• ALGAE
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• v.17 no.1
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• pp.59-68
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• 2002

A phylogenetic affinity between charophytes and embryophytes (land plants) has been explained by a few chloroplast genomic characters including gene and intron (Manhart and Palmer 1990; Baldauf et al. 1990; Lew and Manhart 1993). Here we show that a charophyte, Spirogyra maxima, has the largest operon of angiosperm chloroplast genomes, rpl23 operon (trnⅠ-rpl23-rpl2-rps19-rpl22-rps3-rpl16-rpl14-rps8-infA-rpl36-rps11-rpoA) containing both embryophyte introns, rpl16.i and rpl2.i. The rpl23 gene cluster of Spirogyra contains a distinct eubacterial promoter sequence upstream of rpl23, which is the first gene of the green algal rpl23 gene cluster. This sequence is completely absent in angiosperms but is present in non-flowering plants. The results imply that, in the rpl23 gene cluster, early charophytes had at least two promoters, one upstream of trnⅠ and and another upstream of rpl23, which partially or completely lost its function in land plants. A comparison of gene clusters of prokaryotes, algal chloroplast DNAs and land plant cpDNAs indicated a loss of numerous genes in chlorophyll a+b eukaryotes. A phylogenetic analysis using presence/absence of genes and introns as characters produced trees with a strongly supported clade containing chlorophyll a+b eukaryotes. Spirogyra and embryophytes formed a clade characterized by the loss of rpl5 and rps9 and the gain of trnⅠ (CAU) and introns in rpl2 and rpl16. The analyses support the hypothesis that the rpl23 gene cluster and the rpl2 and rpl16 introns of land plants originated from a common ancestor of Spirogyra and land plants.

• Molecules and Cells
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• v.37 no.5
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• pp.372-382
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• 2014

In this study, the chloroplast (cp) genome sequences from three early diverged leptosporangiate ferns were completed and analyzed in order to understand the evolution of the genome of the fern lineages. The complete cp genome sequence of Osmunda cinnamomea (Osmundales) was 142,812 base pairs (bp). The cp genome structure was similar to that of eusporangiate ferns. The gene/intron losses that frequently occurred in the cp genome of leptosporangiate ferns were not found in the cp genome of O. cinnamomea. In addition, putative RNA editing sites in the cp genome were rare in O. cinnamomea, even though the sites were frequently predicted to be present in leptosporangiate ferns. The complete cp genome sequence of Diplopterygium glaucum (Gleicheniales) was 151,007 bp and has a 9.7 kb inversion between the trnL-CAA and trnV-GCA genes when compared to O. cinnamomea. Several repeated sequences were detected around the inversion break points. The complete cp genome sequence of Lygodium japonicum (Schizaeales) was 157,142 bp and a deletion of the rpoC1 intron was detected. This intron loss was shared by all of the studied species of the genus Lygodium. The GC contents and the effective numbers of codons (ENCs) in ferns varied significantly when compared to seed plants. The ENC values of the early diverged leptosporangiate ferns showed intermediate levels between eusporangiate and core leptosporangiate ferns. However, our phylogenetic tree based on all of the cp gene sequences clearly indicated that the cp genome similarity between O. cinnamomea (Osmundales) and eusporangiate ferns are symplesiomorphies, rather than synapomorphies. Therefore, our data is in agreement with the view that Osmundales is a distinct early diverged lineage in the leptosporangiate ferns.

• Korean Journal of Pharmacognosy
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• v.47 no.2
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• pp.128-136
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• 2016

Tiny leaf fragments were found in the Annals of the Joseon Dynasty, which were compiled about 500 years ago. The records describing the detailed process of compiling the Annals indicate that silk bags packed with the powders of 'Cheongung' and 'Changpo', which have been used as traditional herbal medicines in the northeast Asian countries such as China and Japan as well as Korea, were put in the wooden storage boxes together with the volumes of the Annals. However, there is no record that parts of plants were used in the process of compiling the Annals. The botanical origin of leaf fragments was identified as Ligusticum sinense 'Chuanxiong' by the analysis of trnK of chloroplast DNA as well as the examination of leaf surface with SEM. The comparative analysis of trnK sequences showed that the chloroplast DNA haplotype of 'Tocheongung', a triploid species cultivated in Korea, was identical with Cnidium officinale, but different from L. sinense 'Chuanxiong'. The molecular results provide a new suggestion on the botanical origin of crude drugs used as 'Cheongung', which has been disputed in Korea.

• Korean Journal of Plant Resources
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• v.28 no.3
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• pp.341-349
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• 2015

Magnoliae Flos (Sini in Korean) is one of the most important oriental medicinal plants. In the Korean Herbal Pharmacopeia, the bud of the all species in Manolia denudate and Manolia genus were regarded as the botanical sources for ‘Sini’. Most the dried bud of Manolia denudata, Manolia biondii and Manolia sprengeri were used as ‘Xin-yi’ in China. Therefore, the purpose of this study was to determine and compare the ‘Magnolia’ species, four species including Manolia denudata, M. biondii, M. liliiflora and M. Kobus were analysis of sequencing data revealed DNA polymorphisms. The based on tRNA coding leucine/phenylalanine (trnL-F) and NADH-plastoquinone oxidoreductase subunit 5 (ndhF) sequences in chloroplast DNA. For the identification of ‘Magnolia’ species, polymerase chain reaction (PCR) analysis of chloroplast DNA regions such as ndhF have proven an appropriate method. A single nucleotide polymorphism (SNP) has been identified between genuine “Sini” and their fraudulent and misuse. Specific PCR primers were designed from this polymorphic site within the sequence data, and were used to detect true plants via multiplex PCR.

• CELLMED
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• v.5 no.3
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• pp.15.1-15.12
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• 2015

Comparative studies have established that the North-Eastern (NE) region of India which is a part of the Eastern Himalayan region is affluent in both traditional knowledge based phytomedicine and biodiversity. About 1953 ethno-medicinal plants are detailed from the NE region of India out of which 1400 species are employed both as food and ethnopharmacological resources. Nearly 70% of species diversity has been reported from the two Indian biodiversity hotspots-The Western Ghats and the Eastern Himalayas and these hotspots are protected by tribal communities and their ancient traditional knowledge system. Paris polyphylla Smith belongs to the family Melanthiaceae and is a traditional medicinal herb which is known to cure some major ailments such as different types of Cancer, Alzheimer's disease, abnormal uterine bleeding, leishmaniasis etc. The major phytoconstituents are dioscin, polyphyllin D, and balanitin 7. Phylogeny of Paris was inferred from nuclear ITS and plastid psbA-trnH and trnL-trnF DNA sequence data. Results indicated that Paris is monophyletic in all analyses. Rhizoma Paridis, which is the dried rhizome of Paris polyphylla is mainly used in Traditional Chinese Medicine and its mode of action is known for only a few cancer cell lines. The current review determines to sketch an extensive picture of the potency, diversity, distribution and efficacy of Paris polyphylla from the Eastern Himalayan region and the future validation of its phytotherapeutical and molecular attributes by recognizing the Intellectual Property Rights of the Traditional Knowledge holders.

• Journal of Species Research
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• v.6 no.1
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• pp.76-90
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• 2017

Aster altaicus var. uchiyamae Kitam. is an endemic taxon of Korea and is protected by law as an endanger taxon. The genetic information of A. altaicus var. uchiyamae is unavailable in Genbank. Here we sequenced chloroplast genome of A. altaicus var. uchiyamae. The cp-genome of Aster altaicus var. uchiyamae was 152,446 bps in size: LSC was 84,240 bps, IR 25,005 bps, SSC 18,196 bps. The cp-genome contains 112 genes and 21 introns consisted of 79 protein coding genes(PCGs), 4 RNA genes, and 29 tRNA genes, with 20 group II introns and one group I intron. There were three pseudo-genes including ${\psi}$-ycf1, ${\psi}$-rps19, and ${\psi}$-trnT_GGU. Eighteen genes, five introns, and parts of two genes and an intron are found within the IR, which has two copies. The cp-DNA of Aster altaicus var. uchiyamae is distinguished from A. spathulifolius, only known cp-genome of the genus Aster, by 172 SNP in genic regions of 43 PCGs and 21 indels in 11 PCGs and SSU. The chloroplast genome sequence was deposited at GenBank (KX35265).

• Journal of Ginseng Research
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• v.27 no.3
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• pp.146-150
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• 2003

This study was carried out to obtain basic information on breeding using PCR-aided RFLP technology which can identify the variation inter- and intra-species of ginseng in the level of DNA. It was intended to investigate banding pattern on psbA and rbeL genes of chloroplast DNA in ginseng after treating with restriction enzymes. To isolate psbA and rbcL genes of chloroplast, both psbA-N, psbA-C primer and rbcL-N, PX-1 primer were used. As a result, 1,008 bp band of psbA gene and 1,336 bp band of rbcL gene were appeared, which was optimal and expected molecular weight. In addition, primers to isolate atpB, rpoB, trnL, and trnF genes were used, resulting in the expected 1366, 900, 1500 and 1008 bp bands. Genes of psbA and rbcL isolated by PCR were cut by restriction enzymes, Sau3A, TaqI, AluI, HaeIII, and RFLP pattern was investigated. KG line and other species of ginseng were cut by TaqI treatment, and bands were located in 800 bp. The treatment treated by AluI also showed the same 800 bp band in KG line and other species. In HaeIII treatment, 500 bp of faint bands were shown in case of KG line, whereas any bands were not observed in other species. All chloroplast genes formed bands by PCR amplification. However, it was not evident to distinguish intra-or inter-species of ginseng after restriction enzyme treatment. Therefore, more restriction enzyme treatment or sequence comparison method should be considered for further experiment.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2018.04a
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• pp.37-37
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• 2018

The genus Crepidiastrum (Asteraceae), containing ca. 20 species, is mainly distributed in Asia. Crepidiastrum denticulatum, an edible plant that commonly call "e-go-deulppae-gi" in Korean, distributes in Korea, Japan, and China. The complete chloroplast (cp) genome sequences of C. denticulatum was characterized from MiSeq2000 (Illumina Co.) pair-end sequencing data. The cp genome of C. denticulatum has a total sequence length of 152,689 bp and show a typical quadripartite structure. It consists of the large single copy (LSC: 84,022 bp), small single copy (SSC: 18,519 bp), separated by a pair of inverted repeats (IRs: 25,074 bp) and contains 110 unique genes and 18 genes duplicated in the IR regions. Our comparative analysis identified three cpDNA regions (matK, rbcL, and psbA-trnH) from three Crepidiastrum species, which may be useful for molecular identification of each species, and providing a guideline for its clear confirming about dried medical herb.

• Korean Journal of Plant Taxonomy
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• v.50 no.3
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• pp.253-261
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• 2020

Carex splendentissima U. Kang & J. M. Chung, endemic to the Korean peninsula, is characterized by staminate terminal spikes and glabrous elliptic perigynia. Based on its broad leaves, androgynous spikes, and tri-stigmatic features, the species has been placed in Carex sect. Siderostictae Franch. ex Ohwi, an East Asian section and a basal group in the genus. To clarify the monophyly and phylogenetic position of the species, a molecular study using the internal transcribed spacer region of nuclear ribosomal DNA and chloroplast DNA (trnL-F) data was conducted. The DNA sequence data of ten taxa in sect. Siderostictae and closely related taxa (two taxa in sect. Surculosae) with outgroups were analyzed based on maximum parsimony and maximum likelihood (ML) criteria. In the analyses, C. splendentissima was monophyletic and placed within the Siderostictae clade (sect. Siderostictae + two species of sect. Surculosae), forming a clade with C. ciliatomarginata and C. pachygyna (endemic to Japan). The clade (C. splendentissima + C. ciliatomarginata + C. pachygyna) shows evidence of diploidy. Furthermore, C. splendentissima is a sister to C. ciliatomarginata in the ML tree, and the two taxa have staminate terminal spikes. This study also updates the distribution of C. splendentissima and provides keys to the four Korean taxa in sect. Siderostictae. To conserve the endemic species C. splendentissima, further research on its genetic and ecological features should be conducted at the population level.

• Korean Journal of Plant Taxonomy
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• v.37 no.1
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• pp.1-15
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• 2007

Phylogenetic studies were conducted for 42 populations of Korean viola based on matK gene and atpB-rbcL intergenic spacer region of chloroplast DNA. In the matK tree, section Chamaemelanium and Dischidium were formed as a distinct group. Five subsections of section Nomimium were paraphyletic. In atpB-rbcL intergenic spacer region analysis, two species of sect. Chamaemelanium were monophyletic, and section Dischidium was placed sister to subsection patellares clade except for V. keiskei. Five subsections of section Nomimium were also paraphyletic as matK tree. the separate data analyses were incongruent in the relationships among 42 populations, especially for the position of section Dischidium and V. keiskei. The combined analyses of two chloroplast regions showed three major clades; section Chamaemelanium and Dischidium (x=6) formed a sister to subsections Hypocarpae and Trigonocarpae (x=10) clade; subsections Bilobatae and vaginatae (x=10 or 12) formed a clade with V. keiskei; and 19 populations of subsection patellares (x=12) except for V. keiskei were recognized as an independent clade within section Nomimium. Although combined data suggest three major clades of Korean viola, the origins of each clade from outgroup were discordance with previous ITS and trnL-F data.