• Journal of Species Research
• /
• v.13 no.3
• /
• pp.332-339
• /
• 2024

The filamentous freshwater red alga Compsopogon caeruleus(Compsopogonophyceae, Compsopogonaceae, Rhodophyta) occurs in tropical and subtropical regions of worldwide. This species has been reported from Asia, America, Africa, Europe and Oceania, and the worldwide distribution of Compsopogon caeruleus is in variable water habitats. Several morphospecies of the genus Compsopogon had been recorded, but recent molecular phylogenetic analyses with worldwide sampling identified a monospecific genus, C. caeruleus. In the present study, we first report a freshwater red alga Compsopogon caeruleus from Korea. We identified Compsopogon caeruleus in an urban river in Yongin City, and analyzed its morphological and genetic characteristics. Nuclear 18S rDNA, plastidal rbcL gene and mitochondrial cox1 gene sequences isolated from Korean Compsopogon caeruleus showed high sequences similarity with Compsopogon caeruleus from worldwide (98.6-100% (18S rDNA), 99-100% (rbcL) and 97.7-100% (cox1)). These sequences similarities support the identification of a red alga found in Korea as Compsopogon caeruleus. This new geographical report provides the useful information for understanding the distribution and habitat range of Compsopogon caeruleus especially concerning urban freshwater environments.

• Journal of Life Science
• /
• v.29 no.1
• /
• pp.123-128
• /
• 2019

The use of 16S rDNA is commonplace in the determination of prokaryotic species. However, it has limitations, and there are few studies at the genus level. We investigated conserved genes and metabolic pathways at the genus level in 28 strains of 13 genera of prokaryotes using the COG database (conserved genes) and MetaCyc database (metabolic pathways). Conserved genes compared to total genes (core genome) at the genus level ranged from 27.62%(Nostoc genus) to 71.76%(Spiribacter genus), with an average of 46.72%. The lower ratio of core genome meant the higher ratio of peculiar genes of a prokaryote, namely specific biological activities or the habitat may be varied. The ratio of common metabolic pathways at the genus level was higher than the ratio of core genomes, from 58.79% (Clostridium genus) to 96.31%(Mycoplasma genus), with an average of 75.86%. When compared among other genera, members of the same genus were positioned in the closest nodes to each other. Interestingly, Bacillus and Clostridium genera were positioned in closer nodes than those of the other genera. Archaebacterial genera were grouped together in the ortholog and metabolic pathway nodes in a phylogenetic tree. The genera Granulicella, Nostoc, and Bradyrhizobium of the Acidobacteria, Cyanobacteria, and Proteobacteria phyla, respectively, were grouped in an ortholog content tree. The results of this study can be used for (i) the identification of common genes and metabolic pathways at each phylogenetic level and (ii) the improvement of strains through horizontal gene transfer or site-directed mutagenesis.

• Korean Journal of Fisheries and Aquatic Sciences
• /
• v.50 no.4
• /
• pp.447-452
• /
• 2017

In this study, we tried to identify a sea anemone collected from the coast of Gijang, Busan. The anemone was morphologically similar to species belonging to the genus Anthopleura, but its morphological characteristics did not allow for confirmed identification to species level. Multiple genes from mitochondrial cytochrome oxidase III, 12S and 16S rRNA, and nuclear 18S and 28S rRNA, were amplified for multilocus sequence typing (MLST) analysis using genomic DNA extracted from the sampled anemone and a different primer set. Based on the MLST analysis, the anemone obtained in this study was identified as Anthopleura artemisia. Also, the sequence of internal transcribed spacer-2 was most closely related to A. artemisia, indicating that this single region might be useful for anemone identification. This study shows significance of molecular identification for sea anemones, and will be helpful in studies of sea anemone identification using genotyping-by-sequencing.

• Journal of fish pathology
• /
• v.22 no.3
• /
• pp.391-400
• /
• 2009

Genetic identification of 17 fish-derived Aeromonas strains was attempted using 5 housekeeping genes. 16S rRNA, gyrB, rpoD, dnaJ and recA genes from the 17 strains were amplified, and total of 85 amplicons were sequenced. DNA sequences of the strains and type strains of the 17 Aeromonas homology groups were used for genetic identification and phylogenetic analyses. None of the strains was identified as a single species using the 16S rRNA gene, showing the same identities (average = 99.7%) with several Aeromonas species. According to gyrB, rpoD, dnaJ, and recA, 9 strains and RFAS-1 used in this study were identified as A. hydrophila and A. salmonicida, respectively. However, the other strains were closely related to 2 or more Aeromonas species (i.e., A. salmonicida, A. veronii, A. jandaei, A. media and A. troda) depending on the genetic marker used. In this study, gyrB, rpoD, dnaJ and recA gene sequences proved to be advantageous over 16S rRNA for the identification of field Aeromonas isolates obtained from fish. However, there are discrepancies between analyses of different phylogenetic markers, indicating there are still difficulties in genetic identification of the genus Aeromonas using the housekeeping genes used in this study. Advantages and disadvantages of each housekeeping gene should be taken into account when the gene is used for identification of Aeromonas species.

• International Journal of Industrial Entomology and Biomaterials
• /
• v.8 no.1
• /
• pp.77-80
• /
• 2004

For the development of the alternative control system against the major forest pests, Beauveria spp. F-101, isolated from a dead larva of Thecodiplosis japonensis, was selected because this isolate showed high pathogenicities against T. japonensis and Acantholyda parki. Beauveria spp. F-101 had irregular clustered conidio-phores and conidia borne on a distinctive apical zigzag extension, and it showed typical characteristic of the genus, Beauveria in morphology. For molecular based-identification, the ribosomal ITS region of Beauveria spp. F-101 was amplified with ITS1 and ITS4 primers, and cloned into pGEM- T Easy vector. The amplified PCR product was 569 bp in size and completely sequenced. The similarities of the cloned ITS sequence were 99 ％ and 97％ to those of B. bassiana and B. brongniartii, respectively. In comparison to other species among the genus Beauveria, the ITS region of Beauveria spp. F-101 showed a similarity of 95％ to B. amorpha, 95％ to B. tenella, 89％ to B. vermiconia and 69％ to B. alba, respectively. In addition, in comparison to different genus, it had 95％ similarities to Cordyceps militaris and 91％ to Paecilomyces tenuipes. Accordingly, the current result suggests that Beauveria spp. F-101 was a variant of B. bassiana and it seems to be a new isolate considering sequence variation in ITS region.

• Animal Systematics, Evolution and Diversity
• /
• v.11 no.2
• /
• pp.183-197
• /
• 1995

Description and identifications of 6 species belonging to genus Phintella from Korea are in insufficient and inaccurate situation. In the present paper, redescriptions illustrations and identification key are provided for 7 species of genus Phintella including P. popovi newly recorded in Korean spider fauna, and Ocius munitus described by Wesolowska (1981s) was synonymized to P.cavaleriei. For the author's identiication and pairing to be valid multivariate analysis was performed with 13 RVCs below STD 0.05 to 134 individuals. The result of discriminant analysis carried out with 13 RVCs of 134 individuals was not satisfactory, but cluster analysis performed with mean ratio values of 14 OTUs to 13 RVCs showed the same result with author's pairing except P.abnormis , which has larger dissimilarity than the pairs of the others. So pairing of 7 species was possible as a whole because one species only failed in pairing , even though this is imperful result. This method to be helpful to pairing test and identification if it were to improve.

• Journal of Microbiology and Biotechnology
• /
• v.27 no.6
• /
• pp.1128-1137
• /
• 2017

The aim of this study was to explore the accuracy and feasibility of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) in identifying bacteria from environmental sources, as compared with rpoA gene sequencing, and to evaluate the occurrence of bacteria of the genus Enterococcus in wild birds. In addition, a phyloproteomic analysis of certain Enterococcus species with spectral relationships was performed. The enterococci were isolated from 25 species of wild birds in central Europe (Poland). Proteomic (MALDI-TOF MS) and genomic (rpoA gene sequencing) methods were used to identify all the isolates. Using MALDI-TOF MS, all 54 (100%) isolates were identified as Enterococcus spp. Among these, 51 (94.4%) isolates were identified to the species level (log(score) ${\geq}2.0$), and three isolates (5.6%) were identified at a level of probable genus identification (log(score) 1.88-1.927). Phylogenetic analysis based on rpoA sequences confirmed that all enterococci had been correctly identified. Enterococcus faecalis was the most prevalent enterococcal species (50%) and Enterococcus faecium (33.3%) the second most frequent species, followed by Enterococcus hirae (9.3%), Enterococcus durans (3.7%), and Enterococcus casseliflavus (3.7%). The phyloproteomic analysis of the spectral profiles of the isolates showed that MALDI-TOF MS is able to differentiate among similar species of the genus Enterococcus.

• Mycobiology
• /
• v.36 no.3
• /
• pp.143-147
• /
• 2008

We have detected the slime mold, Diachea leucopodia (GNU06-10) in a strawberry greenhouse located in Sancheong-gun, Gyeongnam. Typical fruiting bodies had developed gregariously on the strawberry leaves, petioles, and plant debris on ground soil habitat, and also surprisingly on plastic pipes and a vinyl covering. Field samples were examined via stereomicroscopy, light microscopy, and SEM for the determination of morphological characteristics. Dark-brown to black spores formed gregariously within the stipitate cylindrical sporangium, and were covered by an iridescent peridium, which may be intact at maturity, or may have disintegrated. The upper portion of the peridium generally breaks up to expose the spores, whereas the lower portion was usually persistent. The results of energy dispersive X-ray spectrometer (EDS) analysis showed that lime was present in the stalk and columella but absent from the spores, capillitium, and peridium. The above characteristics confirm its taxonomic position in the genus Diachea. However, this genus is intermediate in character between the Physarales and Stemonitales of the Myxogastromycetidae. Hence, this genus had been classified as a member of the Stemonitales until the mid-1970's, on the basis of its iridescent peridium and noncalcareous capillitial system, similar to Comatricha of the Stemonitaceae. By way of contrast, emphasis on morphological characteristics, most notably the calcareous stalk and typical columella, places Diachea within the order Physarales. The presence of a phaneroplasmodium during the trophic stage and lime deposition in its sporophores, as was confirmed in this work, supported the inclusion of Diachea in the Physarales, and the noncalcareous capillitial system verified its identification as a member of the Didymiaceae. Further characteristics of the species D. leucopodia include the following: phaneroplasmodium, spore globose 7.5 ${\mu}m$ in diameter, very minutely roughened; sporangia $500{\mu}m\times1mm$, more or less cylindrical, gregarious, stalked 1.2mm; stalk and columella white.

• Mycobiology
• /
• v.48 no.6
• /
• pp.476-483
• /
• 2020

The genus Pholiota (Strophariaceae, Basidiomycota) is made up of wood-rotting saprotrophic mushrooms characterized by a yellow or brown pileus with scales and/or slimy, and by a brownish smooth spore with a germ pore. However, these features are not enough to distinguish its species, or separate the genus Pholiota from other brown-spored wood-rotting genera such as Hypholoma and Stropharia. Although internal transcribed spacer (ITS) sequencebased identification has improved identification accuracy for species of Pholiota, most Pholiota species in Korea are reported based on morphological features. To evaluate the taxonomy of Pholiota species, we investigated 62 specimens collected from 1999 to 2019 in Korea using ITS sequence analysis and morphological observation. Twelve of the 16 recorded Pholiota species in Korea were identified. While eight species were clearly separated, the ITS analysis did not distinguish three in the Pholiota adiposa complex. Therefore, further investigation is required to distinguish these three species. ITS sequences deposited in GenBank confirm that P. highlandensis exists in Korea. The presence of the other four Pholiota species could not be confirmed through specimens or sequence information in GenBank. A taxonomic key and the ITS sequence data for Korean Pholiota species are included and can be good baselines for further research on Pholiota taxonomy and diversity.

• Microbiology and Biotechnology Letters
• /
• v.23 no.2
• /
• pp.123-130
• /
• 1995

DNA topoisomerase I have been shown to be important therapeutic target in cancer chemotherapy. Chemotaxonomy and numerical identification were carried out for an isolate strain No.7489 producing an antibiotic that inhibits DNA topoisomerase I activity. The genus of strain No.7489 was determined as Streptomyces sp. from culture, morphological and chemotaxonomic data. Thirty-nine taxonomic unit characters were tested and the data were analyzed numerically using the TAXON program. The isolate was best matched to Streptomyces melanosporofaciens in the major cluster 32 of Streptomyces. Therefore, it was concluded that the isolate was identified to be a member of Streptomyces melanosporofaciens.