• Journal of Korean Society of Forest Science
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• v.96 no.4
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• pp.425-431
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• 2007

To investigate genetic diversity and PCR detection of Rhizina undulata, PCR detection and sequence analysis of rDNA ITS region of R. undulata in soil were analyzed and developed. The length of partial 18S rDNA from four R. undulata isolates were 1,375 nt. The sequence similarity of R. undulata isolates was 100%. The rDNA ITS regions of R. undulata isolates were 585 nt long. Nucleotide sequencing of the ITS regions showed that PDK-1, PTT-1 and PDJ-9 isolates had 100% sequence identity. But, PDS-5 isolate differed from the three isolates by two nucleotide substitution. R. undulata-specific primers designed by the sequence of ITS region were used in PCR detection of R. undulata. PCR products about 525 bp size, which is specific to R. undulata, were amplified from total DNAs of R. undulata isolates. To assay the sensitivity of PCR detection by R. undulata ITS-specific primer, purely cultured mycelial suspension of R. undulata was serially diluted and mixed with 100g of sterile sandy loam soil, respectively. And then, PCR products of total DNAs extracted from each mycelium-soil mixtures were analysed. The PCR protocol could detected up to 1ng mycelium of R. undulata within 100g of soil.

• Journal of Life Science
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• v.23 no.10
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• pp.1260-1266
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• 2013

The ribosomal DNA (rDNA) clusters of Hypsizygus marmoreus 3-10 and H. marmoreus 1-1 were analyzed in this study. The small subunit (SSU) and intergenic spacer 2 (IGS 2) was partially sequenced. The internal transcribed spacer 1 (ITS 1), 5.8S, internal transcribed spacer 2 (ITS 2), large subunit (LSU), intergenic spacer 1 (IGS 1), and 5S were completely sequenced. The rDNA clusters of H. marmoreus 3-10 and H. marmoreus 1-1 were 7,049 bp in length. The sequence of SSU rDNA, which corresponded to 18S rDNA, was 1,796 bp in length, and the sequence of LSU rDNA, which corresponded to 28S rDNA, was 3,348 bp in length. The ITS region that variable region and IGS region that non-transcribed spacer was 462 bp and 1,290 bp in length. The sequence of 5.8S rDNA and 5S rDNA was 153 bp and 43 bp in length, respectively. The 17 bp of the rDNA cluster in the H. marmoreus 3-10 strain was different to that in the H. marmoreus 1-1 strain, with 2 bp in the SSU, 3 bp in the ITS, 9 bp in the LSU, and 3 bp in the IGS. The analysis of the secondary structure revealed that the ITS regions of H. marmoreus 3-10 and H. marmoreus 1-1 have five stem-loop structures. Interestingly, among these structures, one different nucleotide sequence resulted in a different secondary structure in stem-loop V.

• The Korean Journal of Mycology
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• v.32 no.1
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• pp.1-7
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• 2004

To establish the phylogenetic relationships of Dictyophora spp., rDNA-ITS regions of 11 strains of veiled lady mushroom collected from various countries were amplified and sequenced. It was observed that the 11 strains were divided into four groups based on PCR band patterns of each ITS region cleaved by eight different restriction enzymes in cleaved amplified polymorphic sequence analysis (CAPS). The phylogenic relationship of each group by cleaved amplified polymorphic sequence (CAPS) analysis matches well with previously reported morphological phylogeny, such as 5 strains of D. indusiata, 4 strains of D. echinovolvata, and a strain of Phallus rugulosus. Sequence analysis using the cluster V methods showed more detail classification than CAPS analysis. The 5.8S region showed two point nucleotide base exchanges from G to A according to four groups, and four groups were subdivided by sequence variation of ITS I and ITS II regions. But sequence variation of Phallus rugulosus was not showed in full ITS region. This study further delineates the taxonomic level at which ITS sequences, in comparison to ribosomal gene sequence, are most useful in systematics and other mushroom study.

• Ocean Science Journal
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• v.40 no.3
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• pp.155-166
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• 2005

New PCR primers (N=18) were designed for the isolation of complete SSU to LSU rDNA sequences from the dinoflagellate Alexandrium tamarense. Standard PCR, employing each primer set selected for amplifications of less than 1.5 kb, successfully amplified the expected rDNA regions of A. tamarense (Korean isolate, HY970328M). Complete SSU, LSU rDNAs and ITS sequences, including 5.8S rDNA, were recorded at 1,800 bp, 520 bp and 3,393 bp, respectively. The LSU rDNA sequence was the first report in Alexandrium genus. No intron was found in the LSU rRNA coding region. Twelve D-domains within the LSU rDNA were put together into 1,879 bp (44.4% G+C), and cores into 1514 bp (42.8% G+C). The core sequence was significantly different (0.0867 of genetic distance, 91% sequence similarity) in comparison with Prorocentrum micans (GenBank access. no. X16108). The D2 region was the longest in length (300 bp) and highly variable among the 12 D-domains. In a phylogenetic analysis using complete LSU rDNA sequences of a variety of phytoplankton, A. tamarense was clearly separated with high resolution against other species. The result suggests that the sequence may resolve the taxonomic ambiguities of Alexandrium genus, particularly of the tamarensis complex.

• Mycobiology
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• v.34 no.3
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• pp.154-157
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• 2006

A fungal isolate collected from infected paprika (Capsicum annuum var. grossum) was characterized as Sclerotinia sclerotiorum based on its ability of sclerotium formation, physiological and molecular properties. When the isolate was grown on potato dextrose agar, oatmeal agar, and malt extract agar, it grew most well on PDA. Optimal temperature and pH for its growth were $25^{\circ}C$ and pH 7, respectively. The fungal isolate produced sclerotia on PDA within 10 days, and the color and shape of the sclerotia were similar to those of S. sclerotiorum. The ITS rDNA regions including ITS1 and ITS2 and 5.8S sequences were amplified using ITS1F and ITS4 primers from the genomic DNAs of the paprika isolate and other known pathogenic S. sclerotiorum isolated from different crops in Korea, and their nucleotide sequences were determined. Sequence comparison analysis showed the ITS rDNA of the paprika isolate shares 100% sequence identity with those of S. sclerotiorum isolated from red pepper, lettuce and a S. sclerotiorum isolate registered in GenBank DNA database. Neighbor joining analysis based on the ITS rDNA sequence revealed the paprika isolate has very close phylogenetic relationships with known Sclerotinia sclerotiorum isolates. This is the first report that S. sclerotiorum has been found associated with paprika rot in paprika growing countries.

• The Plant Pathology Journal
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• v.21 no.3
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• pp.229-236
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• 2005

Molecular profIles of PCR-RFLP and sequence analysis of internal transcribed spacer (ITS) regions of rDNA were compared between morphologically distinguishable species of Trichoderma isolated from substrates of oyster mushroom in Korea, T. atroviride, T. citrinoviride, T. harzianum, T. longibrachiatum, T. virens, and two unidentified species, Trichoderma sp. 1 and 2. PCR­RFLP analysis divided the Trichoderma spp. into six RFLP groups, A, B, C, D, E, and F. The RFLP groups were generally agreed with described morphological species, except that the RFLP group A containing the two unidentified species. A neighbor-joining tree based on ITS sequences well supported RFLP groups observed by RFLP analysis of ITS regions of rDNA. Additionally, the two unidentified species, Trichoderma sp. 1 and 2, which could not be distinguished by PCR­RFLP analysis, were separated in sequence analysis of ITS regions of rDNA.

• Journal of Yeungnam Medical Science
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• v.19 no.1
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• pp.1-10
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• 2002

With the establishment of rapid sequence analysis of 16S rRNA and the recognition of its potential to determine the phylogenetic position of any prokaryotic organism, the role of 16S rRNA similarities in the present species definition in bacteriology need to be clarified. Comparative studies clearly reveal the limitations of the sequence analysis of this conserved gene and gene product in the determination of relationship at the pathogenic strain level for which DNA-DNA reassociation experiments still constitute the superior method. Since today the primary structure of 16S rRNA is easier to determine than hybridization between DNA strands, the strength of the sequence analysis is to recognize the level at which DNA pairing studies need to be performed, which certainly applies to similarities of 97% and higher.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.33 no.6
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• pp.489-495
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• 2000

The 185 ribosomal RNA gene (185 rDNA) of the marine alga Porphyra sp. 723 (Bangiales, Rhodophyta) was amplified using the polymerase chain reaction and its sequence was analysed. The Porphyra species was a summer strain collected on rocks in upper intertidal zone at Ikidae, Pusan on 23rd July 1999. The fronds were $1{\~}5 cm$ long, monostromatic, and orbicular or ovate shaped, They had spinulate processes at margin of the frond, Comparison of this 185 rDNA sequence with the other Forphyra species indicates that Porphyra sp. 723 has the same 185 rDNA sequence derived from Porphyra suborbiculata (NCBI access number; AB 013180) except one base pair substitution in 2327 base pairs.

• Korean Journal Plant Pathology
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• v.12 no.1
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• pp.91-98
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• 1996

벼도열병균 14개 균주와 벼 이외 화본과 식물 도열병균 12개 균주를 대상으로 rDNA의 ITS II 부위를 증폭하여 그들의 핵산 구조 차이를 분석함으로 도열병균 균주간 분류를 시도하였다. 5.8S rDNA의 3`-말단 부위와 28S rDNA의 5`-말단 부위의 sequence 중 5`-CCCGGGAATTCGCATCGATCGATCGAATGAAGA-ACGCAGC-3`와 5`-CCCGGGATCCTCCGCTTATT-GATATGC-3`를 이용하여 PCR 증폭을 하였을 때 벼도열병균 14개 균주는 동일한 길이의 단일 밴드를 형성하였으며 벼 이외 화본과 식물 도열병균에서는 레드톱 식물로부터 분리한 도열병균만이 나머지 균주보다 38bp가 더 큰 길이를 가진 밴드를 형성하였다. PCR로 증폭된 DNA를 HaeIII와 MspI 제한효소로 절단하였을 때 벼도열병균 레이스간에는 제한효소 절단에 의한 전기영동 밴드 형태 차이를 관찰할 수 없었으나, 벼 이외 화본과 식물 도열병균 12개 균주는 3군으로 구분할 수 있었다. 벼도열병균 90=054와 강아지풀에서 분리한 도열병균 G90-5, 기장에서 분리한 G88-4, 바랭이에서 분리한 G88-5 그리고 레드톱에서 분리한 RT 균주의 ITS II 부위의 DNA 염기서열 비교 분석에 의하면 G88-4와는 다른 HaeIII와 MspI 제한효소 위치를 가지고 있었기에 제한효소 절단에 의한 전기영동 형태가 상이하였다. 또한 RT균주는 HaeIII와 MspI위치가 존재하지 않았다.

• Journal of Life Science
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• v.20 no.4
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• pp.578-583
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• 2010

It has been reported that extracts of globe thistle (Echinops spp.) and thistle (Circium spp., Carduus spp. and Onopordum spp.) have anti-bacterial and anti-fungal activities. Methanol extracts of Echinops setifer and Carduus spp. were used to test and see if the extracts of these plants could suppress growth of Mycobacterium smegmatis and Mycobacterium fortuitum. Although extract of Echinops setifer showed no anti-mycobacterial activities, extract of Carduus spp. showed inhibition zones when tested with filter discs. Genomic DNA was isolated from Carduus spp. and PCR was performed to clone a DNA fragment containing ITS1, 5.8S rRNA gene and ITS2. A 733-bp PCR product was obtained and its DNA sequence was reported to the GenBank (accession number GU188570). BLAST search of the obtained DNA sequence did not show a match with any DNA sequences in the Genbank. Carduus crispus and Carduus defloratus had the closest phylogenetic relationships to this plant.