• Korean Journal of Plant Taxonomy
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• v.43 no.1
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• pp.12-21
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• 2013

To clarify the taxonomic position for Astragalus nakaianus and provide correct scientific name for A. mongholicus cultivar in South Korea, we examined external morphological characters and sequence variations from ITS and five cp non-coding DNA regions. Genetic structure was also analyzed for 61 individuals from three populations using nine microsatellite loci. We found no significant difference between the South Korean cultivar and A. mongholicus var. dahuricus when morphology and ITS sequences were considered. Morphologically, A. nakaianus specimens varied somewhat from A. mongholicus var. mongholicus and var. dahuricus in habit, plant height, and lengths of leaf axis and leaflet. Although sequence data from ITS and cp noncoding DNA regions could not distinguished A. nakaianus from A. mongholicus, microsatellite analysis revealed strong structuring between the cultivar and A. nakaianus. Therefore, we conclude that the South Korean A. mongholicus cultivar should be treated as A. mongholicus var. dahuricus and that A. nakaianus should be merged into A. mongholicus as a variety, i.e., A. mongholicus var. nakaianus.

• The Korean Journal of Mycology
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• v.39 no.1
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• pp.11-15
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• 2011

To provide basic information for Verticillium spp., molecular methods were applied to analyze genetic characteristics within Verticillium spp. including Verticillium dahliae, isolated from diseased plants in two regions of Korea. Five Korean isolates of V. dahliae causing Verticillium wilt on chrysanthemum were analyzed, together with six other Verticillium spp., using mitochondrial small subunit rRNA gene (rns) sequence and random-amplified polymorphic DNA (RAPD). In a phylogenetic tree based on rns region sequences, Korean V. dahliae isolates formed a single clade with foreign isolates, whereas the other Verticillium spp. formed separate groups. In addition to rns sequence analysis, a dendrogram based on RAPD fragment patterns also showed clustering of all V. dahliae isolates into one group, separate from the six different Verticillium spp., and the V. dahliae isolates formed three subgroups which corresponded to the regions of origin, Kumi, Busan city and Canada. This indicates that high genetic variation exists between regions, although the fungus was isolated from the same host plant, chrysanthemum. These results provide the foundation for the study of genetic diversity and relationships among V. dahliae isolates in Korea.

• The Korean Journal of Malacology
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• v.21 no.2 s.34
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• pp.147-161
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• 2005

To elucidate the phylogenetic relation of the superfamily Veneroidea, we obtained partial 28S rRNA sequences of 14 heterodonts and three pteriomorphs which were collected from Korea and the sequence data of related taxa from GenBank, and analyzed maximum parsimony with PAUP program 750 of the nucleotide positions were variable, 560 of which were informative under conditions of parsimony. Total tree length was 2,765, and consistency index, homoplasy index (HI), and Retention index was 0.4843, 0.5157, and 0.6291, respectively. Intraspecific variation of 28 rRNA of Corbicula fluminea and Sinonovacula constricta was 3.1% and 1.3%, respectively. Pitarinae-Cyclininae-Meretrinae group had a clade and Samaranginae, Chioninae, and Dorsininae were clustered.

• Korean Journal of Plant Tissue Culture
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• v.28 no.5
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• pp.255-261
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• 2001

Vitis vinifera thaumatin-like protein (VVTL1) is a fruit-specific and ripening-related protein in grape. In order to isolate VVTL1-homolog gene and fruit-specific promoter from Campbell cultivar, we isolated a genomic clone containing VVTL1-homolog gene from grape genomic library through plaque hybridization. VVTL1-homolog gene has an intronless genomic structure, which the pattern is matched with those of other PR5 genes such as osmotin and osmotin-like protein genes. Transcription start site was determined by primer extension analysis. The promoter region of VVTL1-homolog gene contains a sequence or structure, especially the location and number of TCA box and ABRE (abscisic acid-responsive element), distinct from other reported plant PR5 genes, though with several known functional elements such as a TATA box and CAAT box. These results suggested that VVTL1-homolog gene may be regulated by a plant hormone, abscisic acid, and one or several stresses such osmotic pressure and pathogen infection. The isolation of fruit-specific promoter may be helpful to breed a genetically modified grape with valuable phenotype or materials in fruits.

• Korean Journal of Plant Taxonomy
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• v.45 no.2
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• pp.158-168
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• 2015

A study of the genus Pilea in Korea including five taxa was carried out using molecular phylogenetic methods. The majority of members of the genus Pilea in Korea are annual herbs, and they live in moist habitats, flowering in summer and fruiting in autumn. The results of a phylogenetic analysis using nrDNA and cpDNA supported the recognition of P. japonica, P. peploides, and P. taquetii. Pilea taquetii from Mt. Sanbangsan in Jeju was nested within P. hamaoi and P. mongolica clade instead of the P. taquetii clade, with P. taquetii from Mt. Jirisan also separated from the P. taquetii clade. This indicates that the separation is not geographical isolation, but is instead related to taxonomic problems. Therefore, further study of the P. taquetii group is necessary.

• The Journal of Korean Academy of Prosthodontics
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• v.49 no.4
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• pp.341-345
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• 2011

Genetic association study has been progressed in medicine along with advance in genetic technology. It focused on the individual differences in genotype due to errors occurring during DNA duplication, which can cause vulnerability to specific diseases. Polymorphism defines the varieties in phenotype due to those genetic variations. Polymorphism due to change in one DNA base sequence is called as a Single Nucleotide Polymorphism. In the near future, the evaluation of relative risk to specific disease according to SNP will be essential part of fundamental of medicine for the diagnosis, treatment and prevention. Dental caries and periodontal diseases has been first subject to genetic association study in dentistry and broaden out to other areas like bone formation and resorption. This article presents the current state of genetic association study and its application to dentistry.

• Journal of Animal Science and Technology
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• v.53 no.4
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• pp.303-310
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• 2011

Phylogenetic relationships of Jeju dogs to other domestic and foreign dog breeds were assessed using mtDNA D-loop sequences. Neighbor-joining trees were constructed using complete sequences (970 bp excluding the tandem repeat region) determined for five Cheju, four Jindo, four Sapsaree, five Pungsan, two of each East and West Laika dogs (Canis familiaris), two gray wolves (Canis lupus) and two coyotes (Canis latrans) and also published complete sequences for dogs. Coyote sequences were used as outgroups. In addition, a total of 214 haplotypes of 598bp D-loop sequences from 30 dog breeds were collected from GenBank and used to investigate genetic structure of population. In the analyses of full D-loop sequence variation and the phylogenetic trees constructed by neighbor-joining method, neither haplotypes nor clades specific for any domestic dog breeds were observed. The inter-species sequence variation (4.51%) between domestic dogs and wolves was much higher than the intra-species sequence variation within domestic dogs (1.63%) and wolves (3.64%). The divergence of the dog and wolf occurred approximately 1~2 million years ago based on these values. The taxa of Jeju dog breed in the phylogenetic tree are clustered separately and intermingled with other taxa of breeds, suggesting that active crossbreeding of Jeju dogs with other domestic breeds.

• Journal of Life Science
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• v.19 no.5
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• pp.684-687
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• 2009

Xanthomonas arboricola pv. pruni, the causal agent of bacterial shot holes in stone fruits, was known to have a low population diversity. To investigate the genetic characteristics of X. arboricola pv. pruni isolated in Korea, three strains which have identical 16S rDNA sequences - including type strain (LMG852), Japanese isolate (MAFF301420) and Korean isolate (XWD1) - were analysed based on the nucleotide sequences of three DNA regions and RAPD pattern. No sequence diversity among the three strains was found within the ITS, glnA and atpD gene sequences. However, five of 756 nucleotides of the atpD gene determined (accession number FJ429319) were different from those of the French strain available from the Genbank database. RAPD analyses performed with 40 different arbitrary primers revealed that two strains isolated from Korea and Japan showed similarity in their band patterns distinguished by type strain. These results suggest that Korean and Japanese strains are very close and belong to a population with a low genetic diversity, and might have a different origin from strains found in West Europe.

• Journal of Plant Biotechnology
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• v.43 no.1
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• pp.82-90
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• 2016

Most Araliaceae plant species distributed in Korea are economically important because of their high medicinal values. This study was conducted to develop barcode markers from sequence analysis of chloroplast DNA in 14 taxa of Araliaceae species grown in South Korea. Sequencing of seven chloroplast DNA regions was performed to establish the DNA barcode markers, as suggested by the Consortium for the Barcode of Life (CBOL). From the sequence analysis of chloroplast DNA, we identified specific sequences and nucleotides that allowed us to discriminate among each other 14 Korean Araliaceae species. The sequence in the region of psbA-trnH revealed the most frequent DNA indels and substitutions of all 7 regions studied. This psbA-trnH marker alone can discriminate among all 14 species. There are no differences between Korean and Chinese Panax ginseng in all seven sequenced chloroplast DNA regions. A phylogenetic tree constructed using the seven chloroplast DNA regions revealed that Tetrapanax papyriferus should be classified as an independent clade. The Aralia and Panax genera showed a close phylogenetic relationship. Five species in the Eleutherococcus genus were more closely related to Kalopanax septemlobus than to any Panax species.

• Journal of Life Science
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• v.32 no.10
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• pp.803-811
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• 2022

Despite the importance of traditional Korean fermented foods, little is known about the microbial communities and diversity of fermented soy products. To gain insight into the unexplored microbial communities of both Doenjang (DJ) and Ganjang (GJ) that may contribute to the fermentation in Korean traditional foods, we carried out next-generation sequencing (NGS) based on the V3-V4 region of 16S rDNA gene analysis. The alpha diversity analysis results revealed that both the Shannon and Simpson diversity indices were significantly different between the two groups, whereas the richness indices, including ACE, CHAO, and Jackknife, were not significant. Firmicutes were the most dominant phylum in both groups, but several taxa were found to be more abundant in DJ than in GJ. The proportions of Bacillus, Kroppenstedtia, Clostridium, and Pseudomonas and most halophiles and halotolerant bacteria, such as Tetragenococcus, Chromohalobacter, Lentibacillus, and Psychrobacter, were lower in DJ than in GJ. Linear discriminant effect size (LEfSe) analysis was carried out to discover discriminative functional biomarkers. Biomarker discovery results showed that Bacillus and Tetragenococcus were identified as the most important features for the classification of subjects to DJ and GJ. Paired-permutational multivariate analysis of variance (PERMANOVA) further revealed that the bacterial community structure between the two groups was statistically different (p=0.001).