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"Junki Lee"

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"Junki Lee"

Research Articles
Characterization of Chloroplast Genomes, Nuclear Ribosomal DNAs, and Polymorphic SSR Markers Using Whole Genome Sequences of Two Euonymus hamiltonianus Phenotypes
Junki Lee, Shin-Jae Kang, Hyeonah Shim, Sang-Choon Lee, Nam-Hoon Kim, Woojong Jang, Jee Young Park, Jeong Hwa Kang, Wan Hee Lee, Taek Joo Lee, Gyoungju Nah, Tae-Jin Yang
Plant Breed. Biotech. 2019;7(1):50-61.   Published online March 1, 2019
DOI: https://doi.org/10.9787/PBB.2019.7.1.50

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
    Balnur Kali, Sara Bekkuzhina, Dilnur Tussipkan, Shuga Manabayeva
    Plants.2024; 13(16): 2174.     CrossRef
  • 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
    Horticulture Research.2023;[Epub]     CrossRef
  • 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
    Yongtan Li, Yan Dong, Yichao Liu, Xiaoyue Yu, Minsheng Yang, Yinran Huang
    Frontiers in Plant Science.2021;[Epub]     CrossRef
  • 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
    Current Issues in Molecular Biology.2021; 43(3): 2177.     CrossRef
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Characterization of Complete Chloroplast Genome of Allium victorialis and Its Application for Barcode Markers
Junki Lee, JaeKyung Chon, JongSung Lim, Eun-Kyoung Kim, Gyoungju Nah
Plant Breed. Biotech. 2017;5(3):221-227.   Published online September 1, 2017
DOI: https://doi.org/10.9787/PBB.2017.5.3.221

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
    Martino Adamo, Valeria Fochi, Marco Mucciarelli
    Mitochondrial DNA Part B.2024; 9(8): 1132.     CrossRef
  • Authentication of Allium ulleungense, A. microdictyon and A. ochotense based on super-barcoding of plastid genome and 45S nrDNA
    Minyoung Lee, Hyo Young Lee, Jong-Soo Kang, Hyeji Lee, Ki-Jin Park, Jee Young Park, Tae-Jin Yang, Yanbin Yin
    PLOS ONE.2023; 18(11): e0294457.     CrossRef
  • Comparative and phylogenetic analysis of the complete chloroplast genome sequences of Allium mongolicum
    Yanan Jin, Ting Zhang, Binke Liu, Chengzhong Zheng, Hongyan Huo, Jixing Zhang
    Scientific Reports.2022;[Epub]     CrossRef
  • Comparative Analysis of the Complete Chloroplast Genomes in Allium Section Bromatorrhiza Species (Amaryllidaceae): Phylogenetic Relationship and Adaptive Evolution
    Junpei Chen, Dengfeng Xie, Xingjin He, Yi Yang, Xufeng Li
    Genes.2022; 13(7): 1279.     CrossRef
  • A Review of Genetic Understanding and Amelioration of EdibleAlliumSpecies
    Geetika Malik, Ajmer Singh Dhatt, Ajaz Ahmed Malik
    Food Reviews International.2021; 37(4): 415.     CrossRef
  • Gene Loss, Pseudogenization in Plastomes of Genus Allium (Amaryllidaceae), and Putative Selection for Adaptation to Environmental Conditions
    Victoria A. Scobeyeva, Ilya V. Artyushin, Anastasiya A. Krinitsina, Pavel A. Nikitin, Maxim I. Antipin, Sergei V. Kuptsov, Maxim S. Belenikin, Denis O. Omelchenko, Maria D. Logacheva, Evgenii A. Konorov, Andrey E. Samoilov, Anna S. Speranskaya
    Frontiers in Genetics.2021;[Epub]     CrossRef
  • Omics approaches inAlliumresearch: Progress and way ahead
    Kiran Khandagale, Ram Krishna, Praveen Roylawar, Avinash B. Ade, Ashwini Benke, Bharat Shinde, Major Singh, Suresh J. Gawande, Ashutosh Rai
    PeerJ.2020; 8: e9824.     CrossRef
  • Complete plastome sequencing of Allium paradoxum reveals unusual rearrangements and the loss of the ndh genes as compared to Allium ursinum and other onions
    Denis O. Omelchenko, Anastasia A. Krinitsina, Maxim S. Belenikin, Evgenii A. Konorov, Sergey V. Kuptsov, Maria D. Logacheva, Anna S. Speranskaya
    Gene.2020; 726: 144154.     CrossRef
  • Insights into phylogeny, age and evolution of Allium (Amaryllidaceae) based on the whole plastome sequences
    Deng-Feng Xie, Jin-Bo Tan, Yan Yu, Lin-Jian Gui, Dan-Mei Su, Song-Dong Zhou, Xing-Jin He
    Annals of Botany.2020; 125(7): 1039.     CrossRef
  • Comparative Analysis of the Complete Chloroplast Genomes in Allium Subgenus Cyathophora (Amaryllidaceae): Phylogenetic Relationship and Adaptive Evolution
    Xin Yang, Deng-Feng Xie, Jun-Pei Chen, Song-Dong Zhou, Yan Yu, Xing-Jin He, Marcelo A. Soares
    BioMed Research International.2020;[Epub]     CrossRef
  • Phylogeny and highland adaptation of Chinese species in Allium section Daghestanica (Amaryllidaceae) revealed by transcriptome sequencing
    Deng-Feng Xie, Yan Yu, Jun Wen, Jiao Huang, Jun-Pei Chen, Juan Li, Song-Dong Zhou, Xing-Jin He
    Molecular Phylogenetics and Evolution.2020; 146: 106737.     CrossRef
  • Development of the chloroplast genome-based InDel markers in Niitaka (Pyrus pyrifolia) and its application
    Ho Yong Chung, So Youn Won, Yoon-Kyung Kim, Jung Sun Kim
    Plant Biotechnology Reports.2019; 13(1): 51.     CrossRef
  • Phylogeny of Chinese Allium Species in Section Daghestanica and Adaptive Evolution of Allium (Amaryllidaceae, Allioideae) Species Revealed by the Chloroplast Complete Genome
    Deng-Feng Xie, Huan-Xi Yu, Megan Price, Chuan Xie, Yi-Qi Deng, Jun-Pei Chen, Yan Yu, Song-Dong Zhou, Xing-Jin He
    Frontiers in Plant Science.2019;[Epub]     CrossRef
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High-Throughput Development of Polymorphic Simple Sequence Repeat Markers Using Two Whole Genome Sequence Data in Peucedanum japonicum
Junki Lee, Ho Jun Joh, Nam-Hoon Kim, Sang-Choon Lee, Woojong Jang, Beom Soon Choi, Yeisoo Yu, Tae-Jin Yang
Plant Breed. Biotech. 2017;5(2):134-142.   Published online June 1, 2017
DOI: https://doi.org/10.9787/PBB.2017.5.2.134

Resource plants are important and have strong potential for a variety of utilities as crops or pharmaceutical materials. However, most resource plants remain wild and thus their utility for breeding and biotechnology is limited. Molecular markers are useful to initiate genetic study and molecular breeding for these understudied resource plants. We collected various wild collections of Peucedanum japonicum which is indigenous resource plants utilized as oriental medicine and leafy vegetables in Korea. In this study, we produced two independent whole genome sequences (WGSs) from two collections and identified large scale polymorphic simple sequence repeat (pSSR) based on our pipeline to develop SSR markers based on comparison of two WGSs. We identified a total of 452 candidate pSSR contigs. To confirm the accuracy and utility of pSSR, we designed ten SSR primer pairs and successfully applied those to seven collections of P. japonicum. The WGS and pSSR candidates identified in this study will be useful resource for genetic research and breeding purpose for the valuable resource plant, P. japonicum.

Citations

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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
    Current Plant Biology.2022; 30: 100244.     CrossRef
  • 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
    Current Issues in Molecular Biology.2021; 43(3): 2177.     CrossRef
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A Glimpse of Panax ginseng Genome Structure Revealed from Ten BAC Clone Sequences Obtained by SMRT Sequencing Platform
Woojong Jang, Nam-Hoon Kim, Junki Lee, Nomar Espinosa Waminal, Sang-Choon Lee, Murukarthick Jayakodi, Hong-Il Choi, Jee Young Park, Jong-Eun Lee, Tae-Jin Yang
Plant Breed. Biotech. 2017;5(1):25-35.   Published online March 1, 2017
DOI: https://doi.org/10.9787/PBB.2017.5.1.25

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.

Citations

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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
    Horticulture Research.2024;[Epub]     CrossRef
  • 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
  • Cytokinin signaling promotes root secondary growth and bud formation in Panax ginseng
    Kyoung Rok Geem, Yookyung Lim, Jeongeui Hong, Wonsil Bae, Jinsu Lee, Soeun Han, Jinsu Gil, Hyunwoo Cho, Hojin Ryu
    Journal of Ginseng Research.2024; 48(2): 220.     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
  • Salinity responses and tolerance mechanisms in underground vegetable crops: an integrative review
    Kumar Nishant Chourasia, Sanket Jijabrao More, Ashok Kumar, Dharmendra Kumar, Brajesh Singh, Vinay Bhardwaj, Awadhesh Kumar, Sourav Kumar Das, Rajesh Kumar Singh, Gaurav Zinta, Rahul Kumar Tiwari, Milan Kumar Lal
    Planta.2022;[Epub]     CrossRef
  • Dynamic evolution of Panax species
    Hyeonah Shim, Nomar Espinosa Waminal, Hyun Hee Kim, Tae-Jin Yang
    Genes & Genomics.2021; 43(3): 209.     CrossRef
  • Gibberellin Signaling Promotes the Secondary Growth of Storage Roots in Panax ginseng
    Chang Pyo Hong, Jinsoo Kim, Jinsu Lee, Seung-il Yoo, Wonsil Bae, Kyoung Rok Geem, Jin Yu, Inbae Jang, Ick Hyun Jo, Hyunwoo Cho, Donghwan Shim, Hojin Ryu
    International Journal of Molecular Sciences.2021; 22(16): 8694.     CrossRef
  • Genetic diversity among cultivated and wild Panax ginseng populations revealed by high-resolution microsatellite markers
    Woojong Jang, Yeeun Jang, Nam-Hoon Kim, Nomar Espinosa Waminal, Young Chang Kim, Jung Woo Lee, Tae-Jin Yang
    Journal of Ginseng Research.2020; 44(4): 637.     CrossRef
  • Till 2018: a survey of biomolecular sequences in genus Panax
    Vinothini Boopathi, Sathiyamoorthy Subramaniyam, Ramya Mathiyalagan, Deok-Chun Yang
    Journal of Ginseng Research.2020; 44(1): 33.     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
  • Complete Mitochondrial Genome and a Set of 10 Novel Kompetitive Allele-Specific PCR Markers in Ginseng (Panax ginseng C. A. Mey.)
    Woojong Jang, Hyun Oh Lee, Jang-Uk Kim, Jung-Woo Lee, Chi-Eun Hong, Kyong-Hwan Bang, Jong-Wook Chung, Ick-Hyun Jo
    Agronomy.2020; 10(12): 1868.     CrossRef
  • Molecular Genetic Diversity and Population Structure of Ginseng Germplasm in RDA-Genebank: Implications for Breeding and Conservation
    Kyung Jun Lee, Jung-Ro Lee, Raveendar Sebastin, Gyu-Taek Cho, Do Yoon Hyun
    Agronomy.2020; 10(1): 68.     CrossRef
  • Genome and evolution of the shade‐requiring medicinal herb Panax ginseng
    Nam‐Hoon Kim, Murukarthick Jayakodi, Sang‐Choon Lee, Beom‐Soon Choi, Woojong Jang, Junki Lee, Hyun Hee Kim, Nomar E. Waminal, Meiyappan Lakshmanan, Binh van Nguyen, Yun Sun Lee, Hyun‐Seung Park, Hyun Jo Koo, Jee Young Park, Sampath Perumal, Ho Jun Joh, Ha
    Plant Biotechnology Journal.2018; 16(11): 1904.     CrossRef
  • Isoform Sequencing Provides a More Comprehensive View of the Panax ginseng Transcriptome
    Ick-Hyun Jo, Jinsu Lee, Chi Hong, Dong Lee, Wonsil Bae, Sin-Gi Park, Yong Ahn, Young Kim, Jang Kim, Jung Lee, Dong Hyun, Sung-Keun Rhee, Chang Hong, Kyong Bang, Hojin Ryu
    Genes.2017; 8(9): 228.     CrossRef
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