• The Plant Pathology Journal
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• v.15 no.4
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• pp.228-235
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• 1999

Genetic diversity of ninety-five Korean isolates of Phytophthora was investigated on the basis of PCR-RFLP of ribosomal DNA. The isolates were previously identified as following fifteen species by mycological and cultural characteristics; P. boehmeriae, P. cactorum, P. cambivora, P. capsici, P. cinnamoni, P. citricola, P. citrophthora, P. cryptogea, P. drechsleri, P. erythroseptica, P. infestans, P. megasperma, P. nicotianae, P. palmivora and P. sojae. The regions of small subunit (SSU) and internal transcribed spacer (ITS) of rDNA were amplified with primer pair, NS1 and ITS4, by polymerase chain reaction (PCR) and digested with nine restriction enzymes. P. boehmeriae, P. cactorum, P. cambivora, P. capsici, P. cinnamomi, P. citricola, P. citrphthora, P. infestans, P. nicotianae and P. palmivora showed specific band patterns for each species. However, P. sojae and P. erythroseptica presented identical band patterns and P. cryptogea, P. drechsleri and P. megasperma were divided into six groups, which were not compatible with delineation of the species. A group originated from cucurbits showed distinct band patterns from other groups, but the other five groups were closely related within 96.0% similarity, forming one complex group. Consequently, Korean isolates of Phytophthora were divided into thirteen genetic groups and each group was readily differentiated by comparing digestion patterns of AvaII, HaeIII, MboI, HhaI and MspI. Therefore, PCR-RFLP of rDNA using the five enzymes can be used to differentiate or identify the Phytophthora species reported in Korea so far.

• Mycobiology
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• v.30 no.1
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• pp.13-17
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• 2002

The genomic DNAs were extracted from roots of Glycine max and Sorghum bicolor, and compared with those from spores of two arbuscular mycorrhizal(AM) fungi, Glomus mosseae and Scutellospora heterogama. The partial small subunit(SSU) of ribosomal RNA genes were synthesized and amplified by polymerase chain reaction with the fungal specific primers, AM1 and NS31. By the recent molecular techniques, the presence of another AM fungal DNA were confirmed in the roots of two plants, and three sequences of rDNA fragments amplified were identified to be close to those of G. caledonium, G. fasiculatum and G. proliferum. The two AM fungi, both, were found to colonize at the cortical layers of plant roots collected in the fields, together.

• Korean Journal Plant Pathology
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• v.14 no.5
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• pp.519-525
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• 1998

Intraspecific genetic diversity of Korean isolates of Phytophthora drechsleri was investigated based on PCR-RFLP of rDNA along with closely related species in the genus; P. cryptogea, P. melonis, P. erythroseptica, P. cinnamomi, P. cambivora and P. cactorum. Gene regions of nuclear small subunit and internal transcribed spacer (ITS) in rDNA were amplified with polymerase chain reaction and digested with 9 restriction enzymes. Phytophthora species was readily differentiated from each other based on the digestion patterns, however, P. cryptogea was not separable from some isolates of P. drechsleri. Twenty one isolates of P. drechsleri originated from 15 host plants were divided into three distinct groups designated as PdG1, PdG2 and PdG3, respectively. Four isolates in PdG1 were originated from green vegetables and tomato and nine isolates in PdG2 were mainly isolated from medicinal plants. The two groups showed 95.3% homology and four isolates of P. cyptogea came under the groups. However, Eight isolates in PdG3 collected from cucurbits were clearly differentiated from those of PdG1 and PdG2 by 66.5% homology, but completely matched with a Taiwan isolate of P. melonis. Results indicated that three distinct groups exist in Korean isolates of P. drechleri and each group has host preference. In addition, reclassification of the cucurbits isolates are reserved because of their distinct genetic characters from other intraspecific groups in P. drechsleri.

• Parasites, Hosts and Diseases
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• v.34 no.4
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• pp.259-266
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• 1996

The taxonomic validity of morphological group III Accnthamoeba app. is uncertain. In the present study. six type strains of group III Aconthamoeba spry. , A. culbertsoni, A. heniyi, A. pustulosc, A. palestinensis, A. royrebn and A. lenticulnto were subjected for the evaluation or their taxonomic validity by comparison of the isoeneyme patterns by isoelectic focusing on polyacrylamide gels, mitochondrial DNA (Mt DNA) restriction fragment length polymorphism (RFLP) . and small subunit ribosomal DNA (ssu rDNA) PCR-RFLP patterns. The Mt DNA RFLP patterns were heterogeneous between the species. The type strains of A. pclestinensls and A. pustulosc showed almost identical patterns of isoenrymes and rDNA PCR-RFLP with an estimated sequence divergence of 2.6%. The other species showed heterogeneous patterns of isoenxymes and rDNA PCR- RFLP. It is likely that A. pustuLosc is closely related with A. palestinensis and that the former may be regarded as a junior synonym of the latter.

• The Korean Journal of Mycology
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• v.46 no.2
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• pp.134-144
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• 2018

Three fungal strains belonging to the class Sordariomycetes, namely BH-06, 17-039 and BE12-1, were isolated from soils in Korea and identified as Chaunopycnis alba, Myrothecium cinctum and Humicola olivacea, respectively. These species were confirmed according to their morphological characteristics and phylogenetic relationships determined based on internal transcribed spacer regions, as well as large subunit, small subunit, ${\beta}$-Tubulin and RNA polymerase II largest subunit sequences of ribosomal DNA. These three species are the first members of the Sordariomycetes reported in Korea.

• Mycobiology
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• v.31 no.2
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• pp.68-73
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• 2003

Roots of Glycine max and Miscanthus sinensis and soil samples were collected from various field sites at Goesan, Chungbuk in Korea. Microscopic observations of the roots indicated high colonization rates of both arbuscular mycorrhizal fungi(AMF) and other fungi. The partial small subunit of ribosomal DNA genes were amplified with the genomic DNA extracted from their roots by nested polymerase chain reaction(PCR) with universal primer NS1 and fungal specific primers AML Restriction fragment length polymorphism(RFLP) was analyzed using the combinations of three restriction enzymes, HinfI, AluI and AsuC21. Nucleotides sequence analysis revealed that ten sequences from Miscanthus sinensis and one sequence from Glycine max were close to those of arbuscular mycorrhizal fungi. Also, 33% of total clones amplified with NS31-AM1 primers from M. sinensis and 97% from G. max were close to Fusarium oxysporum or other pathogenic fungi, and they were successfully distinguished from AME Results suggested that these techniques could help to distinguish arbuscular mycorrhizal fungi from root pathogenic fungi in the plant roots. Especially, DNA amplified by these primers showed distinct polymorphisms between AMF and plant pathogenic species of Fusarium when digested with AsuC21.

• Animal cells and systems
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• v.13 no.3
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• pp.351-356
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• 2009

Ciliates are undoubtedly one of the most diverse protozoans that play a significant role in ecology. However, molecular examination, based on comparing the DNA sequences, has been done on a limited number of the species. Because most ciliates are uncultivable and their population sizes are often too small, it is usually difficult to obtain sufficient genomic DNA required for PCR based experiments. In the present study, we evaluated the effectiveness of four commercial DNA extraction procedures that extract high quality genomic DNA from a single ciliate cell. It was discovered that RED Extract-N-$Amp^{TM}$ PCR kit is the best method for removing PCR-inhibiting substances and minimizing DNA loss during purification. This method can also amplify more than 25 reactions of PCR. In addition, this technique was applied to single cells of 19 species belonged to 7 orders under 5 classes that isolated from mixed natural populations. Their small subunit ribosomal DNA (SSU rDNA) was successfully amplified. In summary, we developed a simple technique for the high-yield extraction of purified DNA from a single ciliate cell that may be more useful for rare ciliates, such as tiny and uncultivable marine microbes.

• ALGAE
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• v.24 no.4
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• pp.205-212
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• 2009

Molecular genetic tools are widely used to learn more about the identical characterization of obscure microalgal strains. At the Korea Marine Microalgae Culture Center (KMMCC), the authors deduced the genetic relationship of 41 strains of the genus Tetraselmis by analysing a small subunit ribosomal DNA (18S rDNA) sequences. Forty-one strains were seperated into five groups, which showed over a 98-99% similarity to Tetraselmis striata or Tetraselmis sp. Tsbre. Also, 13 strains among them had an identical genotype to Tetraselmis striata while 5 strains had with Tetraselmis sp. Tsbre, respectively. The mean size of each strain generally showed the tendency of different variation according to the groups.

• Korean Journal Plant Pathology
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• v.14 no.6
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• pp.589-593
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• 1998

DNA amplification by polymerase chain reaction (PCR) was used to specifically detect Plasmodiophora brassicae, causing clubroot of crucifers. On the basis of DNA sequence informations, an oligonucleotide primer set specific for the pathogen was designed form small subunit gene (18S-like) and internal transcribed spacer (ITS) region of ribosomal DNA. Primer ITS 5/PB-C produced an amplification product of approximately 520 bp in length with DNA from P. brassicae. However, no amplification product was produced with DNAs from several soil-borne fungi, Didymella bryoniae and Rhizopus stolonifer. Using these primers, the clubroot pathogen was readily detected from infected roots of crucifers, but not from healthy roots. Southern hybridization analysis further confirmed that the amplification product was originated from P. brassicae.

• 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.