• Korean Journal of Microbiology
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• v.32 no.3
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• pp.186-191
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• 1994

The origin of the leading strand replication (ori) and of lagging strand replication (M-O) of R-plasmid pSBK203 was identified and its base sequence was determined. About 50 bp of ori sequence residues overlapped with the structural gene of rep. Sequence comparison reveals that pSBK-ori shares obvious identities with those of pT181 family and consists of two regions, one is conserved and the other is variable region. Of two palindrome sequence located one after another in upstream region of rep gene, palA' instead of palA which shares sequence homology with diverse family of plasmids such as pOX6, pC194, and pE194 seems to act as a signal for conversion of primarily replicated ssDNA to dsDNA (minus origin (M-O)).

• The Korean Journal of Mycology
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• v.45 no.4
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• pp.355-361
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• 2017

In this study, endophytic fungi were isolated from the roots of three native orchid species from Korea: Bletilla striata, Oreorchis patens, and Cephalanthera longibracteata. The isolated fungal endophytes were identified based on the morphological and molecular characteristics including sequence analysis of internal transcribed spacer (ITS) and 28S ribosomal DNA regions. As a result, we discovered 5 species of fungal endophytes that have not been previously reported in Korea: Phialocephala bamuru, Coniochaeta mutabilis, Phialophora foetens, Calonectria canadensis, and Neonectria ramulariae.

• The Plant Pathology Journal
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• v.22 no.1
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• pp.36-45
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• 2006

Twenty isolates of Didymella bryoniae were isolated from infected cucurbit plants in various growing areas of southern Korea in 2001 and 2002. Random Amplified Polymorphic DNA (RAPD) group [RG] I of D. bryoniae was more virulent than RG IV to watermelon. Virulence of the RG I isolate was strong to moderate to cucumber, whereas that of the RG IV varied from strong, moderate to weak. Two hundred seventy-three amplified fragments were produced with 40 primers, and were analyzed by a cluster analysis using UPGMA method with an arithmetic average program of NTSYSPC. At the distance level of 0.7, two major genomic DNA RAPD groups were differentiated among 20 isolates. The RG I included 7 isolates from watermelon and one isolate from melon, whereas the RG IV included 12 isolates from squash, cucumber, watermelon and melon. Amplification of internal transcribed spacer (ITS) region and small subunit rRNA region from the 20 isolates yielded respectively a single fragment. Restriction pattern with 12 restriction enzymes was identical for all isolates tested, suggesting that variation in the ITS and small subunit within the D. bryoniae were low. Amplification of the genomic DNAs of the tested isolates with the sequence characterized amplified regions (SCAR) primer RG IF-RG IR specific for RG I group resulted in a single band of 650bp fragment for 8 isolates out of the 20 isolates. Therefore, these 8 isolates could be assigned into RG I. The same experiments done with RG IIF-RG IIR resulted in no amplified PCR product for the 20 isolates tested. An about 1.4 kb-fragment amplified from the RG IV isolates was specifically hybridized with PCR fragments amplified from genomic DNAs of the RG IV isolates only, suggesting that this PCR product could be used for discriminating the RG IV isolates from the RG I isolates as well other fungal species.

• The Korean Journal of Mycology
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• v.45 no.4
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• pp.394-398
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• 2017

A survey to assess the diversity of wound-associated Ophiostomatales and Microascales, the so-called ophiostomatoid fungi, on Korean native trees, was undertaken in 2017. Wounds were artificially created, and a fungus resembling a species of Sporendocladia was consistently isolated from the exposed cambium and inner bark of artificially induced wounds on Quercus variabilis. Morphological examination and DNA sequence comparisons based on the internal transcribed spacer (ITS) and 5.8S regions of the rDNA confirmed the identity of the fungus as Sporendocladia bactrospora. This is the first report on S. bactrospora occurring on Q. variabilis in Korea.

• ALGAE
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• v.36 no.2
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• pp.111-121
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• 2021

Two cyanobacterial morphotypes isolated from Signy Island, South Orkney Islands, maritime Antarctica were characterised using a polyphasic approach combining morphological, cytological and molecular analyses. These analyses showed that the strains grouped with members of the genus Wilmottia. This genus currently includes three species, W. murrayi, W. stricta, and W. koreana. Both morphotypes analysed in this study were placed within the clade of W. murrayi. This clade showed a well-supported separation from Antarctic and New Zealand strains, as well as strains from other regions. W. murrayi was first described from Antarctica and is now known from several Antarctic regions. Confirmation of the occurrence of W. murrayi at Signy Island significantly extends its known distribution in Antarctica. In addition, a new combination, W. arthurensis, is suggested for Phormidium arthurensis.

• Mycobiology
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• v.47 no.3
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• pp.261-272
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• 2019

Oomycetes are widely distributed in various environments, including desert and polar regions. Depending upon different habits and hosts, they have evolved with both saprophytic and pathogenic nutritional modes. Freshwater ecosystem is one of the most important habitats for members of oomycetes. Most studies on oomycete diversity, however, have been biased mostly towards terrestrial phytopathogenic species, rather than aquatic species, although their roles as saprophytes and parasites are essential for freshwater ecosystems. In this study, we isolated oomycete strains from soil sediment, algae, and decaying plant debris in freshwater streams of Korea. The strains were identified based on cultural and morphological characteristics, as well as molecular phylogenetic analyses of ITS rDNA, cox1, and cox2 mtDNA sequences. As a result, we discovered eight oomycete species previously unknown in Korea, namely Phytopythium chamaehyphon, Phytopythium litorale, Phytopythium vexans, Pythium diclinum, Pythium heterothallicum, Pythium inflatum, Pythium intermedium, and Pythium oopapillum. Diversity and ecology of freshwater oomycetes in Korea are poorly understood. This study could contribute to understand their distribution and ecological function in freshwater ecosystem.

• Journal of Microbiology and Biotechnology
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• v.11 no.3
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• pp.529-533
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• 2001

The ${\beta}$-Amylase cDNA fragment from the oomcete Saprolegnia parasitica was cloned by reverse transcription-polymerase chain reaction (RT-PCR) using degenerate oligonucleotide primers derived from conserved ${\beta}$-amylase sequences. The 5'and 3'regions of the $\beta$-amylase gene were amplified using the rapid amplification of cDNA ends (rACE) system. It consisted of an open reading frame of 1,350 bp for a protein of 450 amino acids. Comparison between the genomic and cDNA sequences revealed that the intron was not present in the coding region. The deduced amino acid sequence of the ${\beta}$-amylase gene had a 97% similarity to the ${\beta}$-amylase of Saprolegnia ferax, followed by 41% similarity to those of Arabidopsis thaliana, Hordeum vulgare, and Zea mays. The ${\beta}$-amylase gene was also expressed in Saccharomyces cerevisiae by placing it under the control of the alcohol dehydrogenase gene (ADC1) promoter.

• The Plant Pathology Journal
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• v.23 no.2
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• pp.37-44
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• 2007

Colletotrichum contains many important pathogens which cause economically significant diseases of crops like pepper, strawberry, tomato and apple. Forty four isolates were collected to characterize the diversity of Colletotrichum causing apple anthracnose in various regions of Korea. They were analyzed by random amplified polymorphic DNA (RAPD), internal transcribed spacer (ITS) of rDNA and partial $\beta$-tubulin gene DNA sequence, and culture characteristics on PDA and PDA-Benomyl. From the results of molecular analyses, 31 strains belonged to Colletotrichum gloeosporioides, ribosomal DNA group (RG) 4 of Moriwaki et al. (2002), 8 strains belonged to C. acutatum, A2 group of Talhinhas et al. (2005) and 5 strains to C. acutatum, A3 group of Talhinhas et al. (2005). Most isolates of C. gloeosporioides RG4 grew faster on PDA than strains of C. acutatum, A2 and A3 groups and most RG4 strains were sensitive to Benomyl. However, a few strains of RG4 grew slower and were resistant to Benomyl. On the basis of molecular characteristics, apple isolates of C. acutatum were clearly differentiated from red pepper isolates of the species, but apple isolates of C. gloeosporioides were not.

• Fisheries and Aquatic Sciences
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• v.21 no.3
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• pp.8.1-8.6
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• 2018

Desmarestia japonica (Phaeophyceae, Desmarestiales) was recently established from the Japanese ligulate Desmarestia and is morphologically similar to D. ligulata. This species has been reported only from Japan. However, the taxonomic reports based on additional regional distributions are needed to clarify this taxonomic entity and its species boundaries. Because Desmarestia species have restricted distributions in Korea, we reexamined herbarium specimens of D. ligulata deposited at the National Institute of Biological Resources (South Korea). To improve the amplification efficiency of the polymerase chain reaction and avoid contamination by the DNA of other organisms, we developed taxon-specific molecular markers suitable for DNA barcoding of Desmarestia species. Nuclear ribosomal small subunit RNA (18S rDNA) and mitochondrial cytochrome c oxidase 1 (cox1) regions were selected as target DNA. As a result, both were successfully isolated from herbarium specimens of D. japonica acquired over 10 years. These molecular markers provide useful genetic information for herbarium specimens for which conventional molecular analysis is challenging.

• Korean Journal of Ecology and Environment
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• v.54 no.3
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• pp.209-220
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• 2021

Pacific herring, Clupea pallasii, a keystone species with significant ecological and commercial importance, is declining globally throughout much of its range. While traditional fishing equipment methods remain limited, new sensitive and rapid detection methods should be developed to monitor fisheries resources. To monitor the presence and quantity of C. pallasii from environmental DNA (eDNA) extracted from seawater samples, a pair of primers and a TaqMan^® probe specific to this fish based on mitochondrial cytochrome b (COB) sequences were designed for the real-time PCR (qPCR) assay. The combination of our molecular markers showed high specificity in the qPCR assay, which affirmed the success of presenting a positive signal only in the C. pallasii specimens. The markers also showed a high sensitivity for detecting C. pallasii genomic DNA in the range of 1 pg~100 ng rxn^-1 and its DNA plasmid containing COB amplicon in the range of 1~100,000copies rxn^-1, which produced linear standard calibration curves (r²=0.99). We performed a qPCR assay for environmental water samples obtained from 29 sampling stations in the southeastern coastal regions of South Korea using molecular markers. The assay successfully detected the C. pallasii eDNA from 14 stations (48.2%), with the highest mean concentration in Jinhae Bay with a value of 76.09±18.39 pg L^-1 (246.20±58.58 copies L^-1). Our preliminary application of molecular monitoring of C. pallasii will provide essential information for efficient ecological control and management of this valuable fisheries resource.