• The Korean Journal of Zoology
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• v.16 no.2
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• pp.97-108
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• 1973

Karyological characteristics and relative DNA values were investigated in four species of the family Cyprinidae of Korean fresh-water. The results obtained were as follows; 1) The two Hemibarus species, H. longirostris and H. labeo, had the aiploid chromosome number of 50. The compliment of former consisted of 7 metacentric, 14 submets- and subtelocentric and 4 telo- or acrocentric pairs, whereas latter had 9, 11 and 5 pairs respectively, Total arm numbers (AN) were 92 and 90. 2) In the case of two species of genus Moroce, M. oxycephalus and M. lagowskii, their diploid number and karyotype showed in identical pattern for each other (2n=50); 6 pairs of metacentrics, 14 pairs of submeta- and subtelocentrics and 5 pairs of telo- or acrocentrics. The AN of both species were 90. 3) Relative DNA values of all species were measured as about 60% that of gold fish. From the above observation, the cytogenetical character was discussed with special concern to the phylogenetic significance.

• BMB Reports
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• v.37 no.2
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• pp.144-147
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• 2004

Molecular amplification and sequencing of genomic DNA that encodes camel polyubiquitin (PUBC1) was performed by a polymerase chain reaction (PCR) using various sets of primers. The amplification generated a number of DNA fragments, which were sequenced and compared with the polyubiquitin coding sequences of various species. One DNA fragment that conformed to 325 bp was found to be 95 and 88% homologous to the sequences of human polyubiquitin B and C, respectively. The DNA translated into 108 amino acids that corresponded to two fused units of ubiquitin with no intervening sequence, which indicates that it is a polyubiquitin and contains at least two units of ubiquitin. Although, variations were found in the nucleotide sequence when compared to those of other species, the amino acid sequence was 100% homologous to the polyubiquitin sequences of humans, mice, and rats. This is the first report of the polyubiquitin DNA coding sequence and its corresponding amino acid sequence from camels, amplified using direct genomic DNA preparations.

• ALGAE
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• v.33 no.1
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• pp.69-84
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• 2018

We examined the species diversity of Herposiphonia on Korean coasts, based on a combination of morphology and molecular analyses of the mitochondrial COI-5P DNA barcode marker and plastid rbcL gene. We report the presence of eight species including three novel species: H. donghaensis sp. nov., H. jejuinsula sp. nov., H. sparsa sp. nov., H. caespitosa, H. fissidentoides, H. insidiosa, H. parca, and H. subdisticha. Specimens were separated into eight clades in both the COI-5P and rbcL gene analyses, with 1.3-19.6 and 6.6-15% interspecific sequence divergence, respectively. These eight species are also distinguishable by several morphological characteristics such as: branching pattern (d/i pattern in H. donghaensis sp. nov. and H. sparsa sp. nov.; d/d/d/i pattern in others), shape of determinate branch (ligulate in H. fissidentoides; terete in others), number of vegetative trichoblasts (1-2 in H. insidiosa and H. sparsa sp. nov.; 3-4 in H. caespitosa; absent in others), and number of segments and pericentral cells in determinate branches. About three novel species revealed by our analyses, H. donghaensis sp. nov. is newly discovered, and H. jejuinsula sp. nov. and H. sparsa sp. nov. were previously reported in Korea as H. nuda and H. secunda, respectively. Our results show that DNA barcoding and rbcL analyses are useful for delimiting species boundaries and discovering cryptic species diversity in the genus Herposiphonia.

• The Korean Journal of Ecology
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• v.23 no.4
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• pp.331-337
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• 2000

Fourteen different taxa of dictyostelid cellular slime molds were recovered from the alpine and subalpine zone in Mt. Paektu. In subalpine zone, six species were recovered : Dictyostelium minutum, D. brefeldianum, D. crassicaule, D. capitatum, Polysphondylium solitarium and P. pallidum. One of these species which were isolated from the soils of Larix olgensis community exhibited several distinctive features which differed from the published species. This species was designated as a new species, Polysphondylium solitarium Kang et Chang, sp. nov. When cultivated at 22~24$^{\circ}C$ on low-nutrient agar media with Escherichia coli, Polysphondylium solitarium is distinguishable from other species by the following combination of features: (ⅰ) the sorocarps with vinaceous pigmentation; (ⅱ) pseudoplasmodia radial. usually centralized and rarely subdivided; (ⅲ) the various number of whorls; (ⅳ) the spores with unconsolidated and nonconspicuous polar granules. Also, we confirmed this new species by analyzing ribosomal DNA (ITS1, ITS2 and 5.8s DNA) sequences of P. solitarium and P. violaceum.

• Korean Journal of Medicinal Crop Science
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• v.18 no.3
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• pp.186-190
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• 2010

The chromosome number was identified and fluorescence in situ hybridization(FISH) mapping of 5S and 45S rDNAs were conducted for C. minima and C. lanceolata in the genus Codonopsis from Jeju island. In this study, we have confirmed that the somatic metaphase chromosome number determined as 2n=2x=16 was the same as the findings from the previous studies. While the conventional staining method makes it rather difficult to distinguish satellite chromosomes due to high degree of variability, FISH analysis produced the exact number and location of 5S and 45S rDNAs. Both species in the genus Codonopsis have a pair of 5S rDNA and their gene loci were observed on chromosome 3. Although two pairs of 45S rDNAs (one on chromosome 1 and the other on chromosome 8) were identified in both species, the 45S rDNA signals on chromosome 8 in C. minima were significantly weaker than those on chromosome 1. In addition, the 45S rDNA signals on chromosome 1 in C. lanceolata showed that the chromosome is non-homologus. In this study, we have determined cytogenetic characteristics of C. minima and C. lanceolata according to their gene replication patterns.

• Korean Journal of Ecology and Environment
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• v.54 no.3
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• pp.199-208
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• 2021

Environmental DNA (eDNA) metabarcoding is effective method with high detection sensitivity for evaluating fish biodiversity and detecting endangered fish from natural water samples. We compared the richness of operational taxonomic units(OTUs) and composition of freshwater fishes according to filters(cellulose nitrate filter vs. glass fiber filter), extraction kits(DNeasy2^® Blood & Tissue Kit vs. DNeasy2^® PowerWater Kit), primer sets (12S rDNA vs. 16S rDNA), and PCR methods (conventional PCR vs. touchdown PCR) to determine the optimal conditions for metabarcoding analysis of Korean freshwater fish. The glass fiber filter and DNeasy2^® Blood & Tissue Kit combination showed the highest number of freshwater fish OTUs in both 12S and 16S rDNA. Among the four types, the primer sets only showed statistically significant difference in the average number of OTUs in class Actinopterygii (non-parametric Wilcoxon signed ranks test, p=0.005). However, there was no difference in the average number of OTUs in freshwater fish. The species composition also showed significant difference according to primer sets (PERMANOVA, Pseudo-F=6.9489, p=0.006), but no differences were observed in the other three types. The non-metric multidimensional scaling (NMDS) results revealed that species composition clustered together according to primer sets based on similarity of 65%; 16S rDNA primer set was mainly attributed to endangered species such as Microphysogobio koreensis and Pseudogobio brevicorpus. In contrast, the 12S rDNA primer set was mainly attributed to common species such as Zacco platypus and Coreoperca herzi. This study provides essential information on species diversity analysis using metabarcoding for environmental water samples obtained from rivers in Korea.

• ALGAE
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• v.33 no.1
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• pp.1-19
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• 2018

Members of the family Parviluciferaceae (Alveolata, Perkinsozoa) are the well-known dinoflagellate parasitoids along with Amoebophrya ceratii species complex and parasitic chytrid Dinomyces arenysensis and contain six species across three genera (i.e., Parvilucifera infectans, P. sinerae, P. rostrata, and P. corolla, Dinovorax pyriformis, and Snorkelia prorocentri) so far. Among Parvilucifera species, the two species, P. infectans and P. sinerae, are very similar or almost identical each other morphologically and genetically, thereby make it difficult to distinguish between the two. The only main difference between the two species known so far is the number of sporangium wall (i.e., 2 layers in P. infectans vs. 3 layers in P. sinerae). During sampling in Masan bay, Korea during the spring season of 2015, the dinoflagellate Akashiwo sanguinea cells infected by the parasite Parvilucifera were observed and this host-parasite system was established in culture. Using this culture, its morphological and ultrastructural features with special emphasis on the variation in the number of sporangium wall over developmental times, were investigated. In addition, the sequences of rDNA regions and ${\beta}-tubulin$ genes were determined. The result clearly demonstrated that the trophocyte at 36 h was covered with 4 layers, and then outer layer of the sporocyte gradually degraded over time, resulting in wall structure consisting of two layers, with even processes being detached from 7-day-old sporangium with smooth surface, indicating that the difference in the number of layers seems not to be an appropriate ultrastructural character for distinguishing P. infectans and P. sinerae. While pairwise comparison of the large subunit rDNA sequences showed 100% identity among P. infectans / P. sinerae species complex, genetic differences were found in the small subunit (SSU) rDNA sequences but the differences were relatively small (11-13 nucleotides) compared with those (190-272 nucleotides) found among the rest of Parvilucifera species (P. rostrata and P. corolla). Those small differences in SSU rDNA sequences of P. infectans / P. sinerae species complex may reflect the variations within inter- strains of the same species from different geographical areas. Taken together, all morphological, ultrastructural, and molecular data from the present study suggest that they are the same species.

• Animal cells and systems
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• v.13 no.3
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• pp.351-356
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• 2009

Ciliates are undoubtedly one of the most diverse protozoans that play a significant role in ecology. However, molecular examination, based on comparing the DNA sequences, has been done on a limited number of the species. Because most ciliates are uncultivable and their population sizes are often too small, it is usually difficult to obtain sufficient genomic DNA required for PCR based experiments. In the present study, we evaluated the effectiveness of four commercial DNA extraction procedures that extract high quality genomic DNA from a single ciliate cell. It was discovered that RED Extract-N-$Amp^{TM}$ PCR kit is the best method for removing PCR-inhibiting substances and minimizing DNA loss during purification. This method can also amplify more than 25 reactions of PCR. In addition, this technique was applied to single cells of 19 species belonged to 7 orders under 5 classes that isolated from mixed natural populations. Their small subunit ribosomal DNA (SSU rDNA) was successfully amplified. In summary, we developed a simple technique for the high-yield extraction of purified DNA from a single ciliate cell that may be more useful for rare ciliates, such as tiny and uncultivable marine microbes.

• Animal Systematics, Evolution and Diversity
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• v.27 no.2
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• pp.159-163
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• 2011

DNA barcoding of Bryozoa or "moss animals" has hardly advanced and lacks reference sequences for correct species identification. To date only a small number of cytochrome c oxidase subunit I (COI) sequences from 82 bryozoan species have been deposited in the National Center for Biotechnology Information (NCBI) GenBank and Barcode of Life Data Systems (BOLD). We here report COI data from 53 individual samples of 29 bryozoan species collected from Korean seawater. To our knowledge this is the single largest gathering of COI barcode data of bryozoans to date. The average genetic divergence was estimated as 23.3% among species of the same genus, 25% among genera of the same family, and 1.7% at intraspecific level with a few rare exceptions having a large difference, indicating a possibility of presence of cryptic species. Our data show that COI is a very appropriate marker for species identification of bryozoans, but does not provide enough phylogenetic information at higher taxonomic ranks. Greater effort involving larger taxon sampling for the barcode analyses is needed for bryozoan taxonomy.

• Parasites, Hosts and Diseases
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• v.40 no.1
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• pp.25-31
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• 2002

We describe a riboprinting scheme for identification of unknown Acanthamoeba isolates at the species level. It involved the use of PCR-RFLP of small subunit ribosomal RNA gene (riboprint) of 24 reference strains by 4 kinds of restriction enzymes. Seven strains in morphological group I and III were identified at species level with their unique sizes of PCR product and riboprint type by Rsa 1. Unique RFCP of 17 strains in group II by Dde I. Taq I and Hae III were classified into: (1) four taxa that were identifiable at the species level. (2) a subgroup of 4 taxa and a pair of 2 taxi that were identical with each other. and (3) a species complex of 7 taxa assigned to A. castellanii complex that were closely related. These results were consistent with those obtained by 18s rDNA sequence analysis. This approach provides an alternative to the rDNA sequencing for rapid identification of a new clinical isolate or a large number of environmental isolates of Acanthamoeba.