• Journal of Microbiology and Biotechnology
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• v.10 no.3
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• pp.363-366
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• 2000

The sequences of the D1/D2 region of 26S rDNA from seven Sporobolomyces species, Bensingtonia subrosea, and Rhodosporicium toruloides were determined and compared with those from representatives of the genera Leucosporidium, Rhodosporidium, Rhodotorula, and Sporidiobolus. The five species of Sporobolomyces analyzed were distantly related to a monophyletic clade consisting of species of Sporidiobolaceae and Sporobolomycetaceae. Sporobolomyces falcatus was found to be closely related to Tremella exigua. The members of Sporidiobolaceae and Sporobolomycetaceae were divided into four groups. Group 1 was composed of Leucosporidium scottii and two Rhodotorula species, and group 2 contained three Rhodotorula species. Group 3 was designeate as the Sporobolomyces/Sporidiobolus core group, as it contained Sporidiobolus johnsonii, the type species of Sporidiobolus and the teleomorphic state of Sporobolomyces salmonicolor (the type species of Sporobolomyces). Group 4, named the Rhodotorula/Rhodosporidium core group, included Rhodosporidium toruloides and Rhodotorula glutinis, the type species of the genera Fhodosporidium and Rhodotorula, respectively. The four groups were differentiated on the basis of their physiological characteristics including the assimilation of D-glucosamine, glucuronate, 2-keto-gluconate, L-arabinitol, raffinose, methyl-$\alpha$-glucoside, and satrch. The taxonomy of the genera Leucosporidium, Rhodosporidium, Rhodotorula, Sporidiobolus, and Sporobolomyces will require a major revision when more data becomes available.

• Korean Journal of Plant Resources
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• v.25 no.1
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• pp.96-104
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• 2012

Phylogenetic analyses were conducted to evaluate relationships of 7 taxa of Korean Carpesium including three outgroup (Inula britannica L., Inula germanica L., Rhanteriopsis lannginosa (DC.) Rauschert) by using ITS (internal transcribed spacer) sequences of nuclear ribosomal DNA. Phylogenetic studies used maximum parsimony, neighbor-joining and maximum likelihood methods analysis. The length of the ITS sequences was 731 bp, and the lengths of the ITS1, ITS2 and 5.8S regions were 284~297 bp, 264~266 bp and 164 bp, respectively. The total number of variable sites was 111 for the entire sequences, and a parsimony informative sites of 64 are valid. Base change appeared variously in ITS1 rather than in ITS2. As the result, Korean Carpesium were formed monophyletic group and C. abrotanoides situated as the most basal clade. The results show that C. macrocephalum is closely related with C. triste. C. rosulatum has the closest relationship with C. glossophyllum. C. cernuum is close to C. divaricatum. These results suggest that the ITS data used in this study could be useful for the phylogenetic analysis of Korean Carpesium.

• 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 fish pathology
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• v.36 no.2
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• pp.277-286
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• 2023

Korean rockfish, Sebastes schlegelii, is a representative bony fish that belongs to the family Scorpaenidae and the order Scorpaeniformes. It has high ecological and economic value and is widely cultivated in many East Asian countries, including South Korea, Japan and China. One of streptococci, Streptococcus iniae, is Gram-positive cocci with a negative reaction for catalase and oxidase. The Korean rockfish shows clinical signs when infected with S. iniae, such as body darkening, bleeding, enlarged kidneys, blurred eyes, abdominal distension, etc., ultimately leading to death. The Korean rockfish causes significant economic losses every year in South Korea due to streptococcosis. In this study, we identified bacteria from the fish using polymerase chain reaction and conducted analyses of hemolytic activity and biochemical tests using API 20 STREP and API ZYM systems. Results of confirming the hemolytic activity (n=4) observed in alpha-type hemolysis (25%), beta-type hemol- ysis (50%), and gamma-type hemolysis (25%) of isolates. The biochemical test results exhibited sig- nificant variation among S. iniae. Additionally, we performed intraperitoneal injection with S. iniae in the fish and analyzed the phylogenetic tree using housekeeping genes of S. iniae, including cpsD, arcC, glnA, groEL, gyrB, mutS, pheT, prkC, rpoB, and tkt, via multilocus sequence typing (MLST). The lethal dose (LD₅₀) showed strong pathogenicity, such as 3.34 × 10 colony-forming unit (CFU)/ml for 23FBStr0601 strain and 7.16 × 10 CFU/ml for 23FBStr0602 strain. 23FBStr0603 strain showed relatively low pathogenicity at 1.73 × 10⁵ CFU/ml. The strains 23FBStr0601 and 23FBStr0602, which showed strong pathogenicity, clustered into one monophyletic group. The 23FBStr0603 strain showed weak pathogenicity and formed a monophyletic group with KCTC 3657.

• ALGAE
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• v.27 no.2
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• pp.75-82
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• 2012

$Arthrospira$ $platensis$ and $Arthrospira$ $maxima$ are species of cyanobacteria used in health foods, animal feed, food additives, and fine chemicals. This study conducted a comparison of the 16S rRNA gene and $cpcBA$-intergenic spacer ($cpcBA$-IGS) sequences in $Arthrospira$ strains from culture collections around the world. A cluster analysis divided the 10 $Arthrospira$ strains into two main genotypic clusters, designated I and II, where Group I contained $A.$ $platensis$ SAG 86.79, UTEX 2340, $A.$ $maxima$ KCTC AG30054, and SAG 49.88, while Group II contained $A.$ $platensis$ PCC 9108, NIES 39, NIES 46, and SAG 257.80. However, although $A.$ $platensis$ PCC 9223 belonged to Group II-2 based on its $cpcBA$-IGS sequence, this strain also belonged to Group I based on its 16S rRNA gene sequence. Phylogenetic analyses based on the 16S rRNA gene and $cpcBA$-IGS sequences showed no division between $A.$ $platensis$ and $A.$ $maxima$, plus the 16S rRNA gene and $cpcBA$-IGS sequence clusters did not indicate any well-defined geographical distribution, instead overlapping in a rather interesting way. Therefore, the current study supports some previous conclusions based on 16S rRNA gene and $cpcBA$-IGS sequences, which found that $Arthrospira$ taxa are monophyletic. However, when compared with 16S rRNA sequences, $cpcBA$-IGS sequences may be better suited to resolve close relationships and intraspecies variability.

• Korean Journal of Plant Taxonomy
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• v.36 no.2
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• pp.91-108
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• 2006

Phylogenetic analyses were conducted to evaluate evolution and relationship of 16 taxa of Korean Geranium including 3 outgroups using ITS (internal transcribed spacer) squences of nuclear ribosomal DNA. Phylogenetic studies used most parsimony and neighbor-joining methods including bootstrapping and jackknifing analysis. As the result, Korean Geranium forms monophyletic group. In the parsimony tree G. koraiense var. hallasanense situated as the most basal clade and Erianthum group forms one clade by high bootstrap ans jackknife values (100% of bootstrap and jackknife values). G.dahuricum as one of the Krameri group is closely related with Palustre group by very weak relationship (37% of bootstrap and 44% of jackknife values) and the node collapse in the strict tree. G. Knuthii which was one of wilfordii group is closely related with Koreanum group. G. sibiricum, one of Sibiricum group, is the most closest relationship with G. soboliferum and these species are sister to G. krameri. G. tripartitum and G. wilfordii which are wilfordii group are linked to G. nepalense, G. thunbergii f. pallidum and G. thunbergii. This result suggested that the phylogenetic analysis of ITS sequences should be useful to address phylogenetic questions on the genus Korean Geranium.

• Journal of Microbiology and Biotechnology
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• v.19 no.1
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• pp.5-10
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• 2009

A freshwater bacterium, designated $IMCC1713^T$, was isolated from a highly eutrophic artificial pond. Cells of the strain were Gram-negative, chemoheterotrophic, poly-$\beta$-hydroxybutyrate granule containing and obligately aerobic short rods that were motile with a single polar flagellum. The 16S rRNA gene sequence similarity analysis showed that the novel strain was most closely related to the species Roseateles depolymerans (96.3%), Mitsuaria chitosanitabida (96.2%), Ideonella dechloratans (96.2%), and Pelomonas saccharophila (96.1%) in the Sphaerotilus-Leptothrix group within the order Burkholderiales. Phylogenetic trees based on 16S rRNA gene sequences indicated that the isolate formed an independent monophyletic clade within the order Burkholderiales. The relatively low DNA G+C content (57.4mol%), together with several phenotypic characteristics, differentiated the novel strain from other members of the Sphaerotilus-Leptothrix group. From the taxonomic data, therefore, the strain should be classified as a novel genus and species, for which the name Inhella inkyongensis gen. nov., sp. nov. is proposed. The type strain of the proposed species is strain $IMCC1713^T$ (=KCTC $12791^T$=NBRC $103252^T$=CCUG $54308^T$).

• Molecules and Cells
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• v.28 no.3
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• pp.155-165
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• 2009

The newly sequenced complete mitochondrial genome of the brown marmorated stink bug, Halyomorpha halys($St{\aa}l$) (Hemiptera: Pentatomidae), is a circular molecule of 16,518 bp with a total A+T content of 76.4% and two extensive repeat regions in A+T rich region. Nucleotide composition and codon usage of H. halys are about average when compared with values observed in 19 other published hemipteran mitochondrial genomes. Phylogenetic analyses using these 20 hemipteran mitochondrial genomes support the currently accepted hypothesis that suborders Heteroptera and Auchenorrhyncha form a monophyletic group. The mitochondrial gene arrangements of the 20 genomes are also consistent with our results.

• Ocean and Polar Research
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• v.42 no.3
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• pp.263-270
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• 2020

The distribution and genotypes of the sea nettle Chrysaora pacifica have been reported in the South Sea of Korea; however, little research work has been attempted in the East Sea. Here, we collected similar jellyfishes from the East Sea coasts (Goseong, Yangyang and Sokcho), and identified them to the sea nettle morphologically. In addition, the genotypes of these sea nettle were compared with those from the South Sea (Tongyeong and Geoje). Phylogenetic analysis by using the mitochondrial COI sequences showed that the genus Chrysaora was clearly separated from other taxa to be formed a monophyletic group, with each species distinctly separated. C. pacifica in the East and South Seas was separated geographically by the COI phylogeography, representing potentially different populations. The COI gene of the Korean C. pacifica had approximately 7 times more genetic variation than the nuclear ITS rDNA, and thus it might be considered as a useful marker for genetic analysis of the jellyfish population.