• Journal of Microbiology
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• v.38 no.2
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• pp.62-65
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• 2000

Partial sequence comparisons of mitochondrial small subunit rDNA (mt SSU rDNA) were used to examine taxonomic and evolutionary relationships among seven Penicillium species : two monoverticillate species, two biverticillate species, and three terverticillate species. Amplified fragments of mt SSU rDNA highly varied among seven species in size, suggesting the existence of multiple insertions or deletions in the region. A phylogengtic tree was constructed by exhaustive search of parsimony analysis. The phylogenetic tree distinguished two statistically supported monophyletic groups, one for two monoverticillate species and the other for three terverticillate species and ont biverticillate species, P. vulpinum. The phylogenetic relationship of P. waksmanii, the biverticillate species, was not clear.

• Parasites, Hosts and Diseases
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• v.37 no.3
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• pp.181-188
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• 1999

We investigated the value of mitochondrial small subunit rRNA gene (mt SSU rDNA) PCR-RFLP as a taxonomic tool for Acanthamoeba isolates with close inter-relationships. Twenty-five isolates representing 20 species were included in the analysis. As in nuclear 18s rDNA analysis, two type strains (A. astronyxis and A. tubiashi) of morphological group 1 diverged earliest from the other strains, but the divergence between them was less than in 18s riboprinting. Acanthamoeba griffini of morhological group 2 branched between pathogenic (A. culbertsoni A-1 and A. healyi OC-3A) and nonpathogenic (A.palestinensis Reich, A. pustulosa GE-3a, A. royreba Oak Ridge, and A lenticulata PD2S) strains of morphological group 3. Among the remaining isolates of morphological group 2, the Chang strain had the identical mitochondrial riboprints as the type strain of A. hatchetti. AA2 and AA1, the type strains of A. divionensis and A. paradivionensis, respectively, had the identical riboprints as A. quina Vil3 and A. castellanii Ma. Although the branching orders of A. castellanii Neff, A. polyphaga P23, A. triangularis SH621, and A. lugdunensis L3a were different from those in 18S riboprinting analysis, the results obtained from this study generally coincided well with those from 18S riboprinting. Mitochondrial riboprinting may have an advantage over nuclear 18S rDNA riboprinting beacuse the mt SSU rDNAs do not seem to have introns that are found in the 18S genes of Acanthamoeba and that distort phylogenetic analyses.

• Journal of Microbiology
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• v.34 no.1
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• pp.38-39
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• 1996

The internal regions of nuclear small subunit rRNA from 6 plaeurotus species and 5 Pleurotus ostreatus strains were amplified by PCR and sequenced. The DNA sequences of 8 Pleurotus strains (P. ostreatus NFFA2, NFFA4501, NFFA4001, KFFA4001, KFCC11635, P florida, P. florida, P. sajor-cuju, P. pulmonarius, and P. spodoleucus) were idential, but P. cornucopiae differed from them in two bases out of 605 bases. However, p[hylogenetic analysis of the sequences by DNA-distance matrix and UPGMA methods showed that P. ostreatus NFFA2m1 and NFFA2m2, known as mutants of P. ostreatus NFFA2, belonged to anther group of Basidiomycotina, which is close to the genus Auricularia. The difference of the SSU rDNA sequences of P. cornucopiae from other Pleurotus species tested corresponds to the difference of mitochondrial plasmid type present in Pleurotus species as observed by Kim et al. (1993, Korean J. Microbiol. 31, 141-147).

• Journal of Microbiology
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• v.34 no.1
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• pp.37-37
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• 1996

The internal regions of nuclear small subunit rRNA from 6 plaeurotus species and 5 Pleurotus ostreatus strains were amplified by PCR and sequenced. The DNA sequences of 8 Pleurotus strains (P. ostreatus NFFA2, NFFA4501, NFFA4001, KFFA4001, KFCC11635, P florida, P. florida, P. sajor-cuju, P. pulmonarius, and P. spodoleucus) were idential, but P. cornucopiae differed from them in two bases out of 605 bases. However, p[hylogenetic analysis of the sequences by DNA-distance matrix and UPGMA methods showed that P. ostreatus NFFA2m1 and NFFA2m2, known as mutants of P. ostreatus NFFA2, belonged to anther group of Basidiomycotina, which is close to the genus Auricularia. The difference of the SSU rDNA sequences of P. cornucopiae from other Pleurotus species tested corresponds to the difference of mitochondrial plasmid type present in Pleurotus species as observed by Kim et al. (1993, Korean J. Microbiol. 31, 141-147).ishement of silencing at the HMR/hsp82 locus can occur in G1-arrested cells. Cell cycle arrest at G1 phase was achieved by treatment of early log a cell cultures with .alpha.-factor mating pheromone, which induces G1 arrest. The result suggests that passage through S phase (and therefore DNA replication) is nor required for re-establishing silencer-mediated repression at the HMNRa/HSP82 locus. Finally, to test whether de nono protein synthesis is required for re-establishment of silencer-mediated repression, cells were pretreated with cycloheximide (500 /.mu.g/ml) 120 min. It was apparent that inhibiting protein synthesis delays, but does not prevent, re-establishment of silencer-mediated repression. Altogether, these results indicate that re-establishment of silencer-mediated repression is not dependent on the DNA replication and has no requirement for protein synthesis.

• Journal of Microbiology
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• v.35 no.4
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• pp.259-263
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• 1997

To study the phylogenetic relationships of species of Trichaptum and to infer intraspecific dibergence of T. abietinum, partial mitochondrial small subunit rDNA sequences were determined. Six strains of T. abietinum, two of T. biforme, and one of T. fusco-violaceum were examined. Parsimony and distance analyses showed that each Trichaptum species forms a distinct group and that T. abietinum consists of two or more subgroups. Strains from North America were distantly related to one another but the European strain formed an independent group with three Korean strains, suggesting the possibility that Korean taxa may be phylogenetically closer to European taxa than to North American taxa.

• 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.

• Research in Plant Disease
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• v.11 no.1
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• pp.56-65
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• 2005

To establish taxonomic system of morphologically similar species of small-spored Alternaria, phylogenetic analysis of internal transcribed spacer (ITS 1, ITS 2 and 5.8S rDNA) and mitochondrial small subunit (mt SSU) rDNA sequences and URP-PCR fingerprinting analysis from 11 species ofAlternaria were performed. Phylogenetic analysis of ITS and mt SSU rDNA sequences revealed that 10 out of 11 species of the smallspored Alternaria were phylogenetically identical with a bootstrap value of 100%. A. infectoria only was phylogenetically differentiated from the other species. The results suggest that the 10 small-spored Alternaria species are very closely related evolutionally and the markers can not be used for differentiation of the smallspored Alternaria species. URP-PCR fingerprinting analysis from eleven species of smallspored Alternaria using 10 URP primers showed that it was possible to differentiate the species, although genetic similarities were found among the species. The Alternaria sp. from common pokeweed could be distinguished from other species by URP-PCR analysis, and it was considered as a new species. A. infectoria could be easily distinguished from the other 10 species by phylogenetic analysis of ITS and mt SSU rDNA sequences and the URPPCR fingerprinting analysis.

• Mycobiology
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• v.42 no.2
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• pp.174-180
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• 2014

We analyzed the genetic diversity of Cylindrocarpon destructans isolates obtained from Korean ginseng (i.e., Panax ginseng) roots by performing virulence tests and nuclear ribosomal gene internal transcribed spacer (ITS) and mitochondrial small subunit (mt SSU) rDNA sequence analysis. The phylogenetic relationship analysis performed using ITS DNA sequences and isolates from other hosts helped confirm that all the Korean C. destructans isolates belonged to Nectria/Neonectria radicicola complex. The results of in vivo and ex vivo virulence tests showed that the C. destructans isolates could be divided into two groups according to their distinctive difference in virulence and the genetic diversity. The highly virulent Korean isolates in pathogenicity group II (PG II), together with foreign isolates from P. ginseng and P. quinquefolius, formed a single group. The weakly virulent isolates in pathogenicity group I, together with the foreign isolates from other host plants, formed another group and exhibited a greater genetic diversity than the isolates of PG II, as confirmed by the mt SSU rDNA sequence analysis. In addition, as the weakly virulent Korean isolates were genetically very similar to the foreign isolates from other hosts, they were likely to originate from hosts other than the ginseng plants.

• Journal of Microbiology and Biotechnology
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• v.15 no.5
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• pp.1028-1038
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• 2005

To elucidate phylogenetic relationships of Phellinus and its related genera, nuclear internal transcribed spacer and mitochondrial small subunit ribosomal DNA sequences from 65 strains were determined and compared. The combined dataset of two sequences increased informative characters and led to the production of trees with higher levels of resolution. Phylogenetic analysis of the combined dataset revealed thirteen evolutionary lineages and several unresolved species that were together subdivided into two large clusters consisting of oligonucleate species and binucleate species. These results coincided with previous cytological, morphological, and molecular studies. It is newly recognized that the Phellinus linteus complex forms a sister clade to Inonotus, and that Fulvifomes is somehow related to Inocutis. The Phellinus linteus complex of dimitic perennial taxa made an independent clade from Inonotus and suggested that hyphal miticity and fruitbody permanence had enough phylogenetic significance to keep the complex within the traditional genus Phellinus. Taxa lacking setae were clustered into Fulvifomes, Phylloporia, Inocutis, and Fomitiporia, and the first three were closely related sister groups, but Fomitiporia was a genus distantly related to them. Several taxa with branched setae were shown among distantly related genera. Molecular evidence indicated that the ancestral nuclear type could be a binucleate feature, and that there might be parallel gains of branched setae and parallel losses of setae in the Hymenochaetales.

• Parasites, Hosts and Diseases
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• v.39 no.2
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• pp.161-170
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• 2001

We conducted both the small subunit ribosomal DNA (SSU rDNA) polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and mitochondrial (mt) DNA RFLP analyses for a genetic characterization of Acanthamoeba isolates from contact lens storage cases of students in Seoul, Korea. Twenty-three strains of Acanthamoeba from the American Type Culture Collection and twelve clinical isolates from Korean patients were used as reference strains. Thirty-nine isolates from contact lens storage cases were classified into seven types (KA/LS1 , KA/LS2, KA/LS4, KA/LS5, KA/LS7 KA/LS18, KA/LS31). Four types (KA/LS1 , KA/LS2, KA/LS5, KA/LS18) including 33 isolates were regarded as A. castellanii complex by riboprints. KA/LS1 type was the most predominant (51.3%) in the present survey area, followed by KA/LS2 (20.9%), and KA/LSS (7.7%) types. Amoebae of KA/LS1 type had the same mtDNA RFLP and riboprint patterns as KA/E2 and KA/E12 strains, clinical isolates from Korean keratitis patients. Amoebae of KA/LS2 type had the identical mtDNA RFLP patterns with A. castellanii Ma strain, a corneal isolate from an American patient as amoebae of KA/LS5 type, with KA/E3 and KA/E8 strains from other Korean keratitis patients. Amoebae of KA/LS 18 type had identical patterns with JAC/E1, an ocular isolate from a Japanese patient. Three types , which remain unidentified at species level, were not corresponded with any clinical isolate in their mtDNA RFLP and riboprint patterns. Out of 39 isolates analyzed in this study, mtDNA RFLP and riboprint patterns of 33 isolates (84.6%) were identical to already known clinical isolates, and therefore, they may be regarded as potentially keratopathogenic. These results suggest that contact lens wearers in Seoul should pay more attention to hygienic maintenance of contact lens storage cases for the prevention of Acanthamoeba keratitis.