• The Korean Journal of Mycology
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• v.33 no.1
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• pp.1-10
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• 2005

Nineteen strains of Trametes species were collected from the area of Kangwon Province, Korea. They have a variety of color hands and line-up markings on fruit bodies. Most strains were categorized into four types based on color bands, that is, dark brown, light brown, dark gray and light gray. They also have line-up marking shapes from sparse to compact on fruit bodies. In this study, we tried to investigate the relationship between the genetic variation and morphological appearance of these species using the nuclear ribosomal ITS1-5.8S-ITS2 region sequence, we used nineteen strains collected in nature and four species of five standard strains (T. versicolor KCTC16781, KCTC26203, T. villosa KCTC06866, T. suaveolens KCTC26205 and T. hirusta KCTC26200). The data of ITS sequences indicated that nineteen strains of T. versicolor have the difference of $1{\sim}6$ base pairs, comparing with standard strains of T. versicolor KCTC16781, and KCTC26203. Phylogenetic analysis of the Trametes species showed that they grouped into a wide range of single clade. Standard strains except T. versicolor KCTC16781 and KCTC26203, formed separated subgroup.

• Korean Journal of Microbiology
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• v.53 no.1
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• pp.9-19
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• 2017

We studied soil composition, $N_2O$ production, a number of denitrifying bacteria, community structure and T-RFLP patterns of denitrifying bacteria dependent on agricultural methods with the change of seasons. Analyses of the soil chemical composition revealed that total carbon and total organic carbon contents were 1.57% and 1.28% in the organic farming soil, 1.52% and 1.24% in the emptiness farming soil, and 1.40% and 0.95% in traditional farming soil, respectively. So, the amount of organic carbon was relatively high in the environment friendly farming soils than traditional farming soils. In case of $N_2O$ production, the amount of $N_2O$ production was high in May and November soils, but the rate of $N_2O$ production was fast in August soil. The average number of denitrifying bacteria were $1.32{\times}10^4MPN{\cdot}g^{-1}$ in the organic farming soil, $1.17{\times}10^4MPN{\cdot}g^{-1}$ in the emptiness farming soil, and $6.29{\times}10^3MPN{\cdot}g^{-1}$ in the traditional farming soil. It was confirmed that the environment friendly farming soil have a larger number of denitrifying bacteria than the traditional farming soil. As a result of the phylogenetic analyses, it was confirmed that six clusters were included in organic farming soil among total 10 clusters. And the result of PCA profile distribution of T-RFLP pattern on agricultural methods, the range of distribution showed wide in the organic farming method, relatively narrow in the conventional farming method, and middle in the emptiness farming method. Therefore, we could concluded that the distribution and the community structure of denitrifying bacteria were changed according to the agricultural methods and seasons.

• The Korean Journal of Mycology
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• v.46 no.2
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• pp.193-199
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• 2018

The fungus, Podosphaera pannosa, was identified in 1991 as the cause of powdery mildew symptoms on peach (Prunus persica var. persica) fruit from Korea based on the morphological characteristics of the conidial state. Recently, however, in Serbia and France, the cause of 'rusty spot' found on peach fruit was identified as P. leucotricha, and the cause of 'powdery mildew' on nectarine (Prunus persica var. nucipersica) fruit was identified as P. pannosa. To confirm the identity of the Korean pathogen, we collected four samples of powdery mildew from Korean peach fruit: three with the 'powdery mildew' symptom and one with the 'rusty spot' symptom. Morphological examination of the four samples confirmed P. pannosa as the pathogen. Internal transcribed spacer sequences of rDNA were analyzed for molecular characterization. A phylogenetic tree showed that the Korean isolates were clustered into a clade containing P. pannosa from Rosa species, with high sequence similarities of more than 99%. Thus, we showed that the powdery mildew and rusty spot symptoms on peach fruits from Korea are associated with P. pannosa.

• Korean Journal of Microbiology
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• v.54 no.3
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• pp.188-199
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• 2018

Genomic epidemiology exploits various basic microbial research areas. High-throughput sequencing technologies dramatically have been expanding the number of microbial genome sequences available. Abundant genomic data provide an opportunity to perform strain typing more effectively, helping identify microbial species and strains at a higher resolution than ever before. Genomic epidemiology needs to find antimicrobial resistance genes in addition to standard genome annotations. Strain typing and antimicrobial resistance gene finding are static aspects of genomic epidemiology. Finding which hosts infected which other hosts requires the inference of transient transmission routes among infected hosts. The strain typing, antimicrobial resistance gene finding, and transmission tree inference would allow for better surveillance of microbial infectious diseases, which is one of the ultimate goals of genomic epidemiology. Among several high-throughput sequencing technologies, genomic epidemiology will benefit from the more portability and shorter sequencing time of the Oxford Nanopore Technologies's MinION, the third-generation sequencing technology. Here, this study reviewed computational methods for quantifying antimicrobial resistance genes and inferring disease transmission trees. In addition, the MinION's applications to genomic epidemiology were discussed.

• Korean Journal of Soil Science and Fertilizer
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• v.35 no.1
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• pp.12-26
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• 2002

The phylogenetic relationships for 33 strains belonging to the genera Azorhizobium, Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium were conducted by the sequence analyses of the ITS regions. The sequence homologies of these strains showed the high variations(28.0 - 94.9%). According to the phylogenetic analysis of ITS regions. 37 ITS clones from 33 strains of 32 species were classified into four groups. Group I included all strains of the genus Sinorhizobium as core members and R. giardinii as a peripheral member. The genus Rhizobium strains were clustered into group II which was very heterogeneous and the tree toplogy of this group were very unstable. Among the members of group II. the taxonomic position of R. radiobacter and R. rubi was not clearly identified on the basis of ITS I regions. R. undicola and R. vitis were remotely related with other Rhizobium strains including R. leguminosarum, R. galegae, R. gallicum, R. mongolense, R. tropici, R. hainanense, R. rhizogense and R. huautlense of group II were supposed to be loosely related to R. leguminosarum. While the stains of the genera Bradyrhizobium constituted group III with Azorhizobium caulindans, the strains of the genus Mesorhizobium formed group IV on the relatively high sequence homology level.

• Journal of Life Science
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• v.23 no.2
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• pp.182-189
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• 2013

Halophytes are unique land plants that are capable of thriving in a high-salt environment. They are attracting public attention due to their ability to synthesize bioactive substances such as UV protectants or antioxidizing agents. To achieve unaffected growth under high salinity, halophytes may take advantage of the activities of cell growth factors such as expansins. Expansins are well-known cell wall proteins that are responsible for cell enlargement. They loosen cell walls, thereby contributing to actual plant growth. This study aimed to identify positive roles of expansins in the growth of halophytes. Three expansin cDNA clones were isolated from seedlings of Suaeda japonica. Comparing the deduced amino acid sequences of the expansin genes of S. japonica with those of other plant species suggested that the cDNA clones isolated from S. japonica belong to the EXPA (${\alpha}$-expansin) gene family. A phylogenetic tree based on the deduced amino acid sequences revealed that the expansins of S. japonica share a close evolutionary relationship with those of strawberry (Fragaria ananassa) and jujube (Ziziphus jujuba), both of which are woody dicots. SjEXPAs did not show any remarkable change in the gene expression level in different NaCl concentrations, providing a clue to the unaffected seedling growth of S. japonica in a high-salt environment. In conclusion, the present study presents the first report of expansin genes from halophytes and suggests a putative role for these genes in plant growth under high salinity.

• Korean Journal of Ecology and Environment
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• v.40 no.3
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• pp.387-394
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• 2007

Despite geographic barriers such as oceans, many freshwater algal species inhabit different continents of the world. A unicellular freshwater alga, Mallomonas caudeata, commonly occurring in Asia, Europe, and America of the northern Hemisphere, is closely related to human life such as monitoring blooms and defecting changes in climates. In order to demonstrate its occurrence in Korea and to infer its phylogeny, we sequenced nuclear SSU and plastid rbcL genes from isolates collected in six different reservoirs. We have also investigated transmission electron microscopy of the Korean isolates. SSU sequences of the species from Korea and USA were almost identical, having pair-wise divergences of 0.06% in SSU and 0.45% in rbcL. Both gene trees revealed that the species was clearly separated from other species of the genus, while the genus was not monophyletic. Rhizoplasts are composed of microfibrils organised in striated rootlets attached to the multilayered plate of basal bodies and arranged on the surface of the nucleus at their distal ends. The rhizoplast constitutes a basal body-nucleus connector similar to that of typical Synurophyceas. The results that Mallomonas was not supported by both SSU and rbeL data sets require a further study with additional taxon sampling.

• Korean Journal of Plant Taxonomy
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• v.35 no.1
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• pp.7-23
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• 2005

Molecular phylogenetic studies were conducted to evaluate interspecific relationships in 40 populations of Viola including 35 Korean taxa, four Japanese populations and one outgroup using nuclear ribosomal ITS sequences. The phylogenetic analyses were conducted using parsimony and neighbor-joining methods. Subsection Trigonocarpae of section Nomimium appeared as the most basal clade within the Korean Viola. Section Dischidium and Chamaemelanium was monophyletidbootstrap 100%) and placed between subsect. Trigonocarpae and three other subsections of sect. Nomimium. Sect. Nomimium was paraphyletic. Although each subsectional grouping was in accordance with previous infrageneric classification based on morphological characters, yet discordance remained at the series level. Two evolutionary trends observed in the ITS tree were as follows. First, subsect. Trigonocarpae(x=10) was derived from the outgroup(x=6); Second, subsects. Bilobatae and Vaginatae(x=10 or 12), and subsect. Patellares(x=12) of sect. Nomimium were originated from sects. Dischidium and Chamaemelanium(x=6). Viola albida complex including three very closely related taxa was recognized as independent group within subsect. Patellares in parsimony tree. This result suggested that they should be treated as a taxa in series Pinnatae. Phylogenetic position of a putative hybrid species, Viola woosanensis was not supported with previous morphological hypothesis.

• Journal of Life Science
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• v.29 no.6
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• pp.637-644
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• 2019

This study was conducted to analyze the genetic characteristics of the Jeju dog for preservation and protection. A total of 139 dogs from 7 dog breeds, including the Jeju dog, were genotyped using 16 microsatellite markers. The results revealed 2-18 alleles per locus, with a total of 131 alleles among the 16 markers. Most alleles were identified for FH3381, which had 18 alleles, whereas FH2834 had the fewest alleles, with just 2. When the total mean value was observed, the expected heterozygosity and observed heterozygosity were higher for than for outgroup dogs, and the PIC values ranged from 0.000 to 0.862, respectively. The phylogenetic tree analysis of the Jeju dog and other dog varieties revealed that the Jeju dog is closest to the Sapsal dog (0.393). The phylogeny between the Jeju and Korean domestic dogs showed that the Jeju dog is most distant from the Dongkyung dog (0.507). Looking at the distribution individually, the Jeju dog is in the same group as the Labrador Retriever and the Sapsal dog. Meanwhile, the Poongsan, Dongkyung, and Jindo dogs and the German Shepherd were in the same group. Genetic information confirmed through the results of this study can be used as basic data to study the genetic characteristics of the Jeju dog.

• Research in Plant Disease
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• v.24 no.4
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• pp.328-331
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• 2018

A severe disease with leaf spots and necrotic symptoms was observed in cucumber (Cucumis sativus L.) seedlings in April 2018 at a nursery in Kimjae, Korea (35o 47'09.8"N 127o 2'24.3"E). The infected plants initially showed spots on water-soaked cotyledons which, at later stages, enlarged and spread to the leaves, which the lesions becoming dry and chlorotic. The symptomatic samples were collected from cucumber and the isolates were cultured on LB agar. The representative bacterial strain selected for identification showed fluorescent on King's medium B, was potato rot-positive, levan and arginine dihydrolase-negative, oxidase-negative and tobacco hypersensitivity-positive in LOPAT group 2 as determined by LOPAT tests. A pathogenicity test was carried out on a 3-week-old cucumber. After 3 days of inoculation, leaf spots and necrotic symptoms appeared on the cucumber, similar to the originally infected plants. The infecting bacterial strain was identified as Pseudomonas viridiflava, by 16S rDNA sequence analysis. This is the first report of leaf spot diseases on cucumber caused by P. viridiflava.