• Mycobiology
• /
• v.30 no.2
• /
• pp.82-87
• /
• 2002

Species of Phellinus were known to harmful fungi causing white pocket rot and severe plant disease such as canker or heartrot in living trees in the West, but some species have been used to traditional medicines in the Orient for a long time. In this study the partial D1-D2 nucleotide sequences of 28S ribosomal DNA from 13 Phellinus strains were determined and compared with the sequences of 21 strains obtained from GenBank database. According to the neighbor-joining(NJ) method comparing the sequence data the phylogenetic tree was constructed. The phylogenetic tree displayed the presence of four groups. Group I includes P. ferreus, P. gilvus and P. johnsonianus, Group II contains P. laevigatus, P. conchatus and P. tremulae, Group III possesses P. linteus, P. weirianus, P. baumii, P. rhabarbarinus and P. igniarius, and Group IV comprises P. pini, P. chrysoloma. P. linteus and P. baumii, which were used mainly in traditional medicine, belong to the same group, but exactly speaking both were split into two different subgroups. To detect P. linteus only, we developed the PCR primer, D12HR. The primer showed the specific amplification of P linteus, which is permitted to medicinal mushroom in the East. The results make a potential to be incorporated in a PCR identification system that could be used for the rapid identification of this species from its related species, P. linteus especially.

• Korean Journal of Agricultural Science
• /
• v.40 no.2
• /
• pp.115-121
• /
• 2013

Polymorphic bands of two fine-leaf zoysiagrass mutants (CNU 70-1, CNU 70-2) induced via a gamma-ray irradiation on seeds of Zoysia japonica were obtained by using randomly amplified polymorphic DNA (RAPD) primers. The genotype-specific fragments were then converted into PCR-based sequence characterized amplified region (SCAR) markers, which are now amenable to detecting them among other zoysiagrass species widely noticeable in Korea. The CNU 70-1-specific primer set amplified about 900 bp successfully, while the CNU 70-6 marker produced the expected 1,500 bp band, by which those markers were nominated by CNU 70-1_900 and CNU 70-6_1500 SCARs, respectively. The developed SCAR markers can be an applicable tool in sod industry where illegal appropriation hampers breeder's right and profits due to the turfgrass plant vegetatively propagating.

• Proceedings of the National Institute of Ecology of the Republic of Korea
• /
• v.2 no.1
• /
• pp.32-41
• /
• 2021

South Korea presently harbors less than 800 long-tailed gorals (Naemorhedus caudatus), an endangered species. I report for the first time on the taxonomic status and genetic diversity of the Korean species using non-invasive fecal sampling based on mitochondrial cytochrome b gene sequence analyses. To determine the taxonomic status of this species, I reconstructed a consensus neighbor-joining tree and generated a minimum spanning network combining haplotype sequences obtained from feces with a new goral-specific primer set developed using known sequences of the Korean goral and related species (e.g., Russian goral, Chinese goral, Himalayan goral, Japanese serow, etc.). I also examined the genetic diversity of this species. The Korean goral showed only three different haplotypes. The phylogenetic tree and parsimony haplotype network revealed a single cluster of Korean and Russian gorals, separate from related species. Generally, the Korean goral has a relatively low genetic diversity compared with that of other ungulate species (e.g., moose and red deer). I preliminarily showcased the application of non-invasive fecal sampling to the study of genetic characteristics, including the taxonomic status and genetic diversity of gorals, based on mitochondrial DNA. More phylogenetic studies are necessary to ensure the conservation of goral populations throughout South Korea.

• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2004.11a
• /
• pp.21-28
• /
• 2004

모든 생명체의 genetic information에는 보존적 염기서열과 다형적 염기서열이 존재한다. 다형적 염기서열과 보존적 염기서열은 하나의 종(species)을 감별하거나, 여러 종류의 종을 동시에 감별할 수 있는 genotyping의 표지자로 각각 이용될 수 있다. 본 논문은 병원성 감염질환 세균, 식중독 유발 세균, 생물의약품 오염 유발 세균 및 환경오염 세균 등 세균의 존재 유무와 속과 종 감별을 위해 대부분 세균 종의 보존적 염기서열과 다형적인 염기서열을 포함하고 있는 23S rDNA 유전자의 표적 염기 서열로부터 고안된 세균 특이적(bacterial-specific), 속 특이적(genus-specific), 종 특이적(species-specific) 올리고 뉴클레오티드프로브와 프라이머를 디자인하는 시스템을 소개한다. 시스템을 통해서 얻어진 프로브와 프라이머들은 PCR을 통한 검증단계를 거쳐서 디자인 결과의 정확성을 확인하였다. 본 시스템의 이용으로 프로브와 프라이머를 디자인하는데 몇 주가 소요되는 시간을 몇 일 내로 줄일 수 있었으며, 체계적인 데이터의 관리로 결과의 정확성을 높일 수 있었다.

• Korean Journal of Microbiology
• /
• v.45 no.2
• /
• pp.170-176
• /
• 2009

Culture-independent 16S rDNA-DGGE profiling and phylogenetic analysis were used to examine the predominant bacterial communities associated with the two sponges, Dictyonella sp. and Spirastrella abata from Jeju island. The culture-independent approach involved extraction of total bacterial DNA, PCR amplification of the 16S ribosomal DNA using primer pair 341f-GC and 518r, and separation of the amplicons on a denaturing gradient gel. Denaturing gradient gel electrophoresis banding patterns indicated 8 and 7 bands from the two sponge species, Dictyonella sp. and Spirastrella abata, respectively. There were not common major bands in two different sponges. Comparative sequence analysis of variable DGGE bands revealed from 93% to 98% similarity to the known published sequences. The dominant bacterial group of Dictyonella sp. belonged to uncultured Gammaproteobacteria, while, that of Spirastrella abata belonged to uncultured Alphaproeobacteria and Firmicutes. DGGE analysis indicated predominant communities of the sponge-associated bacteria differ in the two sponges from the same geographical location. This result revealed that bacterial community profiles of the sponges were host species-specific.

• Applied Biological Chemistry
• /
• v.46 no.3
• /
• pp.225-228
• /
• 2003

This study was carried out to investigate the simple and rapid detection of Salmonella species in different kinds of food using PCR method. The specific primer sets (SIN1 and SIN2) was designed and utilized to amplify a 617 bp DNA fragment from salmonella species. The sensitivity of PCR was 1 pg of purified template DNA or $10^2$ cells from pure culture. The detection limit of Salmonella typhimurium on agarose gel electrophoresis was $10^3{\sim}10^4$ cells/g in the artificially contaminated food samples. These results suggested that this simple method could be applied to industrial fields for detection of Salmonella species in food.

• Journal of Korean Society of Forest Science
• /
• v.104 no.2
• /
• pp.332-335
• /
• 2015

Taphrina wiesneri, a pathogen of cherry witches' broom, is highly pathogenic to Prunus yedoensis Matsumura which are widely planted in parks and streets in South Korea. In order to control the disease, it is crucial to know the life cycle of the fungus. We attempted to detect the fungus tentatively overwintering in shoots and branches of cherry trees both having witches' broom and healthy before flowering and leafing in spring using PCR with species-specific primer set (TwITSF and TwITSR). Genomic DNAs were extracted from the symptomatic and the asymptomatic shoots or branches. Results indicated that T. wiesneri is present in leaf buds and inner bark not only in symptomatic branches but also in the asymptomatic branches in diseased trees. However, the fungus was not detected in flower buds of the symptomatic trees and any samples of healthy trees.

• Reproductive and Developmental Biology
• /
• v.29 no.4
• /
• pp.213-221
• /
• 2005

We used nine decamer primers to generate DNA fragment sizes ranging from 100 bp to 1,600 bp from two bullhead (Pseudobagrus fulvidraco) populations of Dangjin in Korea. 376 fragments were identified in the cultured bullhead population, and 454 in the population of wild bullhead from Dangjin: 287 specific fragments $(76.3\%)$ in the cultured bullhead population and 207 $(45.6\%)$ in the wild bullhead population. On average, a decamer primer was used to generate 34.2 amplified products in a cultured bullhead. A RAPD primer was used to generate an average of 3.1 amplified bands per sample, ranging between 2.5 and 6.0 fragments in this population. Nine primers also generated 24 polymorphic fragments (24/376 fragment, $6.4\%$) in the cultured bullhead population, and 24 (24/454 fragments, $5.2\%$) in the wild bullhead population. The OPA-16 primer, notably, produced which 11 out of 11 bands $(100\%)$ were monomorphic in the wild bullhead population. 110 intra-population-specific fragments, with an average of 12.2 per primer, were observed in the cultured bullhead population. 99 fragments, with an average of 11.0 per primer, were identified in the wild bullhead. Especially, 55 inter-population-common fragments, with an average of 6.1 per primer, were observed in the two bullhead populations. The bandsharing value (BS value) of individuals within the wild bullhead population was substantially higher than was determined in the cultured bullhead population. The average bandsharing value was $0.596\pm0.010$ within the cultured bullhead population,. and $0.657\pm0.010$ within the wild bullhead population. The dendrogram obtained with the nine primers indicates two genetic clusters, designated cluster $1\;(CULTURED\;01\~CULTURED\;11)$, and cluster $2\;(WILD\;12\~WILD\;22)$. Ultimately, the longest genetic distance displaying significant molecular differences was determined to exist between individuals in the two bullhead populations, namely between individuals WILD no. 19 of the wild bullhead population and CULTURED no. 03 of the cultured bullhead population (genetic distance = 0.714). RAPD-PCR allowed us to detect the existence of population discrimination and genetic variation in Korean population of bullhead. This finding indicates that this method constitutes a suitable tool for DNA comparison, both within and between individuals, populations, species, and genera.

• Asian-Australasian Journal of Animal Sciences
• /
• v.28 no.4
• /
• pp.568-572
• /
• 2015

Acetes chinensis is an economically important shrimp that belongs to the Sergestidae family; following fermentation, A. chinensis' economic value, however, is low in China, and much of the catch in China is exported to Korea at a low price, thus leading to potential false labeling. For this reason, we developed a simple method to identify A. chinensis' origin using allele-specific polymerase chain reaction (PCR). Ten single nucleotide polymorphisms (SNPs) were identified from partial (i.e., 570 bp) DNA sequence analysis of the mitochondrial 16s rRNA gene in 96 Korean and 96 Chinese individual shrimp. Among 10 SNP sites, four sites were observed in populations from both countries, and two sites located in the middle with SNP sites at their 3'-ends were used to design allele-specific primers. Among the eight internal primers, the C220F primer specific to the Chinese A. chinensis population amplified a DNA fragment of 364 bp only from that population. We were able to identify the A. chinensis population origin with 100% accuracy using multiplex PCR performed with two external primers and C220F primers. These results show that the 16S rRNA gene that is generally used for the identification of species can be used for the identification of the origin within species of A. chinensis, which is an important finding for the fair trade of the species between Korea and China.

• The Korea Journal of Herbology
• /
• v.24 no.4
• /
• pp.115-120
• /
• 2009

Objectives : Due to the morphological similarity and frequent occurrence of intermediate forms as well as morphological variations of aerial part, the correct identification between Rhei Radix et Rhizoma and Rhei Undulatai Rhizoma is very difficult. To develop a reliable method for correct identification and improving the quality standards of Rhei Radix et Rhizoma and Rhei Undulatai Rhizoma, we analyzed RAPD and developed SCAR marker. Methods : To amplify target DNA at the genomic level, 32 Operon 10-mer random primers were applied with four Rheum species, R. officinale, R. palmatum, R. tanguticum and R. undulatum. The nucleotide sequences were determined and species-specific primers were prepared depending on the species-specific RAPD amplicons after subcloned into the pGEM-Teasy vector. To develop the SCAR markers, species-specific PCR amplification and multiplex-PCR were carried out using the single species-specific primer pairs and combinations of them, respectively. Results : We used RAPD analysis of four Rheum plant species to obtain several species-specific RAPD amplicons. From nucleotide sequences of these RAPD amplicons, we developed two SCAR markers that amplified 314 bp and 390 bp DNA fragments in only R. undulatum but not in R. officinale, R. palmatum, R. tanguticum and R. undulatum, for distinguishing Rhei Undulatai Rhizoma and Rhei Radix et Rhizoma. Furthermore, we established SCAR markers for the simultaneous discrimination of the three species within a single reaction by using multiplex-PCR. Conclusions : These genetic markers can be used for the efficient discrimination of plants species and commercial herbal medicines between Rhei Undulatai Rhizoma and Rhei Radix et Rhizoma, to ultimately prevent indiscriminate distribution and prescription of these herbal medicines.