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  1. Article: A phylogenomic study of Iridaceae Juss. based on complete plastid genome sequences.

    Kamra, Kashish / Jung, Joonhyung / Kim, Joo-Hwan

    Frontiers in plant science

    2023  Volume 14, Page(s) 1066708

    Abstract: The plastid genome has proven to be an effective tool for examining deep correlations in plant phylogenetics, owing to its highly conserved structure, uniparental inheritance, and limited variation in evolutionary rates. Iridaceae, comprising more than 2, ...

    Abstract The plastid genome has proven to be an effective tool for examining deep correlations in plant phylogenetics, owing to its highly conserved structure, uniparental inheritance, and limited variation in evolutionary rates. Iridaceae, comprising more than 2,000 species, includes numerous economically significant taxa that are frequently utilized in food industries and medicines and for ornamental and horticulture purposes. Molecular studies on chloroplast DNA have confirmed the position of this family in the order Asparagales with non-asparagoids. The current subfamilial classification of Iridaceae recognizes seven subfamilies-Isophysioideae, Nivenioideae, Iridoideae, Crocoideae, Geosiridaceae, Aristeoideae, and Patersonioideae-which are supported by limited plastid DNA regions. To date, no comparative phylogenomic studies have been conducted on the family Iridaceae. We assembled and annotated (
    Language English
    Publishing date 2023-01-31
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2613694-6
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2023.1066708
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Insights into phylogenetic relationships and genome evolution of subfamily Commelinoideae (Commelinaceae Mirb.) inferred from complete chloroplast genomes.

    Jung, Joonhyung / Kim, Changkyun / Kim, Joo-Hwan

    BMC genomics

    2021  Volume 22, Issue 1, Page(s) 231

    Abstract: Background: Commelinaceae (Commelinales) comprise 41 genera and are widely distributed in both the Old and New Worlds, except in Europe. The relationships among genera in this family have been suggested in several morphological and molecular studies. ... ...

    Abstract Background: Commelinaceae (Commelinales) comprise 41 genera and are widely distributed in both the Old and New Worlds, except in Europe. The relationships among genera in this family have been suggested in several morphological and molecular studies. However, it is difficult to explain their relationships due to high morphological variations and low support values. Currently, many researchers have been using complete chloroplast genome data for inferring the evolution of land plants. In this study, we completed 15 new plastid genome sequences of subfamily Commelinoideae using the Mi-seq platform. We utilized genome data to reveal the structural variations and reconstruct the problematic positions of genera for the first time.
    Results: All examined species of Commelinoideae have three pseudogenes (accD, rpoA, and ycf15), and the former two might be a synapomorphy within Commelinales. Only four species in tribe Commelineae presented IR expansion, which affected duplication of the rpl22 gene. We identified inversions that range from approximately 3 to 15 kb in four taxa (Amischotolype, Belosynapsis, Murdannia, and Streptolirion). The phylogenetic analysis using 77 chloroplast protein-coding genes with maximum parsimony, maximum likelihood, and Bayesian inference suggests that Palisota is most closely related to tribe Commelineae, supported by high support values. This result differs significantly from the current classification of Commelinaceae. Also, we resolved the unclear position of Streptoliriinae and the monophyly of Dichorisandrinae. Among the ten CDS (ndhH, rpoC2, ndhA, rps3, ndhG, ndhD, ccsA, ndhF, matK, and ycf1), which have high nucleotide diversity values (Pi > 0.045) and over 500 bp length, four CDS (ndhH, rpoC2, matK, and ycf1) show that they are congruent with the topology derived from 77 chloroplast protein-coding genes.
    Conclusions: In this study, we provide detailed information on the 15 complete plastid genomes of Commelinoideae taxa. We identified characteristic pseudogenes and nucleotide diversity, which can be used to infer the family evolutionary history. Also, further research is needed to revise the position of Palisota in the current classification of Commelinaceae.
    MeSH term(s) Bayes Theorem ; Commelinaceae ; Europe ; Evolution, Molecular ; Genome, Chloroplast ; Phylogeny
    Language English
    Publishing date 2021-04-02
    Publishing country England
    Document type Journal Article
    ISSN 1471-2164
    ISSN (online) 1471-2164
    DOI 10.1186/s12864-021-07541-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Characterization of the complete plastid genome of Korean endemic,

    Kamra, Kashish / Jung, Joonhyung / Kim, Hyuk-Jin / Yoon, Chang-Young / Kim, Joo-Hwan

    Mitochondrial DNA. Part B, Resources

    2023  Volume 8, Issue 1, Page(s) 119–123

    Abstract: ... Ajuga ... ...

    Abstract Ajuga spectabilis
    Language English
    Publishing date 2023-01-15
    Publishing country England
    Document type Journal Article
    ISSN 2380-2359
    ISSN (online) 2380-2359
    DOI 10.1080/23802359.2022.2156258
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Comparative analysis and implications of the chloroplast genomes of three thistles (

    Jung, Joonhyung / Do, Hoang Dang Khoa / Hyun, JongYoung / Kim, Changkyun / Kim, Joo-Hwan

    PeerJ

    2021  Volume 9, Page(s) e10687

    Abstract: Background: Carduus: Methods: We sequenced and assembled the chloroplast genome (cpDNA) sequences of three : Results: The cpDNA sequences ... ...

    Abstract Background: Carduus
    Methods: We sequenced and assembled the chloroplast genome (cpDNA) sequences of three
    Results: The cpDNA sequences of
    Language English
    Publishing date 2021-01-14
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2703241-3
    ISSN 2167-8359
    ISSN 2167-8359
    DOI 10.7717/peerj.10687
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Correction: Development of molecular markers for invasive alien plants in Korea: a case study of a toxic weed,

    Hyun, JongYoung / Do, Hoang Dang Khoa / Jung, Joonhyung / Kim, Joo-Hwan

    PeerJ

    2019  Volume 7

    Abstract: This corrects the article DOI: 10.7717/peerj.7965.]. ...

    Abstract [This corrects the article DOI: 10.7717/peerj.7965.].
    Language English
    Publishing date 2019-12-16
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 2703241-3
    ISSN 2167-8359
    ISSN 2167-8359
    DOI 10.7717/peerj.7965/correction-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Development of molecular markers for invasive alien plants in Korea: a case study of a toxic weed,

    Hyun, JongYoung / Do, Hoang Dang Khoa / Jung, Joonhyung / Kim, Joo-Hwan

    PeerJ

    2019  Volume 7, Page(s) e7965

    Abstract: Background: Genomic data play an important role in plant research because of its implications in studying genomic evolution, phylogeny, and developing molecular markers. Although the information of invasive alien plants was collected, the genomic data ... ...

    Abstract Background: Genomic data play an important role in plant research because of its implications in studying genomic evolution, phylogeny, and developing molecular markers. Although the information of invasive alien plants was collected, the genomic data of those species have not been intensively studied.
    Methods: We employ the next generation sequencing and PCR methods to explore the genomic data as well as to develop and test the molecular markers.
    Results: In this study, we characterize the chloroplast genomes (cpDNA) of
    Language English
    Publishing date 2019-11-11
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2703241-3
    ISSN 2167-8359
    ISSN 2167-8359
    DOI 10.7717/peerj.7965
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Characterization of the complete chloroplast genome of Korean endemic,

    Kim, Changkyun / Do, Hoang Dang Khoa / Jung, Joonhyung / Kim, Dong-Kap / Kim, Joo-Hwan

    Mitochondrial DNA. Part B, Resources

    2020  Volume 5, Issue 3, Page(s) 3269–3271

    Abstract: Habenaria ... ...

    Abstract Habenaria cruciformis
    Language English
    Publishing date 2020-08-31
    Publishing country England
    Document type Journal Article
    ISSN 2380-2359
    ISSN (online) 2380-2359
    DOI 10.1080/23802359.2020.1812448
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: The newly developed single nucleotide polymorphism (SNP) markers for a potentially medicinal plant, Crepidiastrum denticulatum (Asteraceae), inferred from complete chloroplast genome data.

    Do, Hoang Dang Khoa / Jung, Joonhyung / Hyun, JongYoung / Yoon, Seok Jeong / Lim, Chaejin / Park, Keedon / Kim, Joo-Hwan

    Molecular biology reports

    2019  Volume 46, Issue 3, Page(s) 3287–3297

    Abstract: Medicinal effects of Crepidiastrum denticulatum have been previously reported. However, the genomic resources of this species and its applications have not been studied. In this study, based on the next generation sequencing method (Miseq sequencing ... ...

    Abstract Medicinal effects of Crepidiastrum denticulatum have been previously reported. However, the genomic resources of this species and its applications have not been studied. In this study, based on the next generation sequencing method (Miseq sequencing system), we characterize the chloroplast genome of C. denticulatum which contains a large single copy (84,112 bp) and a small single copy (18,519 bp), separated by two inverted repeat regions (25,074 bp). This genome consists of 80 protein-coding gene, 30 tRNAs, and four rRNAs. Notably, the trnT_GGU is pseudogenized because of a small insertion within the coding region. Comparative genomic analysis reveals a high similarity among Asteraceae taxa. However, the junctions between LSC, SSC, and IRs locate in different positions within rps19 and ycf1 among examined species. Also, we describe a newly developed single nucleotide polymorphism (SNP) marker for C. denticulatum based on amplification-refractory mutation system (ARMS) technique. The markers, inferred from SNP in rbcL and matK genes, show effectiveness to recognize C. denticulatum from other related taxa through simple PCR protocol. The chloroplast genome-based molecular markers are effective to distinguish a potentially medicinal species, C. denticulatum, from other related taxa. Additionally, the complete chloroplast genome of C. denticulatum provides initial genomic data for further studies on phylogenomics, population genetics, and evolutionary history of Crepidiastrum as well as other taxa in Asteraceae.
    MeSH term(s) Asteraceae/genetics ; Biomarkers ; Chloroplasts/genetics ; Evolution, Molecular ; Genes, Plant/genetics ; Genome, Chloroplast/genetics ; Genome, Plant/genetics ; Genomics ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Plants, Medicinal/genetics ; Polymorphism, Single Nucleotide/genetics ; Sequence Analysis, DNA
    Chemical Substances Biomarkers
    Language English
    Publishing date 2019-04-12
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 186544-4
    ISSN 1573-4978 ; 0301-4851
    ISSN (online) 1573-4978
    ISSN 0301-4851
    DOI 10.1007/s11033-019-04789-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1140: Show issues Location:
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  9. Article: The newly developed single nucleotide polymorphism (SNP) markers for a potentially medicinal plant, Crepidiastrum denticulatum (Asteraceae), inferred from complete chloroplast genome data

    Do, Hoang Dang Khoa / Jung, Joonhyung / Hyun, JongYoung / Yoon, Seok Jeong / Lim, Chaejin / Park, Keedon / Kim, Joo-Hwan

    Molecular biology reports. 2019 June, v. 46, no. 3

    2019  

    Abstract: Medicinal effects of Crepidiastrum denticulatum have been previously reported. However, the genomic resources of this species and its applications have not been studied. In this study, based on the next generation sequencing method (Miseq sequencing ... ...

    Abstract Medicinal effects of Crepidiastrum denticulatum have been previously reported. However, the genomic resources of this species and its applications have not been studied. In this study, based on the next generation sequencing method (Miseq sequencing system), we characterize the chloroplast genome of C. denticulatum which contains a large single copy (84,112 bp) and a small single copy (18,519 bp), separated by two inverted repeat regions (25,074 bp). This genome consists of 80 protein-coding gene, 30 tRNAs, and four rRNAs. Notably, the trnT_GGU is pseudogenized because of a small insertion within the coding region. Comparative genomic analysis reveals a high similarity among Asteraceae taxa. However, the junctions between LSC, SSC, and IRs locate in different positions within rps19 and ycf1 among examined species. Also, we describe a newly developed single nucleotide polymorphism (SNP) marker for C. denticulatum based on amplification‐refractory mutation system (ARMS) technique. The markers, inferred from SNP in rbcL and matK genes, show effectiveness to recognize C. denticulatum from other related taxa through simple PCR protocol. The chloroplast genome-based molecular markers are effective to distinguish a potentially medicinal species, C. denticulatum, from other related taxa. Additionally, the complete chloroplast genome of C. denticulatum provides initial genomic data for further studies on phylogenomics, population genetics, and evolutionary history of Crepidiastrum as well as other taxa in Asteraceae.
    Keywords Crepidiastrum ; chloroplast genome ; chloroplasts ; genes ; genetic markers ; genomics ; high-throughput nucleotide sequencing ; medicinal plants ; medicinal properties ; polymerase chain reaction ; ribosomal RNA ; single nucleotide polymorphism ; transfer RNA
    Language English
    Dates of publication 2019-06
    Size p. 3287-3297.
    Publishing place Springer Netherlands
    Document type Article
    ZDB-ID 186544-4
    ISSN 1573-4978 ; 0301-4851
    ISSN (online) 1573-4978
    ISSN 0301-4851
    DOI 10.1007/s11033-019-04789-5
    Database NAL-Catalogue (AGRICOLA)

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