• Korean Journal of Plant Taxonomy
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• v.34 no.4
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• pp.335-358
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• 2004

To investigate molecular phylogenetic relationships and to test hypothesis of hybrid origin of Ranunculus cantoniensis (Ranunculaceae), the sequences of nrDNA and chloroplast DNA were analyzed for 8 taxa and 25 accessions including 5 accessions of outgroup. In the phylogenetic trees by analyses of maximum parsimony and maximum likelihood for ITS nrDNA sequences and combined data of psbA-trnH, rps16 and trnL sequences of cpDNA, R. cantoniensis was most closely related to R. chinensis, and then to R. taciroi and R. silerifolius. The molecular phylogenetic relationships were not congruent with the previous report that R. cantoniensis was most closely related to R. silerifolius. In the sequence analysis of ITS and psbA-trnH, rps16, trnL for R. cantoniensis and the related taxa, R. cantoniensis showed polymorphism. It supported that the polymorphism also was reported in chromosome number and karyotype of R. cantoniensis. Ranunculus cantoniensis shared the marker gene of R. chinensis and R. silerifolius in ITS, and one of R. silerifolius in cpDNA. These results supported the hypothesis that R. cantoniensis was caused by hybridization between R. chinensis and R. silerifolius based on chromosome number and karyotype, and also estimated that R. silerifolius might be of maternal origin and R. chinensis be paternal.

• ALGAE
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• v.23 no.1
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• pp.15-29
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• 2008

Many species in Gymnodiniales, which are unarmored dinoflagellates, are responsible for marine algal blooms and some of them have potent toxin in the cell. Their taxonomy has so far been well-defined, and several genera (e.g. Akashiwo, Gymnodinium, Karenia) have recently been re-described. In Korea, few works have been carried out on their taxonomical and molecular studies. This study focused on comparison of both morphological and molecular characteristics of five unarmored dinoflagellates on Korean coastal water: Akashiwo sanguinea, Cochlodinium polykrikoides, Gymnodinium catenatum, Gymnodinium impudicum and Karenia aureolum (=K. mikimotoi). Morphological characteristics observed here was in good accordance with the original descriptions of individual species. In addition, none of difference was found in morphological comparisons between the Korean and foreign strains. Furthermore, molecular analysis showed that the SSU rDNA sequences were generally identical according to each species. In some distinct features, A. sanguinea, which has generally the same morphological features, were divided into two groups: one was Korean isolates including European isolates, the other was American isolates. In the two groups, the nucleus was positioned differently: middle of the cells in the Korean isolates (GnSg02, GnSg03), near the epicone in American isolates (CCMP1593, CCMP1837). In addition, this was strongly supported by phylogenetic analysis, inferred from the SSU rDNA sequences. K. aureolum (GrAr01) was corresponded to European G. aureolum (=K. mikimotoi) in shape and position of nucleus, chloroplast, however, which is similar to K. digitata in view of having a finger-like sulcus. This was in good agreement with phylogenetic study of these species. G. catenatum have identical morphology except the ridge location, and their genotype of SSU rDNA was also identical to GenBank data of the same species. From this study, we found that the five Korean unarmored dinoflagellates are identical morphological characteristics and genotype to each species of foreign isolates.

• Korean Journal of Environment and Ecology
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• v.31 no.4
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• pp.349-364
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• 2017

Duckweed family (Lemnaceae Martinov), including the genus Lemna L., is a typical floating aquatic perennial plant, and about five genera and 40 species in the family are in wide distribution around the world except the polar regions. The genus Lemna is the smallest and the simplest plant among the angiosperms. It has a characteristic of doubling every three days with fast vegetative propagation, which helps the organisms to increase in rapid growth. As such, the plant is ideal for environmental pollution assessment and toxicity test. Although taxonomists and scholars have used different scientific names for the species, many of them have agreed that there is only one member of species of the genus Lemna in Korea. Paying attention to the external morphological variation observed in the Korean genus Lemna, we conducted a molecular phylogenetic analysis to identify the entity of the Korean Lemna species and to investigate the possibility of two or more members of the species existing in Korea. We determined and aligned the DNA sequences of the atpF-H region of the chloroplast DNA in 37 populations of the nationally distributed Lemna species. The results showed that the sequence length of the cp DNA atpF-H region was 463-483 bp, the length of the aligned sequences was 488 bp, and the number of variation site in nucleotide sequences was 47. There were two types of aligned sequences of the cp DNA atpF-H region from 37 populations of Lemna species in Korea. The maximum parsimony analysis revealed that the Korean Lemna consists of two clades, and one of them had two subclades. The results suggest that, contrary to the general understanding, at least two taxa (L.aequinoctialis, L.minor) exist in Korea.

• Korean Journal of Plant Taxonomy
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• v.38 no.4
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• pp.371-388
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• 2008

Phylogenetic studies were conducted for 35 populations of the subfamily Coryloideae (Betulaceae) based on waxy gene of nuclear DNA and atpB-rbcL intergenic spacer region of chloroplast DNA. Waxy data analysis suggest that Coryloideae is monophyletic; Corylus is monophyletic and basally branching within the subfamily Coryloideae; Ostryopsis is sister to the Carpinus and Ostrya clade, and the Ostrya is monophyletic (BS=86, PP=99). AtpB-rbcL intergenic spacer region analysis shows that Ostryopsis appeared as the most basal clade within the Coryloideae; Corylus is monophyletic(BS=98, PP=100) and placed between Carpinus-Ostrya and Ostryopsis clade; Carpinus and Ostrya formed a clade with a high support value(BS=100, PP=100). Carpinus sect. Carpinus is monophyletic, whereas sect. Distegocarpus is paraphyletic in the waxy tree. Corylus formed two subclades, but discordance at the infrageneric classification based on morphological characters. In the atpB-rbcL tree, Carpinus and Corylus taxa form a polytomy within the each clade. Results from the two data sets differ mainly in the relative position of Ostryopsis, the monophyly of Ostrya, and the relationships within the Carpinus-Ostrya clade. Further studies are needed for clarify the taxonomic position and the generic limitation.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.210-210
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• 2022

Silybum marianum is an annual or biennial plant from the Asteraceae family. It can grow in low-nutrient soil and drought conditions, making it easy to cultivate. From the seed, a specialized plant metabolite called silymarin (flavonolignan complex) is produced and is known to alleviate the liver from hepatitis and toxins damages. To infer the phylogenetic placement of a Korean milk thistle, we conducted a chloroplast assembly and annotation following by a comparison with existing Chinese reference genome (NC_028027). The chloroplast genome structure was highly similar with an assembly size of 152,642 bp, an 153,202 bp for Korean and Chinese milk thistle respectively. Moreover, there were similarities at the gene level, coding sequence (n = 82), transfer RNA (n = 31) and ribosomal RNA (n = 4). From all coding sequences gene set, the phylogenetic tree inference placed the Korean cultivar into the milk thistle clade; corroborating the expected tree. Moreover, an investigation the tree based only on the ycf1 gene confirmed the same tree; suggesting that ycf1 gene is a potential marker for DNA barcoding and population diversity study in milk thistle genus. Overall, the provided data represents a valuable resource for population genomics and species-centered determination since several species have been reported in the Silybum genus.

• Journal of Life Science
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• v.23 no.7
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• pp.847-853
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• 2013

The genus Hemerocallis (family Xanthorthoeaceae) is a herbaceous species, some of which are very important in herbal medicines. We evaluated the rps16-trnK region of the chloroplast DNA of a representative sample of eight taxa in Korea to estimate phylogenetic relationships within the taxa of this genus. Due to differences in the number of inserted nucleotides, the aligned data for Hemerocallis ranged from 729 (H. aurantiaca) to 742 nucleotides (H. fulva var. kwanso), with a mean of 736. Although several small indels and 20 inserts were present, sequence variation within the Hemerocallis genus was mostly due to nucleotide substitutions. All rps16-trnK trees generated in Korea exhibited a well-solved topology, with high bootstrap support, irrespective of the methods (parsimony) and the setting used. The node of H. minor and H. littorea was strongly supported, with a high bootstrap value in three trees, and these two taxa were sistered with H. thunbergii. The number of chromosomes was not congruent with that found in a previous study with RAPD, but the number was in agreement with the results of this study.

• Korean Journal of Plant Tissue Culture
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• v.24 no.2
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• pp.93-97
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• 1997

For the molecular genetic study of cold tolerance mechanism in plants, a cDNA encoding fatty acid desaturase (fad3), converting linoleic acid (18:2, $\omega$-6) to linolenic acid (18:3, $\omega$-3), was isolated from $\lambda$ZAPII Arabidopsis thaliana cDNA expression library by plaque hybridization using fad3 cDNA probe derived from Brassica napus. A 1.8 kb-EcoRI fragment from a lambda clone showing a strong positive hybridization signal was subcloned into pGEM7 and analyzed for its nucleotide sequence. From deduced amino acid sequences, the fad3 gene was revealed to have an open reading frame(ORF) consisting of 386 amino acids with a molecular mass of 44,075 Da. The fad3 gene was compared to chloroplast $\omega$-3 fatty acid desaturase (fad7) and endoplasmic reticulum Δ12 fatty acid desaturase (fad2) to show 70% and 58% amino acid sequence homology, respectively, Especially, amino acids of internal (82 to 151) and carboxy terminal (276 to 333) regions were highly conserved, implying their requisite role for enzymatic functioning of fatty acid desaturases. IPTG-induced fad3 cDNA expression in E. coli cells was suggested to be toxic to bacterial growth.

• Korean Journal of Plant Taxonomy
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• v.50 no.3
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• pp.318-326
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• 2020

We found an unrecorded species, Carex molestiformis Reznicek & Rothrock, in Byeokparyeong, Daehwa-myeon, Pyeongchang-gun, Gangwon-do, South Korea. This species is native to southern parts of the United States (ca. 11 states, including Arkansas, Missouri, and Oklahoma). These plants are usually distributed densely in stream flood plains, bottomlands, stream banks, and along roadsides. Belonging to section Ovales Kunth, perennial herbs with gynecandrous spikes, C. molestiformis is closely related to C. maackii Maxim. and C. scoparia Willd. and is distinguished from them by the number (2-4) of spikes in each inflorescence and the width (2.63.4 mm) and number (69) of veins of perigynia. A new Korean name of C. molestiformis 'Ga-Neun-Ta-Rae-Sa-Cho' was given, as it has slender overall appearance compared with C. maackii (Ta-Rae-Sa-Cho). We also provide a description, illustrations, photographs and a key of related taxa in Korea. We compared three DNA barcode region (chloroplast DNA matK, ndhF and nuclear ribosomal DNA internal transcribed spacer) sequences from C. molestiformis with those of C. maackii and C. scoparia, determining eight species-specific single nucleotide polymorphism sites for C. molestiformis.

• Weed & Turfgrass Science
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• v.4 no.1
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• pp.26-34
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• 2015

Korean Poaceae includes approximately 80 species of the agricultural weeds. Precise species identification is the first step for more effective weed management in the agricultural fields. However, the identification of species in Poaceae is not easy without the assistance of taxonomists or identification experts although they are relatively easy to distinguish from the plants of the other family by the unique characteristics of caryopsis. Thus, DNA barcode was suggested as an alternative powerful technique for species identification by using short sections of DNA from a specific region of the genome. Two standard barcode markers of vascular plants, chloroplast rbcL and matK, and a supplementary nuclear ribosomal Internal Transcribed Spacer (ITS) region were used for barcode of major Korean Poaceae weeds, 403 individuals of 84 taxa. All the barcode markers revealed a good level of sequencing success with the lowest 73.7% for matK and the highest 88.8% for rbcL. The barcode sequences were deposited to the National Center for Biotechnology Information (NCBI) database for public use. Combined matK and ITS showed very high resolving power with 92.9%. Besides the identification of weeds for weed managment, the generated DNA barcode data could be used for many other applications such as rapid biodiversity assessment and conservation prioritization.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2020.12a
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• pp.55-55
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• 2020

뫼제비꽃(Viola selkirkii)의 엽록체 DNA 염기서열을 차세대염기서열분석법(NGS)을 이용하여 분석하였다. 재료는 강원도 화천군 일산과 제주도 한라산의 2개체를 사용하였다. 분석결과, 염기서열의 길이는 일산의 뫼제비꽃이 156,774 bp (GC content: 36.30%), 한라산의 뫼제비꽃이 157,451 bp(GC content: 36.30%)로 한라산 개체가 길게 분석되었다. 구간별로 LSC(Large single copy)지역은 한라산 개체(85,950 bp)가 일산 개체(85,930 bp)보다 20 bp 길었으며, SSC(Small single copy)지역은 한라산 개체(17,261 bp)보다 일산 개체가 17,982 bp로 길게 분석되었다. IR(Inverted repeat)지역은 한라산 개체가 27,120 bp로 일산 개체(26,431 bp)보다 길게 분석되었다. 이러한 염기서열 길이의 차이는 종내 개체 간 빈번하게 발생하는 현상으로 IGS와 intron 구간에서 확인 된 단순반복서열의 일부 누락과 IR지역 내의 수축과 확장에 의한 것으로 판단된다. 뫼제비꽃 2개체의 엽록체 게놈을 구성하는 유전자 수는 총 111개로 동일하였으며, protein coding gene 77개, tRNA(transfer RNA) gene 30개, 그리고 rRNA (ribosomal RNA) gene 4개로 구성되어 있었다. 이는 기 발표된 엽록체 DNA 전체 염기서열이 밝혀진 제비꽃속 (Viola) 종류들과 동일한 결과이다.