• Proceedings of the Plant Resources Society of Korea Conference
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• 2018.10a
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• pp.42-42
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• 2018

Two unrecognized species of Sparganium of Korea were found during the our field expeditions and phylogenetic analyses of specimens deposited in the Herbarium of Korea National Arboretum (KH). S. coreanum H. $L{\acute{e}}v$. was first reported as a new species based on the specimen (Taquet, 2150) collected from Jeju Island. It has been recognized as synonym or infraspecific taxa of S. stoloniferum and S. eurycarpum or even never recognized recently. However, phylogenetic tree showed that S. coreanum is monophyletic and has sister relationship with S. eurycarpum. Furthermore, additional distribution localities were also found by herbarium survey. Morphological characteristics and distribution information of S. coreanum will be discussed. Another Sparganium species found from Mt. Daeam is occurring either as floating or emergent. Although we could not identify this species since lack of any flowers or fruits for two year surveys, phylogenetic analyses results showed that this species belong to the clade of S. glomeratum, which is distributed in high elevation lakes and marshes of Europe, Asia, and North America. Additional survey of morphology and report will be needed.

• Animal Systematics, Evolution and Diversity
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• v.33 no.2
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• pp.131-135
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• 2017

Asteroid specimens of the genus Luidia were collected at a depth of 95-100 m in the Korea Strait by bottom trawling in April 2016. The specimens were identified as Luidia avicularia Fisher, 1913 (Luidiidae: Paxillosida) based on morphological characteristics and molecular phylogenetic analyses, and the species is new to the Korean fauna. A 648-bp partial nucleotide sequence of mitochondrial cytochrome c oxidase I (mt-COI) gene was obtained from Korea, and then was compared to sequences of related species stored in GenBank using molecular phylogenetic analyses. No sequence differences were detected between the L. avicularia mt-COI gene sequences from Korea and China, and the species described in this report was clearly distinct from L. maculata, which was previously reported in Korean fauna. Three Luidia species have been reported in Korea.

• Journal of Microbiology
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• v.44 no.1
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• pp.83-91
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• 2006

The sudden appearance and potential lethality of severe acute respiratory syndrome (SARS)-associated coronavirus (SARS-CoV) in humans has resulted in a focusing of new attention on the determination of both its origins and evolution. The relationship existing between SARS-CoV and other groups of coronaviruses was determined via analyses of phylogenetic trees and comparative genomic analyses of the coronavirus genes: polymerase (Orflab), spike (S), envelope (E), membrane (M) and nucleocapsid (N). Although the coronaviruses are traditionally classed into 3 groups, with SARS-CoV forming a $4^{th}$ group, the phylogenetic position and origins of SARS-CoV remain a matter of some controversy. Thus, we conducted extensive phylogeneitc analyses of the genes common to all coronavirus groups, using the Neighbor-joining, Maximum-likelihood, and Bayesian methods. Our data evidenced largely identical topology for all of the obtained phylogenetic trees, thus supporting the hypothesis that the relationship existing between SARS-CoV and group 2 coronavirus is a monophyletic one. Additional comparative genomic studies, including sequence similarity and protein secondary structure analyses, suggested that SARS-Co V may bear a closer relationship with group 2 than with the other coronavirus groups. Although our data strongly suggest that group 2 coronaviruses are most closely related with SARS-CoV, further and more detailed analyses may provide us with an increased amount of information regarding the origins and evolution of the coronaviruses, most notably SARS-CoV.

• Korean Journal of Plant Resources
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• v.27 no.6
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• pp.671-679
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• 2014

Molecular phylogenetic analyses of Korean Elaeagnus L. were conducted using seven species, one variety, one forma and four outgroups to evaluate their relationships and phylogeny. The sequences of internal transcribed spacer regions in nuclear ribosomal DNA were employed to construct phylogenetic relationships using maximum parsimony (MP) and Bayesian analysis. Molecular phylogenetic analysis revealed that Korean Elaeagnus was a polyphyly. E. umbellata var. coreana formed a subclade with E. umbellata. Additionally, the genetic difference between E. submacrophylla and E. macrophylla was very low. Moreover, E. submacrophylla formed a branch from E. macrophylla, indicating that E. submacrophylla can be regarded as a variety. However, several populations of this species were not clustered as a single clade; therefore, further study should be conducted using other molecular markers. Although E. glabra f. oxyphylla was distinct in morphological characters of leaf shape with E. glabra. But E. glabra f. oxyphylla was formed one clade by molecular phylogenetic with E. glabra. Additionally, this study clearly demonstrated that E. pungens occurs in Korea, although it was previously reported near South Korea in Japan and China. According to the results of ITS regions analyses, it showed a resolution and to verify the relationship between interspecies of Korean Elaeagnus.

• Asian-Australasian Journal of Animal Sciences
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• v.17 no.10
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• pp.1355-1359
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• 2004

Japanese Black cattle of Hyogo prefecture (Tajima strain) are famous for its ability to produce high-quality meat and have been maintained as a closed system for more than 80 years. In order to assess the usefulness of microsatellite markers in closed cattle populations, and evaluate the genetic structure of the Tajima strain, we analyzed representative dams of the Tajima strain comprised of the substrains Nakadoi and Kinosaki. Genetic variability analyses indicated low genetic diversity in the Tajima strain. In addition, a recent genetic bottleneck, which could be accounted for by the high level of inbreeding, was detected in both substrains. In phylogenetic analyses, relationship coefficients and genetic distances between individuals were calculated using pedigree and microsatellite information. Two phylogenetic trees were constructed from microsatellite and pedigree information using the UPGMA method. Both trees illustrated that most individuals were distinguished clearly on the basis of the two substrains, although in the microsatellite tree some individuals appeared in clusters of different substrains. Comparing the two phylogenetic trees revealed good consistency between the microsatellite analysis tree and the pedigree information. The correlation coefficient between genetic distances derived from microsatellite and pedigree information was 0.686 with a high significance level (p<0.001). These results indicated that microsatellite information may provide data substantially equivalent to pedigree information even in unusually inbred herds of cattle, and suggested that microsatellite markers may be useful in revealing genetic structure without accurate or complete pedigree nformation. Japanese Black cattle of Hyogo prefecture (Tajima strain) are famous for its ability to produce high-quality meat and have been maintained as a closed system for more than 80 years. In order to assess the usefulness of microsatellite markers in closed cattle populations, and evaluate the genetic structure of the Tajima strain, we analyzed representative dams of the Tajima strain comprised of the substrains Nakadoi and Kinosaki. Genetic variability analyses indicated low genetic diversity in the Tajima strain. In addition, a recent genetic bottleneck, which could be accounted for by the high level of inbreeding, was detected in both substrains. In phylogenetic analyses, relationship coefficients and genetic distances between individuals were calculated using pedigree and microsatellite information. Two phylogenetic trees were constructed from microsatellite and pedigree information using the UPGMA method. Both trees illustrated that most individuals were distinguished clearly on the basis of the two substrains, although in the microsatellite tree some individuals appeared in clusters of different substrains. Comparing the two phylogenetic trees revealed good consistency between the microsatellite analysis tree and the pedigree information. The correlation coefficient between genetic distances derived from microsatellite and pedigree information was 0.686 with a high significance level (p<0.001). These results indicated that microsatellite information may provide data substantially equivalent to pedigree information even in unusually inbred herds of cattle, and suggested that microsatellite markers may be useful in revealing genetic structure without accurate or complete pedigree information.

• Mycobiology
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• v.44 no.3
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• pp.121-130
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• 2016

Recently, the Fusarium genus has been narrowed based upon phylogenetic analyses and a Fusarium-like clade was adopted. The few species of the Fusarium-like clade were moved to new, re-installed or existing genera or provisionally retained as "Fusarium." Only a limited number of reference strains and DNA marker sequences are available for this clade and not much is known about its actual species diversity. Here, we report six strains, preserved by the Belgian fungal culture collection BCCM/IHEM as a Fusarium species, that belong to the Fusarium-like clade. They showed a slow growth and produced pionnotes, typical morphological characteristics of many Fusarium-like species. Multilocus sequencing with comparative sequence analyses in GenBank and phylogenetic analyses, using reference sequences of type material, confirmed that they were indeed member of the Fusarium-like clade. One strain was identified as "Fusarium" ciliatum whereas another strain was identified as Fusicolla merismoides. The four remaining strains were shown to represent a unique phylogenetic lineage in the Fusarium-like clade and were also found morphologically distinct from other members of the Fusarium-like clade. Based upon phylogenetic considerations, a new genus, Pseudofusicolla gen. nov., and a new species, Pseudofusicolla belgica sp. nov., were installed for this lineage. A formal description is provided in this study. Additional sampling will be required to gather isolates other than the historical strains presented in the present study as well as to further reveal the actual species diversity in the Fusarium-like clade.

• Korean Journal of Ichthyology
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• v.18 no.4
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• pp.293-299
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• 2006

Copper,zinc superoxide dismutase (Cu,Zn-SOD) plays a key role to the first antioxidant defense system against oxidative stress in diverse aerobic organisms. Due to the housekeeping action of Cu,Zn-SOD, it was reported that the structure and function have been conserved during evolution. In this study Cu,Zn-SOD from cloudy catshark Scyliorhinus torazame was subjected to phylogenetic analyses to know its evolutionary relationship in the vertebrate lineage. Molecular phylogenetic trees inferred by NJ, MP, ML and/or Bayesian analyses showed two shark species, Prionace glauca and S. torazame grouped together with high statistical supports. In general, they placed at the separated position from bony vertebrates. Thereafter, bony vertebrates composed of teleosts and birds/mammals (amniotes) formed a monophyletic group. Each teleost and amniote clade was also supported by relatively high statistical values. These phylogenetic relationships are well congruent with the phylogenetic hypothesis of the ancestral position of cartilaginous fishes to bony vertebrates.

• Animal cells and systems
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• v.4 no.3
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• pp.257-261
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• 2000

To elucidate phylogenetic relationships among poecilostome families 18S rDNA sequence data were generated for seven poecilostome and one cyclopoid copopods by PCR cloning and sequencing techmiques. Phylogenetic trees were constructed by maximum parsimony, neighbor joining, and maximum likelihood methods using cyclopoid sequence as an outgroup. The results from three different analyses showed that the seven poecilostome families were eiridel into two groups: Clausidiidae-Myicolidae-Synaptiphillidae-bomolochidae and Lichomologidae-Chondracanthidae-Ergasilidae. The molecular phylogenies were consistent with those from the morphological characters. Therefore, these analyses porvide further evidence for the utility of 18S rDNA sequences in addressing phylogenetic relationships among poecilostome families.

• Mycobiology
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• v.44 no.4
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• pp.248-259
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• 2016

During fungal diversity surveys of the order Eurotiales in Korea, two fungal strains, EML-DG33-1 and EML-NCP50, were isolated from samples of rat dung and fig tree leaf collected at a garden located in Gwangju in 2014. To complete the National Species List of Korea, it is a prerequisite to verify whether many questionable species, which were previously recorded but not confirmed, indeed present in Korea. Herein, the isolates were confirmed as undescribed species, Paecilomyces variotii and Talaromyces amestolkiae based on the combination of morphological and phylogenetic analyses of multigenes including the rDNA internal transcribed spacer, ${\beta}-tubulin$, and RNA polymerase II subunit 2.

• Mycobiology
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• v.49 no.2
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• pp.188-195
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• 2021

The genus Pseudoperonospora, an obligate biotrophic group of Oomycota, causes the most destructive foliar downy mildew disease on many economically important crops and wild plants. A previously unreported disease by Pseudoperonospora was found on oriental pickling melon (Cucumis melo var. conomon) in Korea, which is a minor crop cultivated in the temperate climate zone of East Asia, including China, Korea, and Japan. Based on molecular phylogenetic and morphological analyses, the causal agent was identified as Pseudoperonospora cubensis, and its pathogenicity has been proven. Importantly, two phylogenetic clades of P. cubensis, harboring probably two distinct species, were detected within the same plots, suggesting simultaneous coexistence of the two clades. This is the first report of P. cubensis causing downy mildew on oriental pickling melon in Korea, and the confirmation of presence of two phylogenetic clades of this pathogen in Korea. Given the high incidence of P. cubensis and high susceptibility of oriental pickling melon to this disease, phytosanitary measures, including rapid diagnosis and effective control management, are urgently required.