• Mycobiology
• /
• v.41 no.4
• /
• pp.191-201
• /
• 2013

Distinguishing individual Russula species has been difficult due to extensive phenotypic plasticity and obscure morphological and anatomical discontinuities. Due to highly similar macroscopic features, such as the presence of a red-cap, species identification within the Russula subgenus Amoenula is particularly difficult. Three species of the subgenus Amoneula have been reported in Korea. We used a combination of morphology and three molecular markers, the internal transcribed spacer (ITS), 28S nuclear ribosomal large subunit (LSU), and RNA polymerase II gene (RPB2), for identification and study of the genetic diversity of Russula subgenus Amoenula in Korea. We identified only two species in Korea (R. mariae and R. violeipes); these two species were indistinguishable according to morphology and LSU, but were found to be reciprocally monophyletic species using ITS and RPB2. The markers, ITS, LSU, and RPB2, have been tested in the past for use as DNA barcoding markers, and findings of our study suggest that ITS and RPB2 had the best performance for the Russula subgenus Amoneula.

• Animal cells and systems
• /
• v.6 no.2
• /
• pp.145-151
• /
• 2002

Phylogenetic signal present in the mitochondrial 16S ribosomal RNA gene (16S rDNA) and the nuclear large subunit ribosomal RNA gene (28S rDNA) was explored to assess their utility in resolving family level relationships of the superfamily Tephritoidea. These two genes were chosen because they appear to evolve at different rates, and might contribute to resolve both shallow and deeper phylogenetic branches within a highly diversified group. For the 16S rDNA data set, the number of aligned sites was 1,258 bp, but 1,204 bp were used for analysis after excluding sites of ambiguous alignment. Among these 1,204 sites, 662 sites were variable and 450 sites were informative for parsimony analysis. For the 28S rDNA data set, the number of aligned sites was 1,102 bp, but 1,000 bp were used for analysis after excluding sites of ambiguous alignment. Among these 1000 sites, 235 sites were variable and 95 sites were informative for parsimony analysis. Our analyses suggest that: (1) while 16S rDNA is useful for resolving more recent phylogenetic divergences, 28S rDNA can be used to define much deeper phylogenetic branches; (2) the combined analysis of the 16S and 28S rDNAs enhances the overall resolution without losing phylogenetic signal from either single gene analysis; and (3) additional genes that evolve at intermediate rates between the 16S and 28S rDNAs are needed to further resolve relationships among the tephritoid families.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
• /
• v.24 no.3
• /
• pp.422-428
• /
• 2019

Fish killing dinoflagellate Cochlodinium polykrikoides has been separated into four genetically differentiated subpopulations globally based on large-subunit (LSU) ribosomal RNA gene, and two subpopulations have been found in the South Sea, Korea. In this study, distributions of the East Asia and Philippines ribotypes were surveyed in the South Sea for 3 years (2014~2016) using quantitative real-time PCR (qPCR). The East Asia ribotype was detected in all sampling stations of the South Sea (Tongyeong~Wando) by 40~100% positives for 2014~2016, whereas the Philippines ribotype was detected in some areas of Tongyeong~Goheung by 1~2% positives for only 2016 when the Tsushima Warm Current (TWC) was particularly strengthened. These results indicate that the East Asia ribotype is the dominant subpopulation in the South Sea, also some of C. polykrikoides swimming cells might be transported from offshore to the South Sea via TWC.

• Microbiology and Biotechnology Letters
• /
• v.47 no.3
• /
• pp.359-363
• /
• 2019

Meju is a spontaneously fermented soybean product produced in Korea. We isolated the bacteria of the genera Bacillus, Enterococcus, and Staphylococcus from 12 meju samples collected from five regions of Korea using selective media, and we identified them based on the sequence analysis of 16S ribosomal RNA and gmk (guanylate kinase) genes. Bacillus and Enterococcus strains were identified from all samples and the numbers of Bacillus strains in the 11 samples were >15% of the total cell number. Therefore, the genus Bacillus was confirmed as the predominant bacterial group of meju. Staphylococcus strains were identified from six samples. The identified 151 Bacillus isolates predominated in the following order: B. velezensis, B. sonorensis, B. subtilis, and B. licheniformis. Among the 165 Enterococcus isolates, 163 strains were identified as E. faecium. Eighty-two Staphylococcus isolates were classified into six species of coagulase-negative Staphylococcus group and S. xylosus was the predominant species.

• Korean Journal of Microbiology
• /
• v.55 no.3
• /
• pp.248-257
• /
• 2019

In this study, we isolated about 70 bacterial strains from terrestrial and marine environments in Jeju island, and finally, total 21 strains were obtained based on the 16S ribosomal RNA gene sequence analysis. These isolated strains were classified into 16 genera of 5 classes and were identified as an unrecorded species in the Republic of Korea. As a result of the substrate utilization and capability for polymer degradation, the physiological phenotypes for acid resistance and halophilic bacteria were observed to be distinct from each other, except for some acid resistance strains. This study might provide basic information on utilization for indigenous microorganisms.

• Parasites, Hosts and Diseases
• /
• v.47 no.3
• /
• pp.293-297
• /
• 2009

Improved methods for detection of Cryptosporidium oocysts in environmental and clinical samples are urgently needed to improve detection of cryptosporidiosis. We compared the sensitivity of 7 PCR primer sets for detection of Cryptosporidium parvum. Each target gene was amplified by PCR or nested PCR with serially diluted DNA extracted from purified C. parvum oocysts. The target genes included Cryptosporidium oocyst wall protein (COWP), small subunit ribosomal RNA (SSU rRNA), and random amplified polymorphic DNA. The detection limit of the PCR method ranged from $10^3$ to $10^4$ oocysts, and the nested PCR method was able to detect $10^0$ to $10^2$ oocysts. A second-round amplification of target genes showed that the nested primer set specific for the COWP gene proved to be the most sensitive one compared to the other primer sets tested in this study and would therefore be useful for the detection of C. parvum.

• Parasites, Hosts and Diseases
• /
• v.53 no.2
• /
• pp.237-242
• /
• 2015

Analysis of ancient DNA (aDNA) extracted from Ascaris is very important for understanding the phylogenetic lineage of the parasite species. When aDNAs obtained from a Joseon tomb (SN2-19-1) coprolite in which Ascaris eggs were identified were amplified with primers for cytochrome b (cyt b) and 18S small subunit ribosomal RNA (18S rRNA) gene, the outcome exhibited Ascaris specific amplicon bands. By cloning, sequencing, and analysis of the amplified DNA, we obtained information valuable for comprehending genetic lineage of Ascaris prevalent among pre-modern Joseon peoples.

• Parasites, Hosts and Diseases
• /
• v.60 no.1
• /
• pp.45-49
• /
• 2022

The Japanese amberjack Seriolae quinqueradiata is one of the most consumed fish species among the Koreans. However, information regarding parasitic infection in Japanese amberjack is scarce. This study described the morphological and molecular characteristics of a species of philometrid nematode, Philometroides seriolae, which was recovered from Japanese amberjack. This fish was caught in the sea of Goseong-gun, Gangwon-do, Republic of Korea (Korea). Six P. seriolae (Nematoda: Philometridae) were recovered from 2 Japanese amberjacks. These parasites were subgravid female which were 325-420 mm long and 2.95-3.27 mm wide. Furthermore, they had typical papillae distributed on their body surface with 14 papillae at the apical view. Sequence analysis of the small subunits of ribosomal RNA (SSU rRNA) showed high sequence identity (99.8%, 1,607/1,611-bp) with that of P. seriolae (GenBank accession no. FJ155811). This nematode species has been newly added to the Korean nematode fauna.

• International Journal of Industrial Entomology and Biomaterials
• /
• v.2 no.1
• /
• pp.37-53
• /
• 2001

Two regions of mtDNA genome, cytochrome oxidase subunit I (COI) and 165 ribosomal RNA (165 rRNA) genes, were sequenced for 15 species of the long-horned beetle belonging to four subfamilies and geographic samples of mulberry longicorn beetle, Apriona germari, from two localities in Korea. Ten samples of A. germari collected from Suwon and Busan revealed three COI haplotypes ranging in nucleotide divergence of 0.3% to 0.5%, and the two populations shared one common COI haplotype (80%). The sequence divergence among 15 species of the long-horned beetle was much higher in COI gene (12.3%∼39.4%) than 16S rRNA gene (7.2% to 23.1), and the maximum value in the COI gene is exceptional compared with other relevant studies, including that of Coleoptera. The greatly increased divergence in the COI gene, in facto was stemmed from a peculiar sequence of Prionus insularis belonging to Prioninne, divergence of which ranges from 31.2% to 39.3% from other species. We discussed possible reason of the divergence in this species. Due to the abnormality of COI gene divergence, decrease in phylogenetic signal was severe in COI nucleotide and, subsequently, the converted amino acid sequences, rendering us to put more confidence on the 16S5 rRNA gene data. Although the molecular phylogeny confidently supports the monophyletic origin of Lepturinae, the presence of discrepancy between molecular data and traditional taxonomic views also is a testable hyothesis. One such discrepancy includes taxonomic position of Sophronica obrioides and Theophilea cylindricollis belonging to Lamiinae.

• Fisheries and Aquatic Sciences
• /
• v.12 no.3
• /
• pp.171-178
• /
• 2009

The Perciformes include approximately 40% of all bony fishes and are the largest order of vertebrates. This order includes some of the most economically relevant marine fishes, particularly the red seabream, black seabream and rock bream. A 409 bp fragment of the cytochrome b (cyt b) gene and 403 bp and 518 bp fragments of ribosomal RNA (12S and 16S rRNA, respectively) were sequenced from five populations of natural and cultured red seabreams, natural black seabream, and natural and cultured rock breams. The mitochondrial DNA sequences were utilized for the genetic identification and population structural analyses of these three species. Phylogenetic relationships of intra- and inter-species were elucidated using three types of molecular genetic markers from three species of the order Perciformes in Korea. We noted no significant differences in the intra-specific variation of the cyt b and rRNA genes in each population however, inter-specific divergences were greater than intra-specific variation. Inter-specific variation was induced more by transition than transversion type in the cyt b and rRNA genes. The cyt b gene and rRNA genes make it possible to determine the inter-species divergence. The rRNA genes have more conserved sequences than the cyt b gene. Therefore, these genes are expected to prove useful among species belonging to the different genera or families.