37 tRNA genes. A total of seven of these genes are duplicated in the inverted repeat regions, nine genes and six tRNA genes contain one intron, while two genes and a ycf have two introns. Analysis revealed 144 simple sequence repeat (SSR) loci and 96 variants, mostly located in the intergenic regions. The types and abundances of repeat units in Capsicum species were relatively conserved and these loci will be useful for developing C. annuum cp genome vectors.

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