28 results on '"Sungyu Yang"'
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2. Genetic and demographic signatures accompanying the evolution of the selfing syndrome in Daphne kiusiana, an evergreen shrub
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Eun-Kyeong Han, Ichiro Tamaki, Sang-Hun Oh, Jong-Soo Park, Won-Bum Cho, Dong-Pil Jin, Bo-Yun Kim, Sungyu Yang, Dong Chan Son, Hyeok-Jae Choi, Amarsanaa Gantsetseg, Yuji Isagi, and Jung-Hyun Lee
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Plant Science - Abstract
Background and Aims The evolution of mating systems from outcrossing to self-fertilization is a common transition in flowering plants. This shift is often associated with the ‘selfing syndrome’, which is characterized by less visible flowers with functional changes to control outcrossing. In most cases, the evolutionary history and demographic dynamics underlying the evolution of the selfing syndrome remain poorly understood. Methods Here, we characterize differences in the demographic genetic consequences and associated floral-specific traits between two distinct geographical groups of a wild shrub, Daphne kiusiana, endemic to East Asia; plants in the eastern region (southeastern Korea and Kyushu, Japan) exhibit smaller and fewer flowers compared to those of plants in the western region (southwestern Korea). Genetic analyses were conducted using nuclear microsatellites and chloroplast DNA (multiplexed phylogenetic marker sequencing) datasets. Key Results A high selfing rate with significantly increased homozygosity characterized the eastern lineage, associated with lower levels of visibility and herkogamy in the floral traits. The two lineages harboured independent phylogeographical histories. In contrast to the western lineage, the eastern lineage showed a gradual reduction in the effective population size with no signs of a severe bottleneck despite its extreme range contraction during the last glacial period. Conclusions Our results suggest that the selfing-associated morphological changes in D. kiusiana are of relatively old origin (at least 100 000 years ago) and were driven by directional selection for efficient self-pollination. We provide evidence that the evolution of the selfing syndrome in D. kiusiana is not strongly associated with a severe population bottleneck.
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- 2022
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3. A taxonomic revision of Philadelphus (Hydrangeaceae) in South Korea
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Young Moon Kim, Shukherdorj Baasanmunkh, Jun-Ho Song, Sungyu Yang, Dong Chan Son, and Hyeok Jae Choi
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Ecology ,Insect Science ,Animal Science and Zoology ,Plant Science ,Ecology, Evolution, Behavior and Systematics - Published
- 2022
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4. Notes on Allium section Rhizirideum (Amaryllidaceae) in South Korea and northeastern China: with a new species from Ulleungdo Island
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Dong-Kap Kim, Jong-Soo Park, Ju Eun Jang, Sungyu Yang, Ji-Young Jung, and Hyeok Jae Choi
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Synonym ,Liliopsida ,Asparagales ,Plant Science ,DNA barcoding ,Allium ,taxonomy ,morphology ,Botany ,DNA barcode ,distribution ,Plantae ,Ecology, Evolution, Behavior and Systematics ,new species ,biology ,Amaryllidaceae ,food and beverages ,synonym ,biology.organism_classification ,Chromosome number ,Tracheophyta ,Geography ,Herbarium ,QK1-989 ,Key (lock) ,Taxonomy (biology) ,Perianth - Abstract
Allium section Rhizirideum is reviewed for South Korea and neighboring northeastern China based on critical observation of wild populations and herbarium materials. Species delimitations are re-evaluated on the basis of morphological and somatic chromosome numbers, resulting in the recognition of five species. Allium dumebuchum from Ulleungdo Island, South Korea, is described as a new species. This species is most similar to A. senescens due to its habits, but is clearly distinguished particularly by its rhomboid scapes in cross-secion, light purple perianth color, entire and narrowly triangular inner filaments, and flowering season from late September. One previously recognized species is placed into synonymy: A. pseudosenescens (under A. senescens). Photographs and a key to species of Allium section Rhizirideum in South Korea and northeastern China are provided in addition to information on nomenclatural types, synonymies, chromosome numbers, distribution, and specimens examined.
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- 2021
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5. A checklist of Gasan Mt.: an online platform for virtual specimens
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Mi-Jung Choi, Bo-Mi Nam, Sungyu Yang, Hyeok Jae Choi, Kyong-Sook Chung, Goya Choi, and Ju-Eun Jang
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World Wide Web ,Geography ,Plant Science ,Ecology, Evolution, Behavior and Systematics ,Checklist - Published
- 2020
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6. Phylogenetic position of Carex splendentissima, a Korean endemic sedge (Cyperaceae)
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Kyong-Sook CHUNG, Sungyu YANG, and Bo-Mi NAM
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Monophyly ,Carex ,Taxon ,biology ,Phylogenetic tree ,Genus ,Botany ,Plant Science ,Internal transcribed spacer ,biology.organism_classification ,Clade ,Ecology, Evolution, Behavior and Systematics ,Maximum parsimony - Abstract
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.
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- 2020
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7. Chromosome Numbers and Karyotypes of Representatives of Caryophyllaceae from Korea
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Sungyu Yang, Bo-Mi Nam, Gyu Young Chung, and Hyeok Jae Choi
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Genetics ,Silene ,Chromosome number ,biology ,Chromosome (genetic algorithm) ,Caryophyllaceae ,Animal Science and Zoology ,Karyotype ,Cell Biology ,Plant Science ,biology.organism_classification - Published
- 2020
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8. New distribution records of two rare species of Cynanchum (Apocynaceae) in South Korea: Cynanchum thesioides (Freyn) K. Schum. and Cynanchum chinense R. Br
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Gyu Young Chung, Sungyu Yang, and Bo-Mi Nam
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geography ,education.field_of_study ,geography.geographical_feature_category ,biology ,Apocynaceae ,Population ,Rare species ,Asclepiadoideae ,Plant Science ,Cynanchum ,biology.organism_classification ,Taxon ,Peninsula ,Botany ,Conservation status ,education ,Ecology, Evolution, Behavior and Systematics - Abstract
Cynanchum L. in the subfamily Asclepiadoideae (Apocynaceae) includes four recognized species on the Korean peninsula, two of which are native to South Korea. However, the species ranges in South Korea are poorly defined. During a field survey, we discovered C. thesioides, previously unrecorded in South Korea, in Gimpo-si, Gyeonggi-do, and found an additional population of C. chinense, for which only one population has been reported in South Korea. The two taxa are considered rare species with extremely restricted distributions in South Korea, especially C. thesioides. We provide fundamental information, including descriptions, images of the habitats and morphological characters, and a taxonomic key for identification and assessments of the conservation status of Cynanchum species in Korea.
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- 2020
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9. Indirect in vitro Regeneration of the Medicinal Plant, Aspilia africana, and Histological Assessment at Different Developmental Stages
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Denis Okello, Sungyu Yang, Richard Komakech, Yuseong Chung, Endang Rahmat, Roggers Gang, Francis Omujal, Alice V. Lamwaka, and Youngmin Kang
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micropropagation ,anatomical assessment ,callus ,organogenesis ,fungi ,food and beverages ,Plant culture ,Plant Science ,in vitro propagation ,Aspilia africana ,Original Research ,SB1-1110 - Abstract
The medicinal plant, Aspilia africana, has been traditionally used in several African countries to treat many diseases such as tuberculosis, cough, inflammation, malaria, osteoporosis, and diabetes. In this study, we developed a protocol for in vitro propagation of A. africana using indirect shoot organogenesis from leaf and root explants of in vitro-grown seedlings and assessed the tissues at different developmental stages. The highest callus induction (91.9 ± 2.96%) from leaf explants was in the Murashige and Skoog (MS) medium augmented with 1.0 mg/L 6-Benzylaminopurine (BAP) and 1.0 mg/L 2,4-dichlorophenoxyacetic acid (2,4-D) while from root explants, the highest callus induction (92.6 ± 2.80%) was in the same plant tissue culture medium augmented with 0.5 mg/L BAP and 1.0 mg/L 2,4-D. The best shoot regeneration capacity from leaf-derived calli (i.e., 80.0 ± 6.23% regeneration percentage and 12.0 ± 6.23 shoots per callus) was obtained in medium augmented with 1.0 mg/L BAP and 0.05 mg/L α-Naphthaleneacetic acid (NAA); the best regeneration capacity for root-derived calli (i.e., 86.7 ± 6.24% shoot regeneration percentage and 14.7 ± 1.11 shoots per callus) was obtained in the MS medium augmented with 1.0 mg/L BAP, 0.05 mg/L NAA, and 0.1 mg/L Thidiazuron (TDZ). Regenerated plantlets developed a robust root system in 1/2 MS medium augmented with 0.1 mg/L NAA and had a survival rate of 93.6% at acclimatization. The in vitro regenerated stem tissue was fully differentiated, while the young leaf tissue consisted of largely unorganized and poorly differentiated cells with large intercellular airspaces typical of in vitro leaf tissues. Our study established a protocol for the indirect regeneration of A. africana and offers a basis for its domestication, large-scale multiplication, and germplasm preservation. To the best of our knowledge, this is the first study to develop an indirect regeneration protocol for A. africana and conduct anatomical assessment through the different stages of development from callus to a fully developed plantlet.
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- 2021
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10. Allium ulleungense (Amaryllidaceae), a new species endemic to Ulleungdo Island, Korea
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Sungyu Yang, Hyeok Jae Choi, Jong-Cheol Yang, and Nikolai Friesen
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Phylogenetic tree ,Range (biology) ,Botany ,Diploid chromosome number ,Allium ,Close relatives ,Plant Science ,Amaryllidaceae ,Biology ,Microdictyon ,Perianth ,biology.organism_classification ,Ecology, Evolution, Behavior and Systematics - Abstract
Allium ulleungense (subg. Anguinum, Amaryllidaceae), from Ulleungdo Island, Korea, is described as a new species. It is clearly distinguished from its close relatives, A. microdictyon and A. ochotense, by its broader leaves and larger whitish perianth and by its diploid chromosome number, which is 2n = 2x = 16. The lengths of the chromosomes range from 11.3 to 15.75 μm. Molecular phylogenetic analyses using nuclear and chloroplast markers also clearly indicate that A. ulleungense is genetically distinct from other species of the subg. Anguinum.
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- 2019
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11. Taxonomic review of Spiraea chartacea compared with its related species of section Chamaedryon in Korea
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Mi Jung Choi, Hyo Seong Eom, Jung-Hyun Lee, Sungyu Yang, and Hyeok Jae Choi
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0106 biological sciences ,Ecology ,biology ,Range (biology) ,010607 zoology ,Plant Science ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Hypanthium ,Sepal ,Spiraea ,Type (biology) ,Herbarium ,Pedicel ,lcsh:QH540-549.5 ,Insect Science ,Botany ,Key (lock) ,Animal Science and Zoology ,lcsh:Ecology ,Ecology, Evolution, Behavior and Systematics - Abstract
A taxonomic revision of Korean endemic Spiraea chartacea is presented compared with its related three species, S. blumei, S. turczaninowii (≡ S. pubescens Turcz.), and S. chinensis, of section Chamaedryon in Korea. Species delimitations are re-evaluated based on critical observations of wild populations and extensive herbarium material. The shape of leaf, the type and distribution of trichome in stem, leaf, peduncle, pedicel, hypanthium, sepal, carpel, and follicle are useful diagnostic traits at the specific level. Almost all morphological and leaf anatomical observations of S. chartacea belong within the range of S. turczaninowii. Therefore, S. turczaninowii is placed into synonymy of S. chartacea by priority. Photographs and a key to three species of Spiraea section Chamaedryon are provided in addition to complete descriptions including information on nomenclatural types, synonymies, chromosome numbers, distributions, and specimens examined. Keywords: Anatomy, Morphology, Rosaceae, Section Chamaedryon, Spiraea L.
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- 2019
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12. Dissection for Floral Micromorphology and Plastid Genome of Valuable Medicinal Borages Arnebia and Lithospermum (Boraginaceae)
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Sungyu Yang, Byeong Cheol Moon, Inkyu Park, and Jun-Ho Song
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molecular marker ,Gynoecium ,biology ,Phylogenetic tree ,phylogenetic analysis ,Lithospermum ,Plant Science ,lcsh:Plant culture ,micromorphology ,Boraginaceae ,Lithospermum erythrorhizon ,biology.organism_classification ,Genome ,chemistry.chemical_compound ,Sister group ,chemistry ,Evolutionary biology ,Molecular marker ,plastid genome ,lcsh:SB1-1110 ,Arnebia ,Original Research - Abstract
The generaArnebiaandLithospermum(Lithospermeae-Boraginaceae) comprise 25–30 and 50–60 species, respectively. Some of them are economically valuable, as their roots frequently contain a purple-red dye used in the cosmetic industry. Furthermore, dried roots ofArnebia euchroma,A. guttata, andLithospermum erythrorhizon, which have been designated Lithospermi Radix, are used as traditional Korean herbal medicine. This study is the first report on the floral micromorphology and complete chloroplast (cp) genome sequences ofA. guttata(includingA. tibetana),A. euchroma, andL. erythrorhizon. We reveal great diversity in floral epidermal cell patterns, gynoecium, and structure of trichomes. The cp genomes were 149,361–150,465 bp in length, with conserved quadripartite structures. In total, 112 genes were identified, including 78 protein-coding regions, 30 tRNA genes, and four rRNA genes. Gene order, content, and orientation were highly conserved and were consistent with the general structure of angiosperm cp genomes. Comparison of the four cp genomes revealed locally divergent regions, mainly within intergenic spacer regions (atpH-atpI,petN-psbM,rbcL-psaI,ycf4-cemA,ndhF-rpl32, andndhC-trnV-UAC). To facilitate species identification, we developed molecular markerspsaA-ycf3(PSY),trnI-CAU- ycf2(TCY), andndhC-trnV-UAC(NCTV) based on divergence hotspots. High-resolution phylogenetic analysis revealed clear clustering and a close relationship ofArnebiato itsLithospermumsister group, which was supported by strong bootstrap values and posterior probabilities. Overall, gynoecium characteristics and genetic distance of cp genomes suggest thatA. tibetana, might be recognized as an independent species rather than a synonym ofA. guttata. The present morphological and cp genomic results provide useful information for future studies, such as taxonomic, phylogenetic, and evolutionary analysis of Boraginaceae.
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- 2020
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13. A Micropropagation Protocol for the Endangered Medicinal Tree Prunus africana (Hook f.) Kalkman: Genetic Fidelity and Physiological Parameter Assessment
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Richard Komakech, Yong-Goo Kim, Wook Jin Kim, Francis Omujal, Sungyu Yang, Byeong Cheol Moon, Denis Okello, Endang Rahmat, Grace Nambatya Kyeyune, Motlalepula Gilbert Matsabisa, and Youngmin Kang
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0106 biological sciences ,micropropagation ,Recalcitrant seed ,Plant Science ,lcsh:Plant culture ,01 natural sciences ,Acclimatization ,03 medical and health sciences ,medicinal plant ,genetic fidelity ,chlorophyll ,lcsh:SB1-1110 ,030304 developmental biology ,0303 health sciences ,Prunus africana ,photosynthesis ,chemical characterization ,biology ,food and beverages ,biology.organism_classification ,RAPD ,Horticulture ,Micropropagation ,Shoot ,010606 plant biology & botany ,Woody plant ,Explant culture - Abstract
Prunus africana is an endangered medicinal plant and hence new propagation methods are urgently required to increase its populations. Unfortunately, propagation through seeds is challenging due to its long flowering cycle and recalcitrant seeds. We developed a protocol for micropropagation using nodal segment explants. A woody plant medium supplemented with vitamins, 15 g L−1 sucrose, and 1.0 mg L−1 6-benzylaminopurine (BAP) supported the optimum rate (100%) of axillary shoot initiation. Supplementation with 15 g L−1 sucrose and 1.5 mg L−1 indole-3-acetic acid (IAA) provided the optimum rate (75%) of root initiation. Rooted plantlets were successfully planted in sterilized horticultural soil containing perlite (2:1 v/v) and the survival rate was 98% following acclimatization. The photosynthetic rate assessed using FlourPen FP110 series showed that the ratio of variable fluorescence to maximum fluorescence mean value for in vitro regenerated P. africana (0.830 ± 0.0008) was similar to that of the maternal P. africana plant (0.825 ± 0.005), indicating similarity in their photosynthetic performance; a pivotal process for growth and development. The Fourier transform near-IR (FT-NIR) spectrometer analysis of the in vitro regenerated and the maternal P. africana plant samples exhibited homogeneity in the absorbance peaks at 8,273, 6,344, and 4,938–4,500 cm−1 associated with lipids, starch, and proteins. The genetic fidelity of regenerated plants was confirmed using the randomly amplified polymorphic DNA (RAPD) technique. Our protocol is suitable for use in large-scale P. africana to meet the increasing demands for it in the global market.
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- 2020
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14. Three Scrophularia Species (Scrophularia buergeriana, S. koraiensis, and S. takesimensis) Inhibit RANKL-Induced Osteoclast Differentiation in Bone Marrow-Derived Macrophages
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Yun-Soo Seo, Jun-Ho Song, Byeong Cheol Moon, Hyeon-Hwa Nam, Sungyu Yang, Inkyu Park, Jin Mi Chun, Joong Sun Kim, and A Yeong Lee
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Arthritis ,Plant Science ,Scrophularia buergeriana ,Bone resorption ,03 medical and health sciences ,0302 clinical medicine ,Osteoclast ,medicine ,Scrophularia ,Ecology, Evolution, Behavior and Systematics ,S. takesimensis ,030304 developmental biology ,osteoclast differentiation ,0303 health sciences ,Scrophularia ningpoensis ,harpagoside ,Ecology ,biology ,Traditional medicine ,Chemistry ,Acid phosphatase ,RANKL ,Botany ,S. koraiensis ,biology.organism_classification ,medicine.disease ,medicine.anatomical_structure ,030220 oncology & carcinogenesis ,QK1-989 ,biology.protein ,Bone marrow - Abstract
Scrophulariae Radix, derived from the dried roots of Scrophularia ningpoensis Hemsl. or S. buergeriana Miq, is a traditional herbal medicine used in Asia to treat rheumatism, arthritis, and pharyngalgia. However, the effects of Scrophularia buergeriana, S. koraeinsis, and S. takesimensis on osteoclast formation and bone resorption remain unclear. In this study, we investigated the morphological characteristics and harpagoside content of S. buergeriana, S. koraiensis, and S. takesimensis, and compared the effects of ethanol extracts of these species using nuclear factor (NF)-&kappa, B ligand (RANKL)-mediated osteoclast differentiation. The harpagoside content of the three Scrophularia species was analyzed by high-performance liquid chromatography&ndash, mass spectrometry (HPLC/MS). Their therapeutic effects were evaluated by tartrate-resistant acid phosphatase (TRAP)-positive cell formation and bone resorption in bone marrow-derived macrophages (BMMs) harvested from ICR mice. We confirmed the presence of harpagoside in the Scrophularia species. The harpagoside content of S. buergeriana, S. koraiensis, and S. takesimensis was 1.94 ±, 0.24 mg/g, 6.47 ±, 0.02 mg/g, and 5.50 ±, 0.02 mg/g, respectively. Treatment of BMMs with extracts of the three Scrophularia species inhibited TRAP-positive cell formation in a dose-dependent manner. The area of hydroxyapatite-absorbed osteoclasts was markedly decreased after treatment with the three Scrophularia species extracts. Our results indicated that the three species of the genus Scrophularia might exert preventive effects on bone disorders by inhibiting osteoclast differentiation and bone resorption, suggesting that these species may have medicinal and functional value.
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- 2020
15. An Integrated Approach for Efficient and Accurate Medicinal Cuscutae Semen Identification
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Goya Choi, Sungyu Yang, Inkyu Park, Byeong Cheol Moon, and Jun-Ho Song
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0106 biological sciences ,Identification key ,Plant Science ,Computational biology ,010603 evolutionary biology ,01 natural sciences ,DNA barcoding ,Genome ,Article ,barcode primer ,endosperm ,03 medical and health sciences ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,0303 health sciences ,Ecology ,biology ,seed morphology ,Cuscutae Semen ,Botany ,scanning electron microscope ,Integrated approach ,light microscope ,biology.organism_classification ,Cuscuta chinensis ,morphological identification key ,QK1-989 ,Identification (biology) ,Primer (molecular biology) ,Cuscuta ,rbcL gene - Abstract
To guarantee the safety and efficacy of herbal medicines, accurate identification and quality evaluation are crucial. The ripe dried seeds of Cuscuta australis R.Br. and C. chinensis Lam. are known as Cuscutae Semen (CS) and are widely consumed in Northeast Asia, however, the seeds of other species can be misidentified as CS owing to morphological similarities, leading to misuse. In this report, we propose a multilateral strategy combining microscopic techniques with statistical analysis and DNA barcoding using a genus-specific primer to facilitate the identification and authentication of CS. Morphology-based identification using microscopy revealed that the useful diagnostic characteristics included general shape, embryo exudation, hairiness, and testa ornamentation, which were used to develop an effective identification key. In addition, we conducted DNA barcoding-based identification to ensure accurate authentication. A novel DNA barcode primer was produced from the chloroplast rbcL gene by comparative analysis using Cuscuta chloroplast genome sequences, which allowed four Cuscuta species and adulterants to be discriminated completely. Therefore, this investigation overcame the limitations of universal DNA barcodes for Cuscuta species with high variability. We believe that this integrated approach will enable CS to be differentiated from other species, thereby improving its quality control and product safety in medicinal markets.
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- 2020
16. Accurate and Rapid Identification of Longan Arillus and Litchi Semen by a Multiplex PCR Assay
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Min Jee Kim, Inkyu Park, Byeong Cheol Moon, Goya Choi, Wook Kim, Sungyu Yang, and Pureum Noh
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Rambutan ,Dimocarpus ,Longan ,Plant Science ,Sapindaceae ,01 natural sciences ,Article ,law.invention ,0404 agricultural biotechnology ,Litchi ,law ,Aril ,Multiplex polymerase chain reaction ,Ecology, Evolution, Behavior and Systematics ,Ecology ,biology ,Traditional medicine ,010401 analytical chemistry ,Botany ,food and beverages ,04 agricultural and veterinary sciences ,biology.organism_classification ,040401 food science ,0104 chemical sciences ,multiplex PCR assay ,Genetic marker ,QK1-989 ,herbal medicine ,Pharmacopoeia ,Nephelium - Abstract
Dimocarpus longan, Litchi chinensis, and Nephelium lappaceum are commercially valuable subtropical and tropical fruits of the Sapindaceae family. Arillus and seeds of the three species have very similar morphologies, however, the arillus of D. longan is used as the herbal medicine Longan Arillus and seeds of L. chinensis are used as Litchi Semen in Korean and Chinese pharmacopoeias. The adulteration of herbal medicines with inauthentic species, including the use of Aril and seed fractions acquired from a single species for two herbal medicines (e.g., Longan Arillus and Litchi Semen), is often driven by economic motives. DNA markers are a tool for the detection of adulterants in commercial products. To establish rapid and reliable assays for the genetic identification of authentic Longan Arillus and Litchi Semen, we developed DNA markers with high specificity and sensitivity based on internal transcribed spacer (ITS) sequences. The newly developed DNA markers and multiplex PCR assay may contribute to efforts to protect against adulteration, quality control, and the standardization of herbal medicines.
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- 2020
17. The complete chloroplast genome sequence of Fritillaria thunbergii Miq., an important medicinal plant, and identification of DNA markers to authenticate Fritillariae Bulbus
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Inkyu Park, Sungyu Yang, Wook Jin Kim, Byeong Cheol Moon, and Youngmin Kang
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0301 basic medicine ,Whole genome sequencing ,Fritillaria ,Plant Science ,Horticulture ,Biology ,Herbaceous plant ,biology.organism_classification ,Fritillaria thunbergii ,Genome ,03 medical and health sciences ,030104 developmental biology ,Genus ,Genetic marker ,Botany ,Identification (biology) ,Biotechnology - Abstract
The genus Fritillaria is an important herbaceous medicinal plant. The dried bulbs of many Fritillaria species are used as Fritillariae Bulbus in traditional oriental medicines. However, these herbal medicines frequently contain mixtures of different types of Fritillariae Bulbus and other Fritillaria species with little or no medicinal value. The accurate identification of different types of Fritillariae Bulbus is very difficult due to the morphological similarities between the plants and dried bulbs; therefore, it is necessary to accurately identify these herbal medicines and other Fritillaria species based on their genetic characteristics. To find molecular markers for Fritillaria species and elucidate the genomic characteristics of F. thunbergii, we sequenced the complete chloroplast (cp) genome of F. thunbergii and performed a comparative analysis with related plant taxa. The complete cp genome of F. thunbergii is 152,155 bp with a quadripartite structure, which is similar to other plants, and was highly similar to previously reported Fritillaria cp genomes in regard to gene content, order, orientation, and GC contents. Comparative analysis of the cp genomes identified two genes, matK and rps16, that contained sufficient markers to distinguish between two herbal medicines (Fritillariae Thunbergii and Fritillariae Hupehensis Bulbus) and five Fritillaria species. These results provide useful information for identification of Fritillaria species and quality control of Fritillariae Bulbus.
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- 2018
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18. Development and characterization of 21 microsatellite markers in Daphne kiusiana, an evergreen broad-leaved shrub endemic to Korea and Japan
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Eun-Seo Lyu, Sungyu Yang, Goya Choi, Wook Kim, Byeong Cheol Moon, Jung-Hyun Lee, Won-Bum Cho, and Eun-Kyeong Han
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0106 biological sciences ,0301 basic medicine ,education.field_of_study ,Daphne kiusiana ,Ecology ,ved/biology ,Population ,ved/biology.organism_classification_rank.species ,Plant Science ,Evergreen ,010603 evolutionary biology ,01 natural sciences ,Shrub ,DNA sequencing ,03 medical and health sciences ,030104 developmental biology ,Geography ,Threatened species ,Microsatellite ,Tree based ,education ,Ecology, Evolution, Behavior and Systematics - Abstract
Microsatellite markers were isolated for Daphne kiusiana var. kiusiana (Thymelaeaceae), an evergreen broad-leaved shrub endemic to Korea and Japan. Because its populations in Jeju Island are morphologically controversial, and consistently threatened by anthropogenic pressures, taxonomic delimitation and conservation effort are required at the genetic level. We developed 21 polymorphic microsatellite loci from Next Generation Sequencing data. The primer set included di-, tri-, and tetra-nucleotide repeats. Variability in the markers was tested for 80 individuals of D. kiusiana from three natural populations in Jeju Island and Japan. Among the 21 loci, three were unavailable for population JKJU of Japan. The Neighbor-Joining tree based on microsatellite markers described here classified the three populations into two groups according to geographical or morphological traits. These will be a powerful genetics tool for determining the taxonomic boundary and establishing suitable conservation strategies for D. kiusiana in Jeju Island.
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- 2017
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19. Comparative Analysis of Actaea Chloroplast Genomes and Molecular Marker Development for the Identification of Authentic Cimicifugae Rhizoma
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Jun-Ho Song, Inkyu Park, Sungyu Yang, and Byeong Cheol Moon
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0106 biological sciences ,0301 basic medicine ,Cimicifuga ,Sequence analysis ,cimicifuga ,Plant Science ,Biology ,actaea ,010603 evolutionary biology ,01 natural sciences ,Genome ,Article ,03 medical and health sciences ,chemistry.chemical_compound ,Tandem repeat ,Molecular marker ,Indel ,plastid ,Gene ,Ecology, Evolution, Behavior and Systematics ,Ecology ,Phylogenetic tree ,Botany ,indel marker ,Angiosperm Phylogeny Group ,030104 developmental biology ,chemistry ,Evolutionary biology ,QK1-989 ,herbal medicine ,Actaea - Abstract
Actaea (Ranunculaceae, syn. Cimicifuga) is a controversial and complex genus. Dried rhizomes of Actaea species are used as Korean traditional herbal medicine. Although Actaea species are valuable, given their taxonomic classification and medicinal properties, sequence information of Actaea species is limited. In this study, we determined the complete chloroplast (cp) genome sequences of three Actaea species, including A. simplex, A. dahurica, and A. biternata. The cp genomes of these species varied in length from 159,523 to 159,789 bp and contained 112 unique functional genes, including 78 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. Gene order, orientation, and content were well conserved in the three cp genomes. Comparative sequence analysis revealed the presence of hotspots, including ndhC-trnV-UAC, in Actaea cp genomes. High-resolution phylogenetic relationships were established among Actaea species based on cp genome sequences. Actaea species were clustered into each Actaea section, consistent with the Angiosperm Phylogeny Group (APG) IV system of classification. We also developed a novel indel marker, based on copy number variation of tandem repeats, to facilitate the authentication of the herbal medicine Cimicifugae Rhizoma. The availability Actaea cp genomes will provide abundant information for the taxonomic and phylogenetic analyses of Actaea species, and the Actaea (ACT) indel marker will be useful for the authentication of the herbal medicine.
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- 2020
20. Establishment of conventional PCR and real-time PCR assays for accurate, rapid and quantitative authentication of four mistletoe species
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Byeong Cheol Moon, Wook Kim, Hyo Seon Kim, Inkyu Park, Sungyu Yang, Pureum Noh, Goya Choi, and A Yeong Lee
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Adulterant ,Biological Products ,Plants, Medicinal ,Traditional medicine ,Santalaceae ,biology ,ved/biology ,ved/biology.organism_classification_rank.species ,Plant Science ,General Medicine ,Horticulture ,biology.organism_classification ,Real-Time Polymerase Chain Reaction ,Biochemistry ,Mistletoe ,Real-time polymerase chain reaction ,Food products ,Viscum coloratum ,Republic of Korea ,Taxillus sutchuenensis ,Maturase K ,Loranthus ,Molecular Biology - Abstract
Adulterants in processed food and herbal medicines reduce their safety, quality control, or pharmacological efficacy. Four mistletoe species, including Viscum coloratum, inhabit Korea. Leaves and branches of V. coloratum, defined as edible or medicinal mistletoe species in Korean, are used to prepare Korean herbal medicines as well as leached tea. However, other mistletoe species including Taxillus sutchuenensis var. duclouxii, Korthalsella japonica, and Loranthus tanakae are frequently distributed as authentic V. coloratum in Korean markets because of similarities in the branches morphology and Korean names of these species with V. coloratum. Although herbal medicines and food products prepared from the other mistletoe species are inauthentic, they are sold at high prices because of the rarity of these species. Thus, it is important to distinguish between authentic and inauthentic adulterant mistletoe species. In this study, we developed species-specific primer, based on matK sequences, suitable for both conventional PCR and real time PCR (qPCR) assay. These assays allowed rapid discrimination among all four mistletoe species. Moreover, qPCR assay enabled the detection of trace amounts of adulterant mistletoe species in V. coloratum samples. Furthermore, we used these assays to monitor commercial mistletoe products distributed in Korean markets. Our data suggest that these methods would serve as a reliable genetic tool to prevent adulteration and standardize the quality of commercial V. coloratum products.
- Published
- 2019
21. Karyotype and genome size variation in Ajuga L. (Ajugoideae–Lamiaceae)
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Bokyung Choi, Sungyu Yang, Tae-Soo Jang, and Jun‐Ho Song
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0106 biological sciences ,biology ,Chromosome ,Karyotype ,Plant Science ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Genome ,Ajuga ,Genus ,Botany ,Lamiaceae ,Feulgen stain ,Genome size ,Ecology, Evolution, Behavior and Systematics ,010606 plant biology & botany - Abstract
Chromosome number changes and karyotype evolution play an important role in plant genome diversification and eventually in speciation. The genus Ajuga L. (Lamiaceae) has approximately 50 species distributed in temperate to subtropical regions. Four of these species are currently recognized in Korea (A. decumbens Thunb., A. multiflora Bunge, A. nipponensis Makino and A. spectabilis Nakai). Understanding the karyotype evolution in Ajuga has been hampered by the small size of their chromosomes and symmetrical karyotypes. Here we used classic Feulgen staining to establish chromosome numbers and construct karyotypes of the four species of Ajuga recognized in Korea and flow cytometry was used to study their variation in genome. The chromosome number of all investigated plants was 2n = 32. Still, the 2C DNA content ranged from 2.18 pg (A. decumbens) to 4.53 pg (A. multiflora). While the chromosome numbers were the same for all investigated species, the genome size variation could potentially be used as a taxonomic marker.
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- 2019
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22. Taxonomic Implications of Leaf Micromorphology Using Microscopic Analysis: A Tool for Identification and Authentication of Korean Piperales
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Sungyu Yang, Jun-Ho Song, and Goya Choi
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stomatal index ,0106 biological sciences ,leaf epidermis ,Asarum ,Identification key ,Plant Science ,010603 evolutionary biology ,01 natural sciences ,Article ,Piperales ,Aristolochia ,lcsh:Botany ,Botany ,Ecology, Evolution, Behavior and Systematics ,Ecology ,biology ,Idioblast ,biology.organism_classification ,Trichome ,lcsh:QK1-989 ,Taxon ,trichomes ,herbal medicine ,Identification (biology) ,Piper ,scanning electron microscopy ,010606 plant biology & botany - Abstract
A comparative study of the leaf micromorphology of Korean Piperales, including medicinal materials, was performed through light microscopy and scanning electron microscopy, to evaluate their taxonomic significance. Piperales possessed both amphistomatic and hypostomatic leaves. The epidermal area ranged from 38 to 5077 &mu, m2, and the stomatal area ranged from 201 to 2129 &mu, m2. The stomatal index on the abaxial surface was higher than that on the abaxial surface. Anomocytic stomata occurred most commonly, but actinocytic, anisocytic, tetracytic, and staurocytic stomata were also found in certain taxa. Secretory idioblasts were found on all taxa studied except Aristolochia. Three main types of trichomes were defined&mdash, (1) glandular trichome, (2) simple multicellular trichome, and (3) two-armed multicellular Y-shaped trichome. Although the quantitative data on its own had somewhat limited taxonomic value, the various qualitative characteristics (e.g., epidermal surfaces, stomata types and positions, trichome types and density, and secretory idioblast types) had great taxonomic value. These characteristics might be taxonomically relevant and useful for developing an identification key. Additionally, we evaluated and supported the previous taxonomic system of Korean Asarum, using leaf micromorphological characteristics. Finally, through the application for authentication of herbal medicine, we revealed that leaf micromorphological characteristics can be used for accurate authentication.
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- 2020
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23. The Complete Chloroplast Genomes of Six Ipomoea Species and Indel Marker Development for the Discrimination of Authentic Pharbitidis Semen (Seeds of I. nil or I. purpurea)
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Inkyu Park, Byeong C. Moon, Pureum Noh, Hyun Oh Lee, Wook Kim, and Sungyu Yang
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0301 basic medicine ,Phylogenetic tree ,phylogenetic relationship ,food and beverages ,Plant Science ,indel marker ,Biology ,Ribosomal RNA ,lcsh:Plant culture ,Ipomoea ,biology.organism_classification ,Genome ,divergent region ,03 medical and health sciences ,Monophyly ,030104 developmental biology ,Molecular evolution ,Botany ,plastid genome ,lcsh:SB1-1110 ,Indel ,Convolvulaceae ,Original Research ,Ipomoeeae - Abstract
Ipomoea L. is the largest genus within the Convolvulaceae and contains 600-700 species. Ipomoea species (morning glories) are economically valuable as horticultural species and scientifically valuable as ecological model plants to investigate mating systems, molecular evolution, and both plant-herbivore and plant-parasite interactions. Furthermore, the dried seeds of I. nil or I. purpurea are used in Korean traditional herbal medicines. In this study, chloroplast (cp) genomes were sequenced from six Ipomoea species, namely, I. nil and I. purpurea and, for the first time, I. triloba, I. lacunosa, I. hederacea, and I. hederacea var. integriuscula. The cp genomes were 161,354 -161,750 bp in length and exhibited conserved quadripartite structures. In total, 112 genes were identified, including 78 protein-coding regions, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. The gene order, content, and orientation of the six Ipomoea cp genomes were highly conserved and were consistent with the general structure of angiosperm cp genomes. Comparison of the six Ipomoea cp genomes revealed locally divergent regions, mainly within intergenic spacer regions (petN-psbM, trnI-CAU-ycf2, ndhH-ndhF, psbC-trnS, and ccsA-ndhD). In addition, the protein-coding genes accD, cemA, and ycf2 exhibited high sequence variability and were under positive selection (Ka/Ks >1), indicating adaptive evolution to the environment within the Ipomoea genus. Phylogenetic analysis of the six Ipomoea species revealed that these species clustered according to the APG IV system. In particular, I. nil and I. headrace had monophyletic positions, with I. purpurea as a sister. I. triloba and I. lacunosa in the section Batatas and I. hederacea and I. hederacea var. integriuscula in the section Quamoclit were supported in this study with strong bootstrap values and posterior probabilities. We uncovered high-resolution phylogenetic relationships between Ipomoeeae. Finally, indel markers (IPOTY and IPOYCF1) were developed for the discrimination of the important herbal medicine species I. nil and I. purpurea. The cp genomes and analyses in this study provide useful information for taxonomic, phylogenetic, and evolutionary analysis of the Ipomoea genome, and the indel markers will be useful for authentication of herbal medicines.
- Published
- 2018
24. A florisitic study of Ulleungdo Island in Korea
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Ro-Young Lee, Bo Mi Nam, Sungyu Yang, Gyu Young Chung, Byoung-Un Oh, Hyun-Do Jang, and Jae-Hyeon Lee
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Geography ,Botany ,Plant Science ,Archaeology ,Ecology, Evolution, Behavior and Systematics - Published
- 2015
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25. Floristic study of Cheondeungsan Mountain in Korea
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Ki-Hong Kim, Hyun-Do Jang, Sungyu Yang, Byoung-Un Oh, Min-Su Park, Chang-Seok Jang, and Ro-Young Lee
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Aster pilosus ,Endemic plants ,Korea ,Ecology ,Penthorum chinense ,Vascular plants ,Plant Science ,Native plant ,Biology ,Subspecies ,biology.organism_classification ,Floristics ,Ambrosia trifida ,Flora ,lcsh:QH540-549.5 ,Insect Science ,Cheondeungsan ,Botany ,Animal Science and Zoology ,lcsh:Ecology ,Taxonomic rank ,Ecology, Evolution, Behavior and Systematics ,Ambrosia artemisiifolia - Abstract
The distribution of native plants of Cheondeungsan Mountain (807 m, N 37°05'00“–37°05'30”, E 128°00'0“–128°02'0”) in Chungcheongbuk-do was determined and the major flora were identified. During field investigations carried out from May 2011 to October 2011, 87 families, 254 genera, and 369 taxonomic groups (327 species, 4 subspecies, 33 varieties, and 5 forms) were confirmed, and the distribution of 219 taxonomic groups was discovered for the first time. The distribution of four endemic plants of Korea, including Ajuga spectabilis Nakai and Salvia chanryoenica Nakai, and that of Penthorum chinense Pursh, a Grade V specific plant species, was found. There were 20 taxa of naturalized plants at Cheondeungsan; the growth and development of plants that are harmful to the ecosystem, such as Ambrosia artemisiifolia L., Ambrosia trifida L., Eupatorium rugosum Houtt., and Aster pilosus Willd., was observed around the forest paths and lowlands.
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- 2014
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26. Flora of vascular plants in the Chilgapsan Provincial Park, Korea
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Yoon-Young Kim, Hyun-Do Jang, Sungyu Yang, Sung-Jin Ji, Hyeok Jae Choi, Byoung-Un Oh, and Ro-Young Lee
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Flora ,Cultivated plant taxonomy ,Ecology ,Plant Science ,rare plants ,Biology ,Subspecies ,Floristics ,Indicator plant ,flora ,Taxon ,Insect Science ,Chilgapsan Provincial Park ,lcsh:QH540-549.5 ,Botany ,Animal Science and Zoology ,Christian ministry ,vascular plants ,lcsh:Ecology ,endemic plants ,Ecology, Evolution, Behavior and Systematics - Abstract
The flora of Chilgapsan Provincial Park in Cheongyang-gun (Chungcheongnam-do), Korea was surveyed from 2000 to 2014. In 19 field surveys, vascular plants were revealed 490 taxa belonging to 97 families, 309 genera, 433 species, four subspecies, 48 varieties, and five forms. Plants of various categories were discovered in this study. For the Korean endemic plants 15 taxa were recorded, and 11 taxa designated by the Korean Forest Service as rare plants were investigated in this region. The plants above the third degree among the floristic regional indicator plants designated by the Korean Ministry of Environment were 10 taxa. In addition, 33 taxa of naturalized and 73 taxa of cultivated plants were recorded.
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- 2014
27. A taxonomical review of Solidago japonica and its relatives (Asteraceae)
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Sungyu Yang, Chang-Seok Jang, and Byoung-Un Oh
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Taxon ,biology ,Botany ,Gigantea ,Taxonomy (biology) ,Coreana ,Plant Science ,Asteraceae ,biology.organism_classification ,Leiocarpa ,Ecology, Evolution, Behavior and Systematics ,Japonica ,Solidago virgaurea - Abstract
The NE Asiatic Solidago virgaurea complex in Korea has been reported on 5 taxa (S. virgaurea subsp. asiatica, S. virgaurea var. taquetii, S. virgaurea var. coreana, S. virgaurea subsp. leiocarpa, and S. virgaurea subsp. gigantea). However, the broad morphological variations and a lack of diagnostic characteristics have made it difficult to distinguish these taxa and have thus resulted in a complicated taxonomy in the complex. Therefore, to clarify the classification and delimitation of each taxon, the morphological characteristics of the S. virgaurea complex were investigated by examining the original descriptions and type specimens. Field work was also conducted to investigate the morphological and geographic features. In conclusion, S. japonica Kitam., as a legitimate name, was distributed all over the country except for the Is. Ulleung-do in Korea, as distinguished from S. virgaurea L. Both S. virgaurea var. taquetii and S. virgaurea var. coreana were considered as synonyms of S. japonica, as their morphological characteristics were within the variation range of those of S. japonica. Furthermore, S. virgaurea subsp. leiocarpa does not occur in Korea. Additional investigations are required to clarify the classification of S. virgaurea subsp. gigantea, whose populations were not found during the investigation in this study. S. dahurica, meanwhile, was distributed in the northern part of North Korea.
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- 2012
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28. The complete chloroplast genome sequence of Aconitum coreanum and Aconitum carmichaelii and comparative analysis with other Aconitum species
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Wook-jin Kim, Hulin Li, Sang-Min Yeo, Sungyu Yang, Inkyu Park, and Byeong Cheol Moon
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0106 biological sciences ,0301 basic medicine ,Inverted repeat ,lcsh:Medicine ,Plant Genomes ,Plant Science ,Plant Genetics ,01 natural sciences ,Genome ,RNA, Transfer ,Gene Order ,Plant Genomics ,Medicine and Health Sciences ,lcsh:Science ,Phylogeny ,Aconitum ,Data Management ,Genetics ,Base Composition ,Multidisciplinary ,biology ,Phylogenetic tree ,Database and informatics methods ,Sequence analysis ,Phylogenetic Analysis ,Genomics ,Phylogenetics ,Research Article ,Biotechnology ,Computer and Information Sciences ,Bioinformatics ,Herbal Medicine ,Genes, Plant ,Aconitum carmichaelii ,Evolution, Molecular ,03 medical and health sciences ,Species Specificity ,Genomic Medicine ,Complementary and Alternative Medicine ,Chloroplast Genome ,Evolutionary Systematics ,Genome, Chloroplast ,DNA sequence analysis ,DNA Primers ,Taxonomy ,Evolutionary Biology ,lcsh:R ,Biology and Life Sciences ,Computational Biology ,Sequence Analysis, DNA ,Comparative Genomics ,biology.organism_classification ,Research and analysis methods ,030104 developmental biology ,RNA, Ribosomal ,lcsh:Q ,Plant Biotechnology ,GC-content ,Microsatellite Repeats ,010606 plant biology & botany - Abstract
Aconitum species (belonging to the Ranunculaceae) are well known herbaceous medicinal ingredients and have great economic value in Asian countries. However, there are still limited genomic resources available for Aconitum species. In this study, we sequenced the chloroplast (cp) genomes of two Aconitum species, A. coreanum and A. carmichaelii, using the MiSeq platform. The two Aconitum chloroplast genomes were 155,880 and 157,040 bp in length, respectively, and exhibited LSC and SSC regions separated by a pair of inverted repeat regions. Both cp genomes had 38% GC content and contained 131 unique functional genes including 86 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. The gene order, content, and orientation of the two Aconitum cp genomes exhibited the general structure of angiosperms, and were similar to those of other Aconitum species. Comparison of the cp genome structure and gene order with that of other Aconitum species revealed general contraction and expansion of the inverted repeat regions and single copy boundary regions. Divergent regions were also identified. In phylogenetic analysis, Aconitum species positon among the Ranunculaceae was determined with other family cp genomes in the Ranunculales. We obtained a barcoding target sequence in a divergent region, ndhC-trnV, and successfully developed a SCAR (sequence characterized amplified region) marker for discrimination of A. coreanum. Our results provide useful genetic information and a specific barcode for discrimination of Aconitum species.
- Published
- 2017
- Full Text
- View/download PDF
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