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
  Applied Biological Chemistry.2024;[Epub]     CrossRef
• Analysis of silybin A and silybin B in different accessions of Silybum marianum seeds
  Neil Patrick Uy, Jeehyoung Shim, Hak-Dong Lee, Jung Sook Sung, Eunae Yoo, Joong Hyoun Chin, Sanghyun Lee
  Journal of Applied Biological Chemistry.2024;[Epub]     CrossRef
• Agricultural phenotype and silymarin content variations of cultivated milk thistle in Korea
  Jeehyoung Shim, Hyejin Cho, Jung Sook Sung, Eunae Yoo, Joong Hyoun Chin, Sanghyun Lee
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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
  Jeehyoung Shim, Su Young Hong, Jae-Hyuk Han, Yeisoo Yu, Eunae Yoo, Jungsook Sung, Joong Hyoun Chin, O New Lee
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• The complete chloroplast genome of Elephantopus scaber L. (Vernonioideae, Asteraceae), a useful ethnomedicinal plant in asia
  Pham Anh Thi Nguyen, Do Tan Khang, Pham Thien Trang Nguyen, Hoang Dang Khoa Do
  Mitochondrial DNA Part B.2023; 8(9): 936.     CrossRef
• 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
  Korean Journal of Breeding Science.2022; 54(4): 294.     CrossRef

Repetitive DNA elements are ubiquitous in plant genomes. Although repeats provide relevant information for cytogenetic, evolutionary, and genomic studies, identifying and characterizing their sequence and chromosomal distribution are not always easily achieved through conventional methods. However, a high-throughput identification of genomic repeats can be obtained with short reads from next-generation sequencing data. Here, we identified the telomeric and two chromosome-specific repeats in Panax ginseng using low-coverage whole genome sequence data. The telomeric repeat sequence is same with the canonical angiosperm sequence, (TTTAGGG)_n, and localized mostly in every chromosome termini, except for an additional interstitial location in chromosome 10. A dinucleotide (GA) microsatellite, PgGA15, with total genome representation (GR) of more than 33 kb localized in the long arm of chromosome 20. An 11-bp minisatellite, Pgms1, with more than 58 kb of GR localized in the long arm of chromosome 1. This study provides chromosome-specific markers for cytogenetic studies in P. ginseng.

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• Beyond genome: Advanced omics progress of Panax ginseng
  Wenjing Yu, Siyuan Cai, Jiali Zhao, Shuhan Hu, Chen Zang, Jiang Xu, Lianghai Hu
  Plant Science.2024; 341: 112022.     CrossRef
• Identification and functional analysis of COLD-signaling-related genes in Panax ginseng
  Jeongeui Hong, Hojin Ryu
  Journal of Plant Biotechnology.2023;[Epub]     CrossRef
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  Eliazar Alumbro Peniton, Nomar Espinosa Waminal, Tae-Jin Yang, Hyun Hee Kim
  Horticulture, Environment, and Biotechnology.2022; 63(1): 137.     CrossRef
• Gibberellin Signaling Promotes the Secondary Growth of Storage Roots in Panax ginseng
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  International Journal of Molecular Sciences.2021; 22(16): 8694.     CrossRef
• Functional characterization of gibberellin signaling-related genes in Panax ginseng
  Jinsoo Kim, Woo-Ri Shin, Yang-Hoon Kim, Donghwan Shim, Hojin Ryu
  Journal of Plant Biotechnology.2021; 48(3): 148.     CrossRef
• Interstitial Telomeric-like Repeats (ITR) in Seed Plants as Assessed by Molecular Cytogenetic Techniques: A Review
  Alexis J. Maravilla, Marcela Rosato, Josep A. Rosselló
  Plants.2021; 10(11): 2541.     CrossRef
• FISH Karyotype Comparison ofPlatycodon grandiflorus(Jacq.) A. DC. ‘Jangbaek’ and Its Colchicine-Induced Tetraploid ‘Etteumbaek
  Eliazar Alumbro Peniton Jr., Yurry Um, Hyun Hee Kim
  Plant Breeding and Biotechnology.2020; 8(4): 389.     CrossRef
• Five-color fluorescence in situ hybridization system for karyotyping of Panax ginseng
  Nomar Espinosa Waminal, Tae-Jin Yang, Jun-Gyo In, Hyun Hee Kim
  Horticulture, Environment, and Biotechnology.2020; 61(5): 869.     CrossRef
• FISH Karyotype Comparison between Wild and CultivatedPerillaSpecies Using 5S and 45S rDNA Probes
  Eliazar Alumbro Peniton, Nomar Espinosa Waminal, Tae-Ho Kim, Hyun Hee Kim
  Plant Breeding and Biotechnology.2019; 7(3): 237.     CrossRef
• Rapid and Efficient FISH using Pre-Labeled Oligomer Probes
  Nomar Espinosa Waminal, Remnyl Joyce Pellerin, Nam-Soo Kim, Murukarthick Jayakodi, Jee Young Park, Tae-Jin Yang, Hyun Hee Kim
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• Identification of ABSCISIC ACID (ABA) signaling related genes in Panax ginseng
  Jeongeui Hong, Hogyum Kim, Hojin Ryu
  Journal of Plant Biotechnology.2018; 45(4): 306.     CrossRef

With the continual development of genetically modified (GM) crops, it has become necessary to develop detailed and effective molecular characterization methods to select candidate events from a large pool of transformation events. Relative to traditional molecular analysis methods such as the polymerase chain reaction (PCR) and Southern blot hybridization, next generation sequencing (NGS) technology for whole-genome sequencing of complex crop genomes had proven comparatively useful for in-depth molecular characterization. In this study, four transformation events, including one in Bacillus thuringiensis (Bt)-resistant rice, one in resveratrol-producing rice, and two in beta-carotene-enhanced soybeans, were selected for molecular characterization. To merge NGS analysis and Southern blot-hybridization results, we confirmed the transgene insertion sites, insertion construction, and insertion numbers of these four transformation events. In addition, the read-coverage depth assessed by NGS analysis for inserted genes might provide consistent results in terms of inserted T-DNA numbers in case of complex insertion structures and highly duplicated donor genomes; however, PCR-based methods can produce incorrect conclusions. Our combined method provides an effective and complete analytical approach for whole-genome visual inspection of transformation events that require biosafety assessment.

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• Molecular Characterization of CRISPR-Cas9-Edited Rice Across Generations and Associated Technical Challenges in Nucleotide Editing Tracing
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  Plant Breeding and Biotechnology.2025;[Epub]     CrossRef
• Combining Nanopore and Illumina Sequencing Permits Detailed Analysis of Insertion Mutations and Structural Variations Produced by PEG-Mediated Transformation in Ostreococcus tauri
  Julie Thomy, Frederic Sanchez, Marta Gut, Fernando Cruz, Tyler Alioto, Gwenael Piganeau, Nigel Grimsley, Sheree Yau
  Cells.2021; 10(3): 664.     CrossRef
• Comparative transcriptome profiling of different tissues from beta-carotene-enhanced transgenic soybean and its non-transgenic counterpart
  Yang Qin, Hee-Jong Woo, Kong-Sik Shin, Myung-Ho Lim, Seong-Kon Lee
  Plant Cell, Tissue and Organ Culture (PCTOC).2020; 140(2): 341.     CrossRef

Closely-related cultivars generally used for crossing in breeding lack sufficient known DNA polymorphisms with already developed DNA markers even though they exhibit remarkable phenotype difference. However, next-generation sequencing (NGS) enables the identification of massive DNA polymorphisms such as single nucleotide polymorphisms (SNPs) and insertions-deletions (InDels) between highly homologous genomes. This study conducted a whole-genome re-sequencing of two Korean japonica rice varieties, Junam and Nampyeong. The sequencing yielded 16.6 × 10⁹ bps for Junam, and 15.1 × 10⁹ bps for Nampyeong. After quality trimming and read mapping onto the reference genome sequence of Nipponbare, 11.9 × 10⁹ bps from Junam and 10.6 × 10⁹ bps from Nampyeong were mapped onto the reference sequence. The final effective mapping depth was 31.98x for Junam and 28.41x for Nampyeong. This study found 398,123 DNA polymophisms between Junam and Nampyeong. These were classified into 352,478 SNPs (88.5%) and 45,645 InDels (11.5%) by polymorphism types, 338,485 homozygous (85%) and 59,638 (15%) heterozygous by zygosity, and 331,855 intergenic (83.4%) and 66,268 genic (16.6%) by genomic location. To see the availability of these results in DNA marker development, Cleaved Amplified Polymorphic Sequences (CAPS) markers were developed based on 22 SNPs lying in restriction enzyme sites. Among them, 17 CAPS markers showed polymorphisms between Junam and Nampyeong. It is expected that sufficient DNA markers for mapping genes/QTLs with progeny population from a cross between Junam and Nampyeong can be developed based on the results of the study.

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  Molecular Genetics and Genomics.2020; 295(5): 1129.     CrossRef
• Kompetitive Allele-Specific PCR Marker Development and Quantitative Trait Locus Mapping for Bakanae Disease Resistance in Korean Japonica Rice Varieties
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• Mapping of a major quantitative trait locus for bakanae disease resistance in rice by genome resequencing
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• Single Nucleotide Polymorphism (SNP) Discovery and Kompetitive Allele-Specific PCR (KASP) Marker Development with Korean Japonica Rice Varieties
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