• Mycobiology
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• v.50 no.3
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• pp.181-187
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• 2022

To exploit insect-derived fungi, insects were collected from seven different regions in Korea, including Gyeongbuk, Goryeong, and several fungi were isolated from them. A fungal strain designated 21-64-D was isolated from riparian tiger beetle (Cicindela transbaicalica) and morphologically identified as a species belonging to the genus Oidiodendron. Phylogenetic analysis using the nucleotide sequences of internal transcribed spacer (ITS) regions and the partial sequence of the large subunit of the nuclear ribosomal RNA (LSU) gene revealed the distinct phylogenetic position of the isolate among recognized Oidiodendron species including its closest neighbors O. chlamydosporicum, O. citrinum, O. maius, and O. pilicola. The hyphal and conidial morphology of the strain, particularly club-shaped hyphae, clearly differentiated it from its close relatives. Results indicated that 21-64-D is a novel species in the genus Oidiodendron, for which the name Oidiodendron clavatum sp. nov. is proposed.

• The Journal of the Korea institute of electronic communication sciences
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• v.19 no.2
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• pp.467-472
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• 2024

Multiple sequence alignment (MSA) is a method of collecting and aligning multiple protein sequences or nucleic acid sequences that perform the same function in various organisms at once. clustalW, a representative multiple sequence alignment algorithm using BioPython, compares the degree of alignment by column position. In addition, a web logo and phylogenetic tree are created to visualize conserved sequences in order to improve understanding. An example was given to confirm the differences between humans and other species, and applications of BioPython are presented.

• The Plant Pathology Journal
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• v.26 no.1
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• pp.83-89
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• 2010

Taxonomic position of 46 Korean isolates of Rhizoctonia solani which were classified into nine intraspecific groups by anastomosis and cultural characteristics was analyzed by randomly amplified polymorphic DNA (RAPD) and sequence analyses of the internal transcribed spacer (ITS) regions of ribosomal DNA. All the isolates within each group showed highly similar band patterns in RAPD. The ITS regions of the isolates within the same groups showed a high level of sequence similarity above 96.0% whereas similarities among different groups were below 94.4%. When compared with several reference strains of R. solani from foreign countries, all the Korean isolates were clustered with the foreign isolates belonging to the same groups in the phylogenetic tree. All six Korean strains of AG-4 were identified as HG-1 out of 3 subgroup of AG-4. We discussed taxonomic position of Korean isolates of R. solani and showed that sequence analysis with ITS regions could be a rapid and useful method for identification of intraspecific group of R. solani.

• BMB Reports
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• v.39 no.2
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• pp.178-182
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• 2006

Four strains of Acidithiobacillus ferrooxidans with different iron oxidation capacity were isolated from different mine drainage stations. The 16S rRNA gene of these strains were cloned and sequenced. Based on our sequences analysis on the four strain and the data on the other strains deposited in Genbank, all A. ferrooxidans may be classified into three phylogenetic groups. The analysis data showed that nucleotide variables (signature sites) were detected in 21 positions, and most of them were found in the first 800bp from 5' terminal except position 970 and 1375. Interestingly, the first 13 signature sites were located in two main regions:the first region (position 175-234) located in V2 while the second region (position 390-439) were detected in constant region between V2 and V3. Furthermore, the secondary structure and minimal free energy were determined in two regions among strains of three groups. These results may be useful in characterizing the microevolutionary mechanisms of species formation and monitoring in biohydrometallurgical application.

• Korean Journal of Medicinal Crop Science
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• v.16 no.1
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• pp.20-26
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• 2008

Anemarrhena asphodeloides (Korean name "Ji-Mo") has been used for oriental medicinal purposes in Korea, China and Japan. In this study, 29 A. asphodeloides samples were collected including 3 certified A. asphodeloides plants and many commercially marketed A. asphodeloides products. Chloroplast trnL-F regions of the "Ji-Mo" samples were sequenced and used to identify whether the samples were genuine A. asphodeloides or not. As the result, the trnL-F sequences of all the "Ji-Mo" samples were shown to be identical and it was proven that commercially available medicinal products "Ji-Mo" are genuine A. asphodeloides. Phylogenetic tree of. A. asphodeloides using the trnL-F sequences was constructed and compared with phylogenetic tree using rubisco large subunit (rbcL) gene sequences. In these tree, A. asphodeloides was affiliated in the family Agavaceae in the order Asparagales. It is proven that trnL-F phylogenetic tree is useful to study taxonomic position of A. asphodeloides.

• Journal of Life Science
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• v.27 no.3
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• pp.351-354
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• 2017

Cowpea (Vigna unguiculata (L.) Walp.) is recognized as a potential source of protein and other nutrients. The genus Vigna includes 100 wild species of plants. Especially, Vigna unguiculata includes annual cowpeas (ssp. unguiculata) and ten wild perennial subspecies. DNA sequence of internal transcribed spacer (ITS) region was determined for Vigna sinensis, one of native plant, which was found in recent but thought to have gone extinct in Korea. The seeds of Vigna sinensis used in this study were donated from Dong-Young Jo. The DNA sequence of ITS-5.8S-ITS2 for Vigna sinensis obtained from this study was deposited as Vigna sinensis AY195581 on GenBank of NCBI (National Center for Biotechnology Information). We investigated the sequence-based phylogenetic relationships of plants related and clarified its taxonomical position. DNA similarities among subspecies including Vigna unguiculata showed the range 98 to 100% in sequence-based phylogenetic analysis using total 507 base pairs of ITS1, 5.8S and ITS2. Vigna unguiculata and subspecies were grouped independently as one cluster from other Vigna species used in the phylogenetic analysis. In this study, based on the phylogenetic analysis using the ITS1-5.8S-ITS2 sequence of Vigna sinensis, it may be concluded to be classified to one of Vigna unguiculata substrains.

• 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.

• Parasites, Hosts and Diseases
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• v.54 no.6
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• pp.777-786
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• 2016

Raillietina species are prevalent in domestic chickens (Gallus gallus domesticus) in Phayao province, northern Thailand. Their infection may cause disease and death, which affects the public health and economic situation in chicken farms. The identification of Raillietina has been based on morphology and molecular analysis. In this study, morphological observations using light (LM) and scanning electron microscopies (SEM) coupled with molecular analysis of the internal transcribed spacer 2 (ITS2) region and the nicotinamide adenine dinucleotide dehydrogenase subunit 1 (ND1) gene were employed for precise identification and phylogenetic relationship studies of Raillietina spp. Four Raillietina species, including R. echinobothrida, R. tetragona, R. cesticillus, and Raillietina sp., were recovered in domestic chickens from 4 districts in Phayao province, Thailand. LM and SEM observations revealed differences in the morphology of the scolex, position of the genital pore, number of eggs per egg capsule, and rostellar opening surface structures in all 4 species. Phylogenetic relationships were found among the phylogenetic trees obtained by the maximum likelihood and distance-based neighbor-joining methods. ITS2 and ND1 sequence data recorded from Raillietina sp. appeared to be monophyletic. The query sequences of R. echinobothrida, R. tetragona, R. cesticillus, and Raillietina sp. were separated according to the different morphological characters. This study confirmed that morphological studies combined with molecular analyses can differentiate related species within the genus Raillietina in Thailand.

• Mycobiology
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• v.47 no.2
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• pp.191-199
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• 2019

Most of lichens are formed by Ascomycota, less than 1% are lichenized Basidiomycota. The flora investigation of lichenized Ascomycota of South Korea has been well studied in the past three decades; however, prior to this study, none of basidiolichens was discovered. During the recent excursion, an unexpected clavarioid basidiolichen, Sulzbacheromyces sinensis was collected. Morphology and ecology has been recorded in detail. DNA was extracted, and ITS, 18S, 28S nuclear rDNA were generated. In order to further confirm the systematic position of the Korean specimens, maximum likelihood and Bayesian inference analysis including all the species of the order Lepidostromatales were conducted based on the ITS. As a result, the phylogenetic tree of the order Lepidostromatales was reconstructed, which differed from the previous studies. The inferred phylogenetic tree showed that species of Sulzbacheromyces in three different continents (Asia, South Africa and South America) were separated into three clades with support. In this study, the species worldwide distribution map of Lepidostromatales was illustrated, and S. sinensis had a widest distribution range (paleotropical extend to the Sino-Japanese) than other species (paleotropical or neotropical). Prior to this study, the range of distribution, southernmost and northernmost points and the fruiting time of S. sinensis were recorded, and the genus Sulzbacheromyces was firstly reported from Korean peninsula and Philippines.

• Journal of fish pathology
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• v.37 no.1
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• pp.25-36
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• 2024

In this study, we analyzed the phylogenetic classification, epitope prediction, and pathogenicity of red sea bream iridovirus (RSIV) isolated from rock bream between 2019 and 2023. Phylogenetics based on genes encoding MCP and ATPase indicated that all five RSIV isolates belonged to RSIV subtype II. The deduced amino acid sequence of the MCP for the amplicons (1362 bp) obtained from RSIV isolates had a length of 453 amino acids. Among these, the amino acid sequences of the RSIV-19, 21, 22, and 23 isolates showed 100% identity, while the RSIV-20 isolate showed 99.78% identity with one residue difference at position 306. As a result of antigenicity analysis based on amino acid sequence, the antigenicity score of the RSIV-20 isolate was 0.6386 and the other RSIV isolates were 0.6365. Additionally, the prediction of their antigenic determinants resulted in a total of 17 identical antigenic plots. When each RSIV was inoculated into rock bream, no significant differences were observed with 100% cumulative mortality in all groups. This study provides data on the potential for genetic variation of RSIV isolated in the same marine area over the past five years, and the antigenicity and pathogenicity results of each isolate are expected to be useful information for selecting future vaccine strains.