• Journal of fish pathology
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• v.33 no.2
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• pp.111-118
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• 2020

The genus Edwardsiella belonging to the family Enterobacteriaceae is a member of Gram-negative rod-shaped bacteria that cause disease in diverse aquatic organisms such as fish, amphibians and reptiles as well as avians and mammals including human throughout the world. This genus had been composed of three species, E. hoshinae, E. ictaluri and E. tarda, but recent researches erected two novel species, E. anguillarum and E. piscicida that were conventionally identified as E. tarda. In this study, we isolated seven strains belonging to the genus Edwardsiella from freshwater fishes that had been reared at inland fish farms in South Korea and investigated their biochemical characteristics and molecular phylogenetic relationships. The seven strains showed typical characteristics of four Edwardsiella species, E. anguillarum, E. ictaluri, E. piscicida and E. tarda, by biochemical analyses of Gram staining, indole and hydrogen sulfide (H2S) production, and API (Analytic Profile Index) 20E test. Molecular phylogenetic analyses inferred from DNA sequence data of both 16S ribosomal RNA (rRNA) and DNA gyrase subunit B (gyrB) genes were congruent with the biochemical characteristics. As a result, both biochemical and molecular phylogenetic analyses identified four strains isolated from three Anguilla species as E. anguillarum, E. piscicida and E. tarda, two strains from Pelteobagrus fulvidraco and Silurus asotus as E. ictaluri, and one strain from Moroco oxycephalus as E. piscicida. In this study, we isolated and successfully identified recently newly erected species, E. anguillarum and E. piscicida in addition to historically notorious pathogenic species, E. ictaluri and E. tarda. In the future study, systematic and comprehensive monitoring of the four Edwardsiella species are required for studying differences in pathogenicity among freshwater fishes.

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

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

• Korean Journal of Plant Taxonomy
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• v.40 no.1
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• pp.1-15
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• 2010

Recognizing a basal group in a taxon is one of the most important factors involved in understanding the evolutionary history of that group of life. Many botanists have suggested a sister to all other angiosperms to understand the origin and rapid diversification of angiosperms based on morphological and fossil evidence. Recent technical advances in molecular biology and the accumulation of molecular phylogenetic data have provided evidence of the extant basal-most angiosperm which is a sister to all other angiosperms. Although it is still arguable, most plant taxonomists agree that Amborella trichopoda Baill., a species (monotypic genus and monotypic family) distributed in New Caledonia, is a sister to all other extant angiosperms based on evidence from the following molecular approaches: 1) classical phylogenetic analyses based on multiple genes (or DNA regions), 2) analyses of a tree network of duplicated gene families, and 3) gene-structural evidence. As an alternative hypothesis with relatively minor evidence, some researchers have also suggested that Amborella and Nymphaeaceae form a clade that is a sister to all other angiosperms. Debate regarding the basal-most angiosperms is still ongoing and is currently one of the hot issues in plant evolutionary biology. We expect that sequencing of the whole genome of Amborella as an evolutionary model plant and subsequent studies based on this genome sequence will provide information regarding the origin and rapid diversification of angiosperms, which is Darwin's so called abominable mystery.

• The Korean Journal of Mycology
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• v.46 no.4
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• pp.415-425
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• 2018

To study the characteristics of yeasts, 433 strains of the genus Aureobasidium were isolated from the flowers collected from Jeolla-do in Korea, and the diversity of the strains was confirmed through molecular phylogenetic and morphological analyses. Based on phylogenetic analysis of LSU rDNA seguences, the Aureobasidium strains from the Jeolla-do province were classified into six groups. The dominant species of flower-derived yeasts were Groups A and D. Since Groups B, E, and F were found only in Jeollanam-do, we can infer that the Aureobasidium is distributed more widely in Jeollanam-do than in the Jeollabuk-do province. Through LSU and ITS rDNA sequence analyses, Group A was identified as A. pullulans, Group B as A. melanogenum, and Group F as a putative new species of Aureobasidium. Groups C, D, and E do not completely match with A. leucospermi, A. namibiae, or A. subglaciale by LSU or ITS rDNA analysis but are closely related to those species. Comparisons of colony morphology are likely to be more helpful in distinguishing Groups C and D. The results of this study can provide useful characteristics for future studies of the genus Aureobasidium.

• Korean Journal of Microbiology
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• v.49 no.4
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• pp.383-390
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• 2013

Lateral gene transfer (LGT) of genes from other bacteria into Vibrio cholerae is expectable because of the pronounced natural competence of the bacterium. In this study, quantitative aspects of LGT among the three species of Vibrio pathogenic to humans were characterized. Genome sequences of V. cholerae N16961, V. parahaemolyticus RIMD2210633, V. vulnificus CMCP6, and Escherichia coli K12 substrain MG1655 were analyzed to determine orthologous quartets of protein coding genes present in all four genomes. Phylogenetic analyses on the quartets were conducted to resolve vertical versus lateral patterns of gene polymorphisms based on congruence versus incongruence of phylogenetic trees. About 70% of the quartets could be resolved as either cohesive topology (75%) or LGT tree topologies (25%). The amount of LGT genes in Vibrio spp. appeared to be abnormally high for a genus and comparable to those of families. Patched distributions of LGT from different donors were observed on a chromosome. In the small chromosome of V. cholerae, physical linkages among LGT loci spanned half the length of the chromosome. Either accumulative selection for the donor alleles in LGT or presence of large-scale LGT events was hypothesized. These findings warrant further studies on the nature of donor-specificity of LGT alleles and its influence on evolution of Vibrio virulence to humans.

• Korean Journal of Plant Taxonomy
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• v.46 no.2
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• pp.247-255
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• 2016

As an attempt to determine the identity of the old trees of flowering cherries planted in the yard of the Catholic Archdiocese of Daegu, we conducted comparative phylogenetic analyses between wild and cultivated Prunus yedoensis Matsum. We generated the phylogeny (MP) and haplotype network (TCS) of 25 individuals, including wild P. yedoensis, from Jeju Island, cultivated P. ${\times}$yedoensis 'Somei-yoshino' from Korea and Japan, and P. spachiana f. ascendens (Makino) Kitam. from Jeju Island and Japan based on highly informative sequences of two cpDNA regions (rpl16 gene and trnS-trnG intergenic spacer). The wild and cultivated P. yedoensis were distinguished from each other in both the phylogeny and haplotype networks, and the old flowering cherry trees in Daegu had a cpDNA haplotype identical to that of the cultivated P. ${\times}$yedoensis 'Someiyoshino'. Compared to the cultivated P. ${\times}$yedoensis 'Somei-yoshino', wild P. yedoensis appears to have greater haplotype diversity, presumably originating from the genetic diversity of P. spachiana f. ascendens that functioned as a maternal parent in the hybrid origin of wild P. yedoensis. A future detailed study requires extensive sampling of P. spachiana f. ascendens from Japan and Korea to determine their precise phylogenetic relationships relative to wild and cultivated P. yedoensis. We concluded that the old flowering cherry trees planted in the yard of the Catholic Archdiocese of Daegu are highly likely to be of cultivated origin rather than wild types from Jeju Island, as previously speculated.

• Korean Journal of Plant Taxonomy
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• v.44 no.1
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• pp.22-32
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• 2014

The petal and sepal micromorphology of five species of Glechoma (Lamiaceae) was investigated to evaluate their taxonomic significance, and a molecular phylogeny using the sequences of internal transcribed spacers (ITS) regions of nuclear ribosomal DNA was carried out to resolve their phylogenetic relationships. Stomatal complexes were mostly found in the inner and outer part of the sepal from all investigated taxa, and the size length of the guard cell was variable among the taxa. Five types of trichomes (uni-cellular non-glandular trichome, multi-cellular non-glandular trichome, short-stalked capitate glandular trichome, long-stalked capitate glandular trichome, and peltate glandular trichome) were variable among the taxa as well as their distribution and density. In molecular phylogenetic studies, the genus Glechoma was composed of three geographically distinct major monophyletic groups (Europe-U.S.A., China-Korea, Japan). G. longituba in Korea and China formed well-supported monophyletic group. G. hederacea in Europe and U.S.A. formed a monophyletic and well-supported clade with G. sardoa, which are endemic species in Italy, with G. hirsuta falling as a sister to this clade. However, G. grandis did not form any phylogenetic relationships with the remaining taxa. The ITS analyses provided taxonomic boundaries of taxa in Glechoma although the petal and sepal micromorphological characters provided weak evidences of the systematic value. As further studies, incorporating more DNA regions to the matrix including other additional morphological analysis will be significant to provide clearer taxonomic structure in Glechoma.

• Journal of Life Science
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• v.18 no.6
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• pp.753-758
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• 2008

Genus Hemerocallis is a herbaceous species and some species among their taxa are very important herbal medicines. We evaluated representative samples of the eight taxa in Korea with inter simple sequence repeats (ISSR) markers to estimate phylogenetic relationships within taxa of this genus. The studied taxa were Hemerocallis fulva L., H. fulva for. kwanso, H. dumortieri Morren, H. coreana Nakai, H. hongdoensis M.G.Chung & S.S.Kang, H. middendorffi Trautv. et Mayer, H. thunbergii Baker, H. minor Miller. In addition, we investigated the genetic variation and structure of Korean populations of these taxa. The mean genetic diversity was 0.098 across species, varying from 0.068 to 0.123. A low level of genetic variation was found in populations of Hemerocallis species. Specially, gene diversity for H. minor was maintained the highest among genus Hemerocallis. An indirect estimate of the number of migrants per generation (Nm=0.218) indicated that gene flow was not extensive among Korean populations of Hemerocallis species. The phylogenic tree showed distinct three clades. One includes H. fulva, H. fulva for. kwanso and H. middendorffi. Another includes three Hemerocallis species, H. dumortieri, H. thunbergii and H. minor. The H. coreana and H. hongdoensis were shown as the sister group to the second clades. Although the size of sampling was not large enough for eight Korean Hemerocallis species, the analyses of ISSRs will certainly provide an enhanced view on the phylogeny of species.

• Journal of Animal Science and Technology
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• v.51 no.4
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• pp.273-282
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• 2009

DNA marker information is used to identify or distinguish cattle breeds or individual animal. The purpose of this study was to apply Bovine Genotypes Kit Version 1.1/2.1 to bovine DNA samples (National Institute of Animal Science) taken from Australian / American beef (n=148), Holstein beef (n=170) and Hanwoo cattle (n=177) bred in Jeongeub, Jeonbuk, Korea, so that it could distinguish Hanwoo breed. The Bovine Genotype Kits consist of 16 ISAG MS markers, which were used to build a database of genotypes in each group. Genotyping results were analyzed using MS Tool kit and Phylip program to create phylogenetic tree. The GeneClass 2.0 was used to estimate breed identification. These analyses found that this kit had 100% capacity to distinguish Hanwoo beef, 95.3% capacity to differentiate Australian / American beef and 90% capacity to identify Korean Holstein steer beef. Hence, it is expected that 16 commercial microsatellite markers is useful to categorizegenetic characteristics of Hanwoo breed and also identify Hanwoo individuals and the origin of beef. In particular, it is expected that these markers will be advantageous in discriminating domestic Holstein beef from Australian / Americanbeef.

• Korean Journal of Microbiology
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• v.44 no.4
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• pp.352-357
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• 2008

We evaluated cultivation methods to obtain pure cultures of previously uncultivated bacteria from soil. Soil bacteria (suspensions) were inoculated onto various oligotrophic media with one of the following additives: 1) soil extract; 2) anthraquinone disulfonate (humic acid analogue); 3) acyl homoserine lactones (quorum-signaling compounds); 4) catalase (for the protection of bacteria from exogenous peroxides). After the relatively long period (60 days) of incubation with elevated concentrations of $CO_2$ (5%, v/v), the media containing catalase showed the highest colony count. We purified 147 randomly selected colonies from the media and the isolates were subjected to the phylogenetic analyses of their 16S rRNA gene sequences. Phylogenetic analysis revealed that approximately 30% of the isolates might belong to novel species or novel family, suggesting that the media and incubation conditions used could be useful for the cultivation of as-yet-uncultured bacteria. Especially, bacteria belonging to the phylum Acidobacteria, ubiquitous bacterial taxon known as an uncultured bacterial group (at least difficult to culture from environmental samples), were successfully cultured in this study.