• Korean Journal of Microbiology
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• v.35 no.3
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• pp.180-184
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• 1999

Molecular spslemaucs of Agaricus species was investigated on the base of the sequences of the internal transcribed spaceriITS) regions in ribosomal DNA (rDNA). The sequences of the ITS region in 5 species and two group of Agaricus genus were resolved. In the phylogenetic trees. the species generally divided inlo two subclusters, refered to here as the group I and group 11. The group I consisted of Agaricus blazei ATCC 76739, Agarictrs blazei species cultivated in Korean hmings. Ago/-icus anmensis IMSNU 32049 and Agaricus can~pestris VPI-OKM 25665. Between Agaricus blazei NCC 76739 and the Agaricus blazei species cultivated in Korean farmings had the variation in lhe 5 nucleotide on the ITS regions. These varieties were presumed the variation by the geographic and cultivated conditions. In addition the subgroup of group I was formed by Agaricus arvensis LMSNU 32049 and Agaricus carnpests VPI-OKM 25665. The group IT included Agnrictrs bispoms CH 3004 and Agaricus pocillotor DUKE-J 173.

• Journal of Microbiology and Biotechnology
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• v.5 no.4
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• pp.194-199
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• 1995

A portion (7.4 kb) of ribosomal DNA tandem repeat unit from a genome of the mushroom T. matsutake has been cloned. A 1.75 kb EcoRI fragment was cloned first using S. cerevisiae 255 rRNA gene as a probe, and this was then used for further cloning. A chromosomal walking experiment was carried out and the upstream region of the 1.75 kb fragment was cloned using SmaI/BamHI enzyme, the size was estimated to be 5.2 kb in length. Part of the downstream region of the 1.75 kb fragment was also cloned using XbaI/BamHI enzymes. Restriction enzyme maps of three cloned DNA fragments were constructed. Northern hybridization, using total RNA of T. matsutake, and the restriction fragments of three cloned DNAs as probes, revealed that all four ribosomal RNA genes (large subunit[LSU], small subunit [SSU], 5.85 and 5S rRNA genes) are present in the cloned region. The gene organization of the rDNA are regarded as an intergenic spacer [IGS]2 (partial) - SSU rRNA - internal transcribed spacer [ITS]1 - 5.8S rRNA - ITS2 - LSU rRNA - IGS1 -5S rRNA - IG52 (partial).

• Bulletin of the Korean Chemical Society
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• v.35 no.10
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• pp.3005-3008
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• 2014

Human ChlR1 protein (hChlR1), a member of the cohesion establishment factor family, plays an important role in the segregation of sister chromatids for maintenance of genome integrity. We previously reported that hChlR1 interacts with hFen1 and stimulates its nuclease activity on the flap-structured DNA substrate covered with RPA. To elucidate the relationship between hChlR1 and Okazaki fragment processing, the effect of hChlR1 on in vitro nuclease activities of hFen1 and hDna2 was examined. Independent of ATPase activity, hChlR1 stimulated endonuclease activity of hFen1 but not that of hDna2. Our findings suggest that the acceleration of Okazaki fragment processing near cohesions may aid in reducing the size of the replication machinery, thereby facilitating its entry through the cohesin ring.

• Mycobiology
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• v.38 no.3
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• pp.166-170
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• 2010

Gummy stem blight is a major foliar disease of muskmelon (Cucumis melo L.). In this study, morphological characteristics and rDNA internal transcribed spacer (ITS) sequences were analyzed to identify the causal organism of this disease. Morphological examination of the Jeonbuk isolate revealed that the percentage of monoseptal conidia ranged from 0% to 10%, and the average length $\times$ width of the conidia was 70 ($\pm$ 0.96) $\times$ 32.0 ($\pm$ 0.15) ${\mu}m$ on potato dextrose agar. The BLAST analysis showed nucleotide gaps of 1/494, 2/492, and 1/478 with identities of 485/492 (98%), 492/494 (99%), 491/494 (99%), and 476/478 (99%). The similarity in sequence identity between the rDNA ITS region of the Jeonbuk isolate and other Didymella bryoniae from BLAST searches of GenBank was 100% and was 95.0% within the group. Nucleotide sequences of the rDNA ITS region from pure culture ranged from 98.2% to 99.8%. Phylogenetic analysis with related species of D. bryoniae revealed that D. bryoniae is a monophyletic group distinguishable from other Didymella spp., including Ascochyta pinodes, Mycosphaerella pinodes, M. zeae-maydis, D. pinodes, D. applanata, D. exigua, D. rabiei, D. lentis, D. fabae, and D. vitalbina. Phylogenetic analysis, based on rDNA ITS sequence, clearly distinguished D. bryoniae and Didymella spp. from the 10 other species studied. This study identified the Jeonbuk isolate to be D. bryoniae.

• ALGAE
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• v.38 no.4
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• pp.241-252
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• 2023

The genera Carolibrandtia and Chlorella have been described as small green algae with spherical cell shapes that inhabit various environments. Species of these genera are often difficult to identify because of their simple morphology and high phenotypic plasticity. We investigated two small coccoid strains from Antarctica based on morphology, molecular phylogeny by two alignment methods which have been applied to previous phylogenetic studies of the genus Chlorella, and comparison of the secondary structures of nuclear small subunit (SSU) and internal transcribed spacer (ITS) rDNA sequences. Light microscopy of two strains revealed spherical cells containing chloroplasts with pyrenoids, and the morphological characteristics of the strains were nearly identical to those of other Chlorella species. However, based on the phylogenetic analyses of nuclear SSU and ITS rDNA sequences, it was determined that the Antarctic microalgal strains belonged to two genera, as the Chlorella and Carolibrandtia. In addition, the secondary structures of the SSU and ITS2 sequences were analyzed to detect compensatory base changes (CBCs) that were used to identify and describe the two strains. A unique CBC in the SSU rDNA gene was decisive for distinguishing strain CCAP 211/45. The ITS2 rDNA sequences for each strain were compared to those obtained previously from other closely related species. Following the comparison of morphological and molecular characteristics, we propose KSF0092 as a new species, Chlorella terrestris sp. nov., and the reassignment of the strain Chlorella antarctica CCAP 211/45 into Carolibrandtia antarctica comb. nov.

• Korean Journal of Oriental Medicine
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• v.14 no.1
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• pp.129-135
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• 2008

Phylogenetic relationship and DNA polymorphism among local populations of the Asparagus cochinchinensis have been investigated based on nuclear ribosomal DNA ITS sequences and RAPD analysis in Korea. In result, two genetically distinct groups of local populations except Geoje were recognized by the phylogenetic tree both in rDNA-ITS and RAPD. One was called 'western coast group' that includes the Buan 1, 2 and Taean and the other was 'southern coast group' that includes Haenam, Yeosu and Namhae. Thus, the geographical relationship of Asparagus cochinchinensis was two well-typified clades. These results suggest that the geographical genetic variation of Asparagus cochinchinensis is closely connected with the slow and long period of propagation via the coast in Korean Peninsula.

• Journal of Life Science
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• v.13 no.1
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• pp.99-104
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• 2003

Aromatic compounds are of major concern among environmental pollutants due to their toxicity and persistence. To monitor aromatic compounds in a real time with a better sensitivity, a new method of SPR (surface plasmon resonance) based on DNA chip (Biacore 3000) was developed here. It is thought that CapR regulatory protein as a complex with phenol, could bind to their corresponding promoter, Po. Biotinylated DNA oligomers for the promoter was synthesized by PCR and coupled onto streptoavidin-linked CM5-chip. CapR regulatory proteins were purified after cloning their genes in pET21a (+) vector and expressing proteins. The interaction was assessed by the system where the regulatory proteins flowed with or without phenol through the cells of DNA chip. CapR regulatory protein even in the presence of phenol had no response to its promoter, Po, suggesting that other factor(s) might be required for the activation of Po promoter. The present work reveals a promising possibility of the SPR-based DNA chip in monitoring specific environmental pollutants in a real time.

• 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.

• Journal of Life Science
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• v.13 no.4
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• pp.400-411
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• 2003

This study was carried out to identify the phylogenetic relationship and to know the distribution of the entomopathogenic fungi by comparing the DNA sequences of internal transcribed spacer regions (ITS1 and ITS2) and 5.8S ribosomal DNA (rDNA) repeat unit. The entomopathogenic fungi had their specific sequences in ITS1 and 2 regions depending on species. The comparison of the ITS sequences of standard strains indicated that the sequences ITS1 were more variable than those of ITS2. It seems that Paecilomyces tenuipes, Isaria japonicus and P. japonicus are the same species but called as different names because of very similar sequences, and unidentified Paecilomyces sp. KACC 40220 and KACC 40656 showed identical sequences to P. tenuipes. Thirty six strains of the commercial products of entomopathogenic fungi used in this study were divided into four groups by the phylogenetic analysis based on 5.85 rDNA and ITS regions. We found twenty-three strains were P. tenuipes / japonica, eleven strains were C. militaris, and other two strains were Beauveria bassiana and C. multiaxialis, respectively.

• Journal of Life Science
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• v.9 no.1
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• pp.15-21
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• 1999

The random amplified ploymorphic DNAs (RAPD) assay is a simple and useful tool in identification of appropriate genetic markers, that requires no knowledge of target DNA sequence. RAPD products were generated directly from seaweed tissues, without prior nucleic acid extraction, of Porphyra yezoensis, Ulva pertusa and Undaria pinnatifida. The nuclear rDNA internal transcribed spacer (ITS) fragment however was not amplified directly from the seaweed tissues. Using DNA extracted by the LiCl method, both the ITS and RAPD's have been amplified by the polymerase chain reaction. RAPD of P yezoensis, thallus (n) and conchocelis (2n) produced lots of different polymorphic bands (36-50$\%$) depending on the arbitrary primers used. Difference was also observed between direct tissues amplification and DNA extracts amplification (53-57$\%$). Thus it is important to use the same ploidy of tissue for DNA extraction and as a RAPD template.