• Journal of Microbiology
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• v.40 no.4
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• pp.335-339
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• 2002

Partial sequences of 16S rRNA gene of five chroococcalian blue-green algal strains, Aphanothece nidulans KCTC AG10041, Aphanothece naegelii KCTC AG10042, Microcystis aeruginosa KCTC AG10159, Microcystis ichthyoblabe KCTC AG10160, and Microcystis viridis KCTC AG10198, which were isolated from water from the Geumgang River, were determined and were inferred their phylogenetic and taxonomic positions among taxa of order Chroococcales. Most taxa of Chroococcales whose partial 16S rRNA gene sequences were aligned in this study, are clustered with other related taxa. Aphanothece nidulans KCTC AG10041 and Aphanothece naegelii KCTC AG10042 made a cluster with other European species of these genera, which supported 100% of the bootstrap trees with a very high sequence similarity (97.4-99.4%) in this study. Three strains, Microcystis aeruginosa KCTC AG10159, M. ichthyoblabe KCTC AG10160, and M. viridis KCTC AG10198, formed a cluster with other Microcystis spp. supported 100 % of the bootstrap trees with a similarity of 97.0-99.9% except for two strains. However, this phylogentic tree made no resolution among the species of Microcystis spp. The topology of the tree reconfirmed the taxonomic status of three species of Microcystis, identified in this study based on the morphology, as three colonial types of Microcystis aeruginosa com. nov. Otsuka et al. (1999c). The genera of chroococcalian cyanophytes are heterogeneously clustered in these sequence analyses. We suggest that more molecular studies on the genera of Chroococcales with reference strains, widely collected from restricted geographic or environmental ranges, get accurate taxonomic or phylogenetic determinations.

• Journal of Veterinary Science
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• v.22 no.6
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• pp.67.1-67.7
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• 2021

Background: Chlamydophila felis, formerly known as Chlamydia psittaci var. felis, is frequently associated with ocular, respiratory, and occasionally reproduction tract infections. Even though the infection is sometimes asymptomatic, it potentially results in a latent immunosuppressive infection. Objective: This study aimed to identify occurrences of feline chlamydophilosis, rarely reported in cats in Indonesia. Methods: The observation was conducted in three cats with clinical signs of Cp. felis infection, particularly relapsing conjunctivitis. The cats' histories were recorded based on owners' information. Conjunctival swabs were sampled for cytology examination and molecular assay detection. A phylogenetic tree was generated using MEGA-X software to reveal group clustering. A post-mortem examination was performed on the cat that died during an examination. Results: Cp. felis was detected in both cytological examination and polymerase chain reaction assay. The phylogenetic tree demonstrated that the Cp. felis isolated in this study clustered with several other isolates from the other countries. Cp. felis can be isolated from cats with different clinical manifestations and levels of severity. The chronic fatal infection demonstrated interstitial broncho-pneumonia under histopathological examination. Conclusions: Molecular assay of Cp. felis is always recommended to obtain a definitive diagnosis of feline chlamydophilosis since the disease can have various clinical manifestations. Even though it may be subclinical and is often not fatal, an infected cat may be a carrier that could spread the pathogen in the surrounding environment. Serious disease management is suggested to avoid high costs associated with regularly relapsing disease.

• ALGAE
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• v.28 no.4
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• pp.307-330
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• 2013

The genus Cryptomonas is easily recognized by having two flagella, green brownish color, and a swaying behavior. They have relatively simple morphology, and limited diagnostic characters, which present a major difficulty in differentiating between species of the genus. To understand species delineation and phylogenetic relationships among Cryptomonas species, the nuclear-encoded internal transcribed spacer 2 (ITS2), partial large subunit (LSU) and small subunit ribosomal DNA (rDNA), and chloroplast-encoded psbA and LSU rDNA sequences were determined and used for phylogenetic analyses, using Bayesian and maximum likelihood methods. In addition, nuclear-encoded ITS2 sequences were predicted to secondary structures, and were used to determine nine species and four unidentified species from 47 strains. Sequences of helix I, II, and IIIb in ITS2 secondary structure were very useful for the identification of Cryptomonas species. However, the helix IV was the most variable region across species in alignment. The phylogenetic tree showed that fourteen species were monophyletic. However, some strains of C. obovata had chloroplasts with pyrenoid while others were without pyrenoid, which used as a key character in few species. Therefore, classification systems depending solely on morphological characters are inadequate, and require the use of molecular data.

• The Korean Journal of Mycology
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• v.47 no.3
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• pp.181-186
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• 2019

A designated fungal isolate, KNU-US-1802E was isolated from the soil in Uiseong, Korea. To identify characteristics of the isolate, it was cultured on PDA media for 6 days at $35^{\circ}C$. Colonies on PDA are flat, light gray, dense, with entire margins; reverse dark gray to black, with white margins. Aerial mycelia were smooth-walled, hyaline and 40~42 mm diameter after 6 days at $35^{\circ}C$. Conidia were hyaline, one-celled, ellipsoidal to fusiform, forming long chains with average length ${\times}$ width of $5.0{\pm}0.3{\times}2.9{\pm}0.2{\mu}m$. Molecular analysis indicates that the internal transcribed spacer (ITS) region and partial beta-tubulin (tub2) gene sequence showed 100% and 99% similarities, respectively with Acrophialophora ellipsoidea CGMCC 3.15255 collected from China. Phylogenetic analysis by the neighbor-joining (NJ) method shows that the KNU-US-1802E was clustered with A. ellipsoidea CGMCC 3.15255 in a phylogenetic tree constructed using the concatenated sequences of ITS region and tub2 gene sequences with a high bootstrap value. Based on these findings, the isolate KNU-US-1802E was identified as Acrophialophora ellipsoidea, and this is the first report of this isolate in Korea.

• Parasites, Hosts and Diseases
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• v.56 no.6
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• pp.583-588
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• 2018

Although widely studied, the natural diversity of the hard tick is not well known. In this study, we collected 194 sequences from 67 species, covering 7 genera of hard tick. The 5' region of the mitochondrial cytochrome c oxidase subunit 1 region (586 bp) has been used to investigate intra- and inter-species variation and the phylogenetic tree of neighbor joining method has been used for assessment. As a result, by comparing the K2P-distance of intra- and interspecies, 30 samples (15.2%) shown that interspecies distance was larger than the minimum interspecfic distance. From the phylogenetic analysis, 86.8% (49) of the species were identified correctly at the genus level. On deeper analysis on these species suggested the possibility of presence cryptic species. Therefore, further work is required to delineate species boundaries and to develop a more complete understanding of hard tick diversity over larger scale.

• Proceedings of the Korean Aquaculture Society Conference
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• 2003.10a
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• pp.35-35
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• 2003

We, for the first time, reported molecular sequences of large subunit ribosomal DNA Dl-D3 region of A. hiranoi, A. leei and A. satoanum hitherto unreported. In addition, this study presented the full-length sequences of A. affine, A. fraterculus, A. catenella and A. tamarense occurring in Korean coastal waters. In total, 17 Alexandrium morphospecies were subjected to the phylogenetic analysis using the Maximum-likelihood (ML) method. The alignment result of sequences of A. hiranoi and A. pseudogonyaulax showed that there were only two substitutions without length heterogeneity implying their genetic affiliation. In ML tree, A. leei formed a deeply diverging branch probably because of the accelerated evolutionary rate, and its phylogenetic position was so ambiguous to resolve the phylogenetic relationship to the residual taxa. An A. satoanum culture showing morphological variation in the sulcal plate formed an independent divergent branch with consistent sister relationship to A. hiranoi/A. pseudogonyaulax clade supported by the high posterior probability (PP) value. Blast search in GenBank showed the sequence data of A. affine, A. fraterculus, A. catenella and A. tamarense corresponded to their morphological species designation. In ML tree, Alexandrium species were commonly split into four main clades. The inter-clade relationships were not clear and usually supported by the week PP values. In general, the sulcal plate of Alexandrium species seemed to reflect the true phylogeny at the main clade level, and the connection between the 1 and the apical pore complex seemed to reflect the phylogeny at the subclade level.

• Mycobiology
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• v.49 no.2
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• pp.122-132
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• 2021

The reexamination of the fungal genus Botryosphaeria on 12 plant species of 10 families was carried out based on molecular phylogenetic analyses using the regions of translation elongation factor 1-α, β-tubulin, DNA-directed RNA polymerase II subunit, and internal transcribed spacer region of rDNA and morphological characteristics. Japanese isolates were divided into five clades and include Botryosphaeria dothidea, B. qingyuanensis, B. sinensis, and Botryosphaeria spp. Two species, B. qingyuanensis and B. sinensis have been newly added to the Japanese mycoflora, but their host plants are not specified. Botryosphaeria tenuispora isolated from Leucothoe fontanesiana and insect galls on fruits of Aucuba japonica has been proposed as a new species.

• Korean Journal of Plant Taxonomy
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• v.36 no.3
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• pp.189-207
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• 2006

Goodyera rosulacea, which is morphologically similar to G. repens, is described recently as a new species based on its distinct morphological characters such as rosette-formed leaves, short rhizome and habitat. To verify the taxonomic identity of G. rosulacea and its taxonomic relationship within Korean Goodyera taxa, sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA and the trnL region of cpDNA from 24 accessions including 1 outgroup accession were analyzed. Aligned sequences were analyzed using maximum parsimony and distance method, and the taxonomic identity and the taxonomic relationships among the related taxa were estimated by the existence of private marker gene and the phylogenetic tree of the aligned sequences. Molecular data indicate that G. rosulacea gas several private marker genes and shows monophyly in phylogenetic trees of both ITS and trnL sequences. the pairwise distance between G. rosulacea and the orher taxa of Korean Goodyera was 3.49-6.68% for ITS region and 5.05-9.53% for trnL region, indicating that G. rosulacea could be treated as an independent species. Therefore, our molecular data support the taxonomic of G. rosulacea as a distinct species of Korea. In phylogenetic trees, G. rosulacea formed same clade with G. repens, which has similar morphological characters with G. rosulacea, and showed the lowest pairwise distance with G. repens among Korean Goodyera taxa. These molecular data sugguested that G. rosulacea and G. repens are closely related taxa.

• Mycobiology
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• v.47 no.1
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• pp.66-75
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• 2019

A new species of Alternaria causing leaf spots on the rubber tree (Hevea brasiliensis) in Yunnan, China, was isolated, examined, and illustrated. Morphologically, it belongs to the section Porri of Alternaria, which produces relatively large conidia and a simple or branched, filamentous long beak. It is, however, characterized by conidiophores gradually enlarging near the apex into a clavate conidiogenous cell and long ellipsoid to obclavate, smoothwalled conidia with a long filamentous beak. Molecular phylogenetic analyses based on ITS rDNA, GAPDH, and TEF1-alpha sequences demonstrate that the phytopathogen falls in the clade of the section Porri, being most closely related to A. sidae, A. sennae, A. deseriticola, A. cyamopsidis, A. rostellata, A. nitrimali, A. crassa, and A. thunbergiae.

• The Korean Journal of Mycology
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• v.49 no.4
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• pp.531-537
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• 2021

Styrax japonicus is a deciduous shrub or a small tree belonging to the family Styracaceae. Since 1990, a rust fungus has continuously been found on S. japonicus leaves across the country. The morphological characteristics of the rust fungus were most consistent with those of Pucciniastrum styracinum reported on Styrax obassia in Japan. The species identification was confirmed by molecular phylogenetic analysis of the internal transcribed spacer and large subunit rDNA sequences. The current study provides mycological information with morphological measurements and molecular phylogenetic data of P. styracinum found on S. japonicus in Korea. Therefore, this is the first confirmed report on the presence of P. styracinum on S. japonicus in Korea.