• Korean Journal of Ichthyology
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• v.33 no.4
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• pp.217-225
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• 2021

The family Platycephalidae is a taxonomic group of economically important demersal flathead fishes that predominantly occupy tropical or temperate estuaries and coastal environments of the Indo-Pacific oceans and the Mediterranean Sea. In this study, we for the first time analyzed the complete mitochondrial genome (mitogenome) of the flathead Platycephalus cultellatus Richardson, 1846 from Vietnam by Next Generation Sequencing method. Its mitogenome was 16,641 bp in total length, comprising 13 protein-coding genes (PCGs), two ribosomal RNA genes, and 22 transfer RNA genes. The gene composition and order of the mitogenome were identical to those of typical vertebrates. The phylogenetic trees were reconstructed based on the concatenated nucleotide sequence matrix of 13 PCGs and the partial sequence of a DNA barcoding marker, cox1 in order to determine its molecular phylogenetic position among the order Scorpaeniformes. The phylogenetic result revealed that P. cultellatus formed a monophyletic group with species belonging to the same family and consistently clustered with one nominal species, P. indicus, and two Platycephalus sp. specimens. Besides, the cox1 tree confirmed the taxonomic validity of our specimen by forming a monophyletic clade with its conspecific specimens. The mitogenome of P. cultellatus analyzed in this study will contribute valuable information for further study on taxonomy and phylogeny of flatheads.

• Journal of Environmental Impact Assessment
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• v.32 no.2
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• pp.94-111
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• 2023

In order to establish an effective management strategy for invasive species early detection and regular monitoring are required to assess their introduction or dispersal. Environmental DNA (eDNA) is actively applied to evaluate the fauna including the presence of invasive species as it has high detection sensitivity and can detect multiple species simultaneously. In Korea, the applicability evaluation of metabarcoding is being conducted mainly on fish, and research on other taxa is insufficient. Therefore, this study identified the feasibility of detecting invasive species in Korea using eDNA metabarcoding. In addition, to confirm the possibility of detection by taxa, the detection of target species was evaluated using four universal primers (MiFish, MiMammal, Mibird, Amp16S) designed for fish, mammals, birds, and amphibians. As a result, target species (Trachemys scripta, 3 sites; Cervus nippon, 3 sites; Micropterus salmoides, 7 sites; Rana catesbeiana, 4 sites) were detected in 17 of the total 55 sites. Even in the selection of dense sampling sites within the study area, there was a difference in the detection result by reflecting the ecological characteristics of the target species. A comparison of community structures (species richness, abundance and diversity) based on the presence of invasive species focused on M.salmoides and T.scripta, showed higher diversity at the point where invasive species were detected. Also, 1 to 4 more species were detected and abundance was also up to 1.7 times higher. The results of invasive species detection through metabarcoding and the comparison of community structures indicate that the accumulation of large amounts of monitoring data through eDNA can be efficiently utilized for multidimensional ecosystem evaluation. In addition, it suggested that eDNA can be used as major data for evaluation and prediction, such as tracking biological changes caused by artificial and natural factors and environmental impact assessment.

• Korean Journal of Microbiology
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• v.49 no.3
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• pp.228-236
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• 2013

Campylobacter jejuni is one of important food-borne pathogens causing human gastroenteritis. We isolated 42 strains of C. jejuni from diarrhea patients and 4 food-poisoning outbreaks in 2010, Gyeonggi-do. In this study, 42 strains were tested for genetic characteristics, the serotype distribution and antimicrobial resistant rate. The presence of hipO (100%), cdtB (100%), and mutated gyrA (95.2%) genes was detected in C. jejuni by polymerase chain reaction (PCR). Detection of mutated gyrA gene correlated with ciprofloxacin resistance. Forty isolates had mutated gyrA gene and were actually resistant to ciprofloxacin. Furthermore, comparing the gyrA DNA sequence data, ciprofloxacin-resistant isolates had a mutation of the DNA sequence from ACA (threonine) to ATA (isoleucine). But 41 strains (97.6%) of patient isolates were susceptible to erythromycin and azithromycin. A total of 35.7% among 42 C. jejuni isolates were identified into 4 different serotypes. The serotype distribution of C. jejuni strains were shown to be HS2(B), HS3(C), HS4(D), HS19(O). To investigate the genotypes of C. jejuni isolated in Gyeonggi province, repetitive sequence polymerase chain reaction (rep-PCR) analysis and SmaI-digested pulsed-filed gel electrophoresis (PFGE) profile analysis were performed. From the PFGE analysis of 42 C. jejuni strains, 12 clusters of PFGE profile were obtained. On the other hand, 11 clusters of rep-PCR profile were obtained from 42 strains of C. jejuni.

• Asian Journal of Turfgrass Science
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• v.20 no.1
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• pp.65-76
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• 2006

Scz1, an isolate of Sclerotinia homoeocarpa, was recently reported as a novel pathogen responsible for dollar spot disease in Zoysiagrass, a warm season turfgrass. Scz1 possessed different characteristics on mycelial pigment, mycelial affinity and host pathogenecity compared to those of Scb1, a typical isolate, obtained from creeping bentgrass, a cool season turfgrass. In this study, only three isolates, Scz1, Scz2(another analogous isolate of Sclerotinia homoeocarpa from zoysiagrass), and Scb1, were examined at the molecular level using the internal transcribed spacer(ITS) and random amplified polymorphic DNA(RAPD) assays to verify their identification and genetic variation. As a result of ITS assay, partial ITS sequences of three isolates showed 94-97% similarity with a standardized ITS sequence of S. homoeocarpa registered on BLAST. In the analysis of RAPD, range value through similarity matrix was 0.167 between Scz1 and Scb1, 0.139 between Scz2 and Scb1, and 0.713 between Scz1 and Scz2, respectively. Furthermore, tendegram analysis indicated that Scz1 and Scz2, unlike Scb1, were clustered together as accompanying a high genetic similarity. In in vitro fungicide bioassay, $EC_{50}$ value representing the sensitivity degree to propiconazole, a well-known fungicide for dollar spot disease, was 0.012 ${\mu}g/ml$ for Sczl, 0.003 ${\mu}g/ml$ for Scz2, and 0.030 ${\mu}g/ml$ for Scb1. From all data taken, we concluded that both Scz1 and Scz2 belonged to one group of S. homoeocarpa, since they exhibit the same host range and high level of genetic similarity, whereas their chemical competences to a fungicide were different. This study would provide further approach for assessing genetic diversity of S. homoeocarpa isolates as well as characterizing individual isolate against chemical exposure.

• Journal of Plant Biotechnology
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• v.38 no.2
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• pp.176-185
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• 2011

Rice is one of the most important crop in the world, in particular for food resources. With its small genome size of 383 Mb, the Oryza sativa is a model plant for genome research. Indeed, it's grain provides human with a source of carbohydrates and proteins. Rice grain has relatively low protein contents (around 8%) compared to other legume seeds (around 40%). Osborne classified seed proteins into water soluble albumin, salt soluble globulin, alcohol soluble prolamin and acidic/alkaline solution soluble glutelin. Glutelin and prolamin are the major storage proteins in rice. For the gene expression study of seed storage proteins, we analyzed 33,192 EST clones at immature stages in a rice cultivar (Oryza sativa L. cv. 'Ilpum'). Based on the expression analysis, we cloned 11 glutelin genes and figured out the 8 genes are located on Chromosome 2. The expression of glutelin genes appears to be about 28.2% of total level in immature seeds. Interestingly, glu-04 is duplicated as inverted sequences on the same chromosomes as far 4.5 kb. Our results indicate that glutelin genes, evolutionarily, were replicated on the chromosome and thus expressed as specific manners. In a whole protein composition analysis, glu05 (type B7) contains the highest lysin contents (4.51%) among the 11 rice glutelin genes. It will be an interesting future work to increase lysin contents by the gene overexpressor strategy with the aim of improved diet nutritionally fortified.

• The Korean Journal of Mycology
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• v.43 no.3
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• pp.149-157
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• 2015

We examined taxonomic characteristics and safety of eight Nuruk molds that are widely used for making soybean paste, soy sauce and alcoholic beverages in Korea. HK1 from Hakyeong Fermentation Co., SW101 from Suwon Fermentation Co., CF1001, CF1002, CF1003 from Chungmoo Fermaentation Co. and KACC 93210 are yellow-Nuruk molds, and SW201 from Suwon Fermentation Co. and CF1005 from Chungmoo Fermentation Co. are white-Nuruk molds. Six strains of yellow-Nuruk molds were identified as Aspergillus oryzae. HK1, SW101, CF1001 and CF1003 of yellow-Nuruk molds have middle length of stipes ($711{\sim}1,121{\mu}m$), and CF1003 (for sake) produced less conidia and more hyphae than HK1, SW101 and CF1001 (for soybean paste). CF 1002 used for soy sauce has shorter stipes ($543{\mu}m$) and is clustered into IBLB-group based on omtA gene analysis although the other yellow-Nuruk molds are clustered into ICAo group. KACC 93210 isolated from traditional Korean Meju has very short stipes (average $270{\mu}m$), and showed velvety colonies although the others showed floccose colonies. The strain has different DNA sequences of omtA gene from other strains in NCBI GenBank as well as strains used in Korea, suggesting that it is unique from other strains published. SW201 and CF1005 of white-Nuruk molds were identified as Aspergillus luchuensis or A. luchuensis mut. Kawachii that is known as safe, non-toxigenic fungus. The six strains of yellow-Nuruk molds did not produce mycotoxins including aflatoxin, cyclopiazonic acid, and sterigmatocystin. Therefore, eight strains of Nuruk molds used for making soy sauce, soybean paste and alcoholic beverages in Korea were proved to be safe in this study.

• The Korean Journal of Ecology
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• v.28 no.3
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• pp.129-134
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• 2005

The monthly variations of physico-chemical and microbiological water quality were investigate in the artificial Lake Geumgang near estuary barrage. Sixty heterotrophic bacteria were isolated and identified by amplification and sequencing of 16S rDNA. Water temperature, pH, and inorganic nutrients($NH_4$-N, $NO_2$-N, $NO_3$-N, $PO_4$-P) were measured. Concentrations of DO, BOD, and inorganic nutrients were lower than in the middle-stream of Geum river The population densities of heterotrophic bacteria and total coliforms varied from $4.1{\pm}1.0\times10^2$ to $6.7{\pm}1.1{\times}10^3\;cfu\;ml^{-1}$, and 0 to $2.3{\pm}0.6{\times}10^2\;cfu\;ml^{-1}$, respectively. Among the measured numbers of physiological groups of bacteria, cellulolytic bacteria showed higher population densities than those of other physiological groups. Bacterial community structure was analysed based on 16S rDNA partial sequencing. Among 60 isolates, dominant genus was Pseudomones (20 strains).

• Research in Plant Disease
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• v.12 no.3
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• pp.168-177
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• 2006

Thirty-nine strains of Colletotrichum gloeosporioides and 5 strains of C. acutatum stored in Korean Agricultural Culture Collection(KACC) were re-identified based on molecular characteristics of ribosomal internal transcribed spacer(ITS) and partial $\beta$-tubulin gene and cultural characteristics on potato dextrose agar(PDA) and Benomyl-added PDA. As the results, 19 strains were identified as C. acutatum with 13 strains of group A2, 5 strains of group A3, and 1 strain of group A4. In addition, 20 strains were identified as C. gloeosporioides with 18 strains of ribosomal DNA group(RG) 4 and 2 strains of RG6. The rest were identified as C. boninense RG5(2 strains), C. coccodes RG2(2 strains), and C. dematium RG12(1 strain). Out of domestic 31 strains, 12 strains were identified as C. acutatum A2, one strain as C. acutatum A3, 14 strains as C. gloeosporioides RG4, 2 strains as C. gloeosporioides RG6, one strains as C. boninense RG5 and one strain as C. dematium RG12. We also discussed taxonomy of C. gloeosporioides and C. acutatum and composition of C. gloeosporioides/C. acutatum isolates from major crops in Korea.

• Korean Journal of Microbiology
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• v.43 no.3
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• pp.210-216
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• 2007

The principal objective of this study was to analyze 16S rDNA-ARDRA of the humus forest soil via an improved manual method and an ISOIL kit on the basis of the UPGMA clustering of the 16S rDNA combined profile, 44 ARDRA clusters of 76 clones via the ISOIL kit method and 45 ARDRA clusters of 136 clones via the improved manual method. On the basis of the 16S rDNA sequences, 44 clones from the ARDRA clusters by the ISOIL kit were classified into 3 phyla : ${\alpha}-,\;{\beta}-,\;{\gamma}-,\;{\delta}-Proteobacteria$, Acidobacteria and Actinobacteria. Using the improved manual method, the specimens were classified into 6 phyla : the ${\alpha}-,\;{\beta}-,\;{\gamma}-,\;{\delta}-Proteobacteria$, Acidobacteria, Bacteroides, Verrucomicrobia, Planctomycetes and Gemmatomonadetes. As a result, the modified manual method indicated greater phylogenetic diversity than was detected by the ISOIL kit. Approximately 40 percent of the total clones were identified as ${\alpha}-Proteobacteria$ and 30 percent of the total clones were ${\gamma}-Proteobacteria$ and assigned to dominant phylogenetic groups using the ISOIL kit. Using the modified manual method, 41 percent of the total clones were identified as Acidobacteria and 28 percent of total clones were identified as ${\alpha}-proteobacteria$ and assigned to dominant phylogenetic groups.