• Journal of Mushroom
• /
• v.10 no.1
• /
• pp.37-43
• /
• 2012

This study was carried to identify a correct species and asses genetic diversity within the same species of Polyporus spp. preserved in Division of applied Microbiology. Contaminated isolates showed different growth rates, morphology and color of hyphae. We have reconstructed the phylogenetic tree of a select group of Polyporus spp. using nucleotide sequences of the internal transcribed spacer region(ITS) region. The phylogenetic tree was constructed by using the neighbor-joining method. PELF primers of 20-mer were used to assess genetic diversity of preserved isolates. Sequence analysis showed that three strains were different species and four strains were identified completely different nomenclature. According to the analysis of ITS sequences, the genus Polyporus clustered into five distinct group, most of which correlated with species-groups identified by RAPD method. Four isolates included strain PM02 showed high similarity with P. arcularius, four isolates included strain PM03 high similarity with P. alveolaris, three isolates included strain PM01 high similarity with P. tuberaster, and PM 06 and PM04 high similarity with P. brumalis and P. squamossus. Isolates were collected in the United States(PM10, PM11) was identified as P. alveolarius and P. arcularius. RAPD analysis of genetic polymorphisms of genus Polyporus showed a very different band patterns. As the result of RAPD and ITS region sequences analysis for preserved isolates, it seems likely that 6 isolates of Polyporus spp. may be need to reclassify or eliminate from preserved catalogue.

• Proceedings of the Korean Society of Life Science Conference
• /
• 2006.09a
• /
• pp.97.2-97.2
• /
• 2006

• Journal of Microbiology and Biotechnology
• /
• v.12 no.6
• /
• pp.989-992
• /
• 2002

Sweet persimmon (Diospyros kaki Thunb.) is widely cultivated in the southern part of Korea and its cultivation is increasing. However, anthracnose disease caused by Colletotricuhum species is one of the major hinderances to the cultivation and production of sweet persimmon. Therefore, in the current study, PCR was used to specifically detect Colletotrichum spp., based on the sequences of the ITS II regions in the rDNA. Using the sequence data, CO-1 was designated to detect Colletotrichum together the with ITS 4 primer. The result showed that a single segment of ca. 500 bp was observed only in Colletotrichum, but not in any other fungal and bacterial isolates. The annealing temperatures and template DNA quantites were also investigated to identify optimal conditions for detection. Using these species-specific primers, a unique band was obtained at annealing temperatures ranging from $55^{\circ}C\;and\;61^{\circ}C$ and template DNA levels from 10 pg- $10{\mu}g$.

• The Korea Journal of Herbology
• /
• v.30 no.3
• /
• pp.41-47
• /
• 2015

Objectives : Due to the morphological similarity of the pericarp and description of multi-species in National Pharmacopoeia of Korea and China, the Zanthoxylum Pericarpium is difficult to authenticate adulterant in species levels. Therefore, we introduced the sequence analysis of DNA barcode and identification of single nucleotide polymorphism(SNP) to establish a reliable tool for the distinction of Zanthoxylum Pericarpium from its adulterants. Methods : To analyze DNA barcode region, genomic DNA was extracted from twenty-four specimens of authentic Zanthoxylum species and inauthentic adulterant and the individual internal transcribed spacer regions (rDNA-ITS and ITS2) of nuclear ribosomal RNA gene were amplified using ITS1, ITS2-S2F, and ITS4 primer. For identification of species-specific sequences, a comparative analysis was performed using entire DNA barcode sequences. Results : In comparison of four Zanthoxylum ITS2 sequences, we identified 16, 4, 6, and 4 distinct species-specific nucleotides enough to distinguish Z. schinifolium, Z. bungeanum, Z. piperitum, and Z. simulans, respectively. The sequence differences were available genetic marker to discriminate four species. Futhermore, phylogenetic relationship revealed a clear classification between different Zanthoxylum species showing 4 different clusters. These results indicated that comparative analysis of ITS2 DNA barcode was an useful genetic marker to authenticate Zanthoxylum Pericarpium in species levels. Conclusions : The marker nucleotides, enough to distinguish Z. schinifolium, Z. piperitum, Z. bungeanum, and Z. simulans, were obtained at 30 SNP marker nucleotides from ITS2 sequences. These differences could be used to authenticate official Zanthoxylum Pericarpium from its adulterants as well as discriminating each four species.

• Korean Journal of Fisheries and Aquatic Sciences
• /
• v.35 no.6
• /
• pp.633-638
• /
• 2002

Nuclear 18S ribosomal RNA gene (185 rDNA) from the aquaculturable seaweed Porphya yezoensis (Bangiales, Rhodophyta) was amplified using the polymerase chain reaction and its sequence was analysed. Complete 185 rDNA has an 1823 bp exon and a 514 bp intron. The G+ C contents of exon and intron were $48\%$ and $51.4\%$, respectively. The exon sequence showed $99.5\%$ homology to the GenBank accession number AB013177 of the Japanese p. yezoensis. The intron region that was inserted upstream between 568 and 1083 showed $93.4\%$ homology to the AB013177.

• Mycobiology
• /
• v.33 no.2
• /
• pp.109-112
• /
• 2005

The internal transcribed spacer (ITS) regions including the 3'-end of 18S rRNA gene, 5.8S rRNA gene and the 5'-end of the 28S rRNA gene of Rhizopus spp. were amplified by PCR and analyzed by DNASIS program. Length polymorphism of these region ranged from 564 bp in R. oryzae to 789bp in R. stolonifer. The length and sequence of 5.8S was very conserved with $154{\sim}155\;bp$. The sequence of ITS2 was more variable than that of ITS1. The base substitution rates were ranged from 0 to 0.6069 per site, and higher rate was found in R. stolonifer. In general, transition was usually more frequent than transversion. On the basis of sequencing results, four groups were clustered with value of 61.9% similarity; R. oryzae, R. micros pores, R. homothallicus, and R. stolonifer groups.

• Mycobiology
• /
• v.37 no.4
• /
• pp.258-266
• /
• 2009

Pleurotus eryngii, known as king oyster mushroom has been widely used for nutritional and medicinal purposes. This study was initiated to screen the suitable conditions for mycelial growth and to determine the phylogenetic relationship of the selected strains. Optimal mycelial growth was observed at $30{^{\circ}C}$ and minimum mycelial growth observed at $10{^{\circ}C}$. This mushroom tolerates a broad pH range for mycelial growth, with most favorable growth observed at pH 6. Results also indicated that glucose peptone, yeast malt extract and mushroom complete media were favorable growth media, while Hennerberg and Hoppkins media were unfavorable. Dextrin was the best and xylose the least effective carbon sources. Results revealed that inorganic nitrogen sources were less effective than organic sources for the mycelial growth of P. eryngii. Investigation of genetic diversity is necessary to identify the strains. The ITS region of rDNA were amplified using PCR. The size of the ITS1 and ITS2 regions of rDNA from the different strains varied from 214 to 222 bp and 145 to 236 bp, respectively. The sequence of ITS2 was more variable than that of ITS1, and the 5.8S sequences were identical. A phylogenetic tree based on the ITS region sequences indicated that selected strains could be classified into six clusters. Fourteen IUM and ATCC- 90212 strains were also analyzed by RAPD with 20 arbitrary primers. Fourteen of these primers were efficiently amplified the genomic DNA. The number of amplified bands varied with the primers and strains, with polymorphic fragments in the range from 0.2 to 2.3 kb.

• Korean Journal of Microbiology
• /
• v.44 no.1
• /
• pp.63-68
• /
• 2008

Strain Kan-23 was extracted from nematophagous fungi, which were isolated from the soil sample of oriental melon field. The strain exhibited the slow-growing characteristic forming conidia after prolonged incubation for 30 days. Morphological features of strain Kan-23 were observed under scanning electron microscope (SEM). It possesses erect conidiophores which contain $2{\sim}3$ side branches, with each branch producing $5{\sim}10$ conidia. The size of conidiophores were between $160{\sim}450\;{\mu}m$. Conidia were ellipsoidal with three septa[septum] in each conidium. Strain Kan-23 captured nematodes by means of giant constricting rings, which were observed in the glucose peptone agar medium. ITS region of rDNA sequence was analyzed. On the basis of the high sequence similarity of ITS region (99%), the Kan-23 strain was closely related to Drechslerella brochopaga (U51950). This is the first report on Drechslerella brochopaga as a nematophagous fungus in Korea.

• BMB Reports
• /
• v.43 no.6
• /
• pp.400-406
• /
• 2010

Cancer/testis (CT) antigens exhibit highly tissue-restricted expression and are considered promising targets for cancer vaccines. Here we identified a novel CT gene ZNF645 which restrictively expresses in normal human testes and lung cancer patients (68.3%). To investigate the promoter methylation status of ZNF645, we carried out bisulfite genomic sequencing and found that the CpG island in its promoter was heavily methylated in normal lung tissues without the expression of ZNF645, whereas there was high demethylation in normal human testes and lung carcinoma tissues with its expression. Also ZNF645 could be remarkably activated in A549 and HEK293T cells treated by DNA demethylation agent 5'-aza-2'-deoxycytidine. And the dual luciferase assay revealed that the promoter activity of the ZNF645 was inhibited by methylation of the CpG island region. Therefore, we proposed that ZNF645 is a CT gene and activated in human testis and lung cancers by demethylation of its promoter region.

• The Korean Journal of Mycology
• /
• v.47 no.3
• /
• pp.275-280
• /
• 2019

We isolated fungal spores belonging to the phylum Glomeromycota from the rhizospheres of Smilax china, cultured in a greenhouse. We identified the isolated spores using sequence analysis of 18S partial rDNA region, internal transcribed spacer and 28S rDNA regions. We confirmed 2 unreported spores of Glomeromycota fungal species, Diversispora eburnea and Paraglomus laccatum. Here, we described the morphological characteristics and results of phylogenetic analysis of the confirmed species.