• International Journal of Oral Biology
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• v.38 no.1
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• pp.21-27
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• 2013

Anginosus group streptococci (AGS) were classified based on the nucleotide sequences of the 16S rRNA gene (16S rDNA) and comprised Streptococcus anginosus, Streptococcus intermedius, and Streptococcus constellatus. It is known that AGS is a causative factor of oral and systematic diseases. The purpose of this study was to discriminate the 56 clinical strains of AGS isolated from Korean oral cavities using phylogenetic analysis of 16S rDNA and species-specific PCR at the species-level. The 16S rDNA of clinical strains of AGS was sequenced using the dideoxy chain termination method and analyzed using MEGA version 5 software. PCR was performed to identify the clinical strains using species-specific primers described in previous studies and S. intermedius-specific PCR primers developed in our laboratory. The resulting phylogenetic data showed that the 16S rDNA sequences can delineate the S. anginosus, S. intermedius, and S. constellatus strains even though the 16S rDNA sequence similarity between S. intermedius and S. constellatus is above 98%. The PCR data showed that each species-specific PCR primer pair could discriminate between clinical strains at the species-level through phylogenetic analysis of 16S rDNA nucleotide sequences. These results suggest that phylogenetic analysis of 16S rDNA and PCR are useful tools for discriminating between AGS strains at the species-level.

• Parasites, Hosts and Diseases
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• v.55 no.3
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• pp.333-336
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• 2017

Avian trichomoniasis caused by Trichomonas gallinae is a serious protozoan disease worldwide. The domestic pigeon (Columba livia domestica) is the main host for T. gallinae and plays an important role in the spread of the disease. Based on the internal transcribed spacers of nuclear ribosomal DNA of this parasite, a pair of primers (TgF2/TgR2) was designed and used to develop a PCR assay for the diagnosis of T. gallinae infection in domestic pigeons. This approach allowed the identification of T. gallinae, and no amplicons were produced when using DNA from other common avian pathogens. The minimum amount of DNA detectable by the specific PCR assay developed in this study was 15 pg. Clinical samples from Guangzhou, China, were examined using this PCR assay and a standard microscopy method, and their molecular characteristics were determined by phylogenetic analysis. All of the T. gallinae-positive samples detected by microscopic examination were also detected as positive by the PCR assay. Most of the samples identified as negative by microscopic examination were detected as T. gallinae positive by the PCR assay and were confirmed by sequencing. The positive samples of T. gallinae collected from Guangzhou, China, were identified as T. gallinae genotype B by sequencing and phylogenetic analyses, providing relevant data for studying the ecology and population genetic structures of trichomonads and for the prevention and control of the diseases they cause.

• Asian-Australasian Journal of Animal Sciences
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• v.13 no.2
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• pp.137-148
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• 2000

This paper is based on the 9 goat colonies along the middle and lower Yellow River valley and 7 local goat colonies in the Northeast, Tibet and the Yangtze valley. After collecting the same data about the 22 goat colonies in China and other countries, it establishes and composes the matrix of fuzzy similarity relation describing the genetic similarities of different colonies. It also clusters 38 colonies according to their phylogenetic relationship. The establishment of the matrix and the cluster are effected in terms of the frequency of 18 loci and 43 allelomorphs in blood enzyme and other protein variations. The study proves that the middle Yellow River valley is one of the taming and disseminating centers of domestic goats in the South and East of Central Asia. Compared with other goat populations in this vast area, the native goat populations in the west of Mongolian Plateau, the Qinghai-Tibet Plateau and the middle Yellow River valley share the same origin. The colonies in the lower Yellow River valley and those in the middle valley, however, are relatively remote in their phylogenetic relationship. The native goat colonies in the southeast of Central Asia can be classified into two genetic groups: "East Asia" and "South Asia" and the colonies in Southeast Asia belong to either group.

• Animal cells and systems
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• v.6 no.1
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• pp.45-51
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• 2002

We compared the complete mitochondrial cytochrome b gene sequences of Korean and European cobitids to provide independent evidence for assessment of systematic and biogeographic relationships of species in the genus Cobitis. The data suggested monophyly of the genus Cobitis and the inclusion of Korean Cobitis species within the group having one lamina circularis, a primitive condition. Also, all the phylogenetic analyses using maximum parsimony, maximum likelihood, and neighbor joining methods showed a monophyletic relationship among Cobitis. The basal position of the Caspian C. cf. sibirica reported here reflects the eastern Asiatic origin cf. the European Cobitis and establishes C. cf. sibirica as an independent lineage. The Korean C. pacifica diverged next to C. cf. sibirica in basal group from the genus Cobitis. This result is in agreement with the hypothesized Asiatic origin of some European freshwater fish lineages. The phylogenetic relationships in this study showed a close affinity between C. zanadreai and C. sinensis. Two new species, C. tetralineata and C. pacifica in Korea also are closely related to monophyletic group clustering the type species of the Acanestrinia subgenus (C. elongata) with all the endemic Italian species (C. bilineata and C. zanandreai). This may suggest that the affinity between the Korean and Danubian-Italian imply genetic convergence or genetic plesiomorphic state between allopatric species that are separated for the Miocene. The mtDNA-based phylogeny for the species of the genus Cobitis from Kores and Europe permits phylogenetic assessment of the morphological transitions of Iamina circularis.

• Korean Journal of Plant Taxonomy
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• v.44 no.1
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• pp.51-58
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• 2014

This study aims to define the phylogenetic relationship within Korean section sabina and find molecular markers which resolve the phylogenetic relationship in genus Juniperus and section sabina. cpDNA matK and psbA-trnH were used as molecular markers. The combined analyses of two genes suggested that section sabina was a clade supported by 100% BP. The relationships of [J. chinensis var. sargentii+J. davurica] clade and [J. chinensis var. chinensis+J. chinensis var. procumbens+J. chinensis var. horizontalis] clade were supported by 91% BP and 100% BP, respectively. Thus, the classification of Korean section sabina would be appropriate at follows, (1) J. chinensis var. sargentii+J. davurica, and (2) J. chinensis var. chinensis+J. chinensis var. procumbens According to the results of separate analyses, matK seems to work better resolving power to clarify the phylogenetic ambiguity in Juniperus and section sabina than psbA-trnH.

• Korean Journal of Veterinary Research
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• v.55 no.1
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• pp.31-39
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• 2015

The present study was conducted to determine the full rpoB and eight house-keeping gene sequences of 78 and 35, respectively, avian pathogenic E. coli (APEC) strains. Phylogenetic comparison with 66 E. coli and Shigella strains from GenBank and EMBL was also conducted. Based on the full rpoB sequence, 50 different rpoB sequence types (RSTs) were identified. RST 1 was assigned to a major RST that included 34.7% (50/144) of the analyzed strains. RST 2 to RST 50 were then assigned to other strains with higher nucleotide sequence similarity to RST 1 in order. RST 1, 11, and 23 were mixed with APEC along with human commensal and pathogenic strains while RST 2, 6, 9, 13-15, 22, 24, 25, 33, 34, 36, and 41 were unique to APEC strains. Only five APEC strains grouped into RST 32 and 47, which contained human pathogenic E. coli (HPEC). Thus, most of the APEC strains had genetic backgrounds different from HPEC strains. However, the minor APEC strains similar to HPEC should be considered potential zoonotic risks. The resolution power of multi-locus sequence typing (MLST) was better than RST testing. Nevertheless, phylogenetic analysis of rpoB was simpler and more economic than MLST.

• Tuberculosis and Respiratory Diseases
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• v.81 no.3
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• pp.216-221
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• 2018

Background: The number of immigrants with tuberculosis (TB) increases each year in South Korea. Determining the transmission dynamics based on whole genome sequencing (WGS) to cluster the strains has been challenging. Methods: WGS, annotation refinement, and orthology assignment for the GenBank accession number acquisition were performed on two clinical isolates from Chinese immigrants. In addition, the genomes of the two isolates were compared with the genomes of Mycobacterium tuberculosis isolates, from two native Korean and five native Chinese individuals using a phylogenetic topology tree based on the Multiple Alignment of Conserved Genomic Sequence with Rearrangements (Mauve) package. Results: The newly assigned accession numbers for two clinical isolates were CP020381.2 (a Korean-Chinese from Yanbian Province) and CP022014.1 (a Chinese from Shandong Province), respectively. Mauve alignment classified all nine TB isolates into a discriminative collinear set with matched regions. The phylogenetic analysis revealed a rooted phylogenetic tree grouping the nine strains into two lineages: strains from Chinese individuals and strains from Korean individuals. Conclusion: Phylogenetic trees based on the Mauve alignments were supposed to be useful in revealing the dynamics of TB transmission from immigrants in South Korea, which can provide valuable information for scaling up the TB screening policy for immigrants.

• Journal of Ecology and Environment
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• v.41 no.1
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• pp.9-18
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• 2017

Background: Species in the heterokont genus Synura are colonial and have silica scales whose ultrastructural characteristics are used for classification. We examined the ultrastructure of silica scales and molecular data (nuclear SSU rDNA and LSU rDNA, and plastid rbcL sequences) to better understand the taxonomy and phylogeny within the section Petersenianae of genus Synura. In addition, we report the first finding of newly recorded Synura species from Korea. Results: We identified all species by examination of scale ultrastructure using scanning and transmission electron microscopy (SEM and TEM). Three newly recorded species from Korea, Synura americana, Synura conopea, and Synura truttae were described based on morphological characters, such as cell size, scale shape, scale size, keel shape, number of struts, distance between struts, degree of interconnections between struts, size of base plate pores, keel pores, base plate hole, and posterior rim. The scales of the newly recorded species, which belong to the section Petersenianae, have a well-developed keel and a characteristic number of struts on the base plate. We performed molecular phylogenetic analyses based on sequence data from three genes in 32 strains (including three outgroup species). The results provided strong statistical support that the section Petersenianae was monophyletic, and that all taxa within this section had well-developed keels and a defined number of struts on the base plate. Conclusions: The phylogenetic tree based on sequence data of three genes was congruent with the data on scale ultrastructure. The resulting phylogenetic tree strongly supported the existence of the section Petersenianae. In addition, we propose newly recorded Synura species from Korea based on phylogenetic analyses and morphological characters: S. americana, S. conopea, and S. truttae.

• KSBB Journal
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• v.19 no.1
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• pp.42-49
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• 2004

A gene coding for epoxide hydrolase (EH) of Aspergillus niger LK, a fungus possessing the enantioselective hydrolysis activity for racemic epoxides, was characterized by phylogenetic analysis. The deduced protein of A. niger LK epoxide hydrolase shares significant sequence similarity with several bacterial EHs and mammalian microsomal EHs (mEH) and belongs to the a/${\beta}$ hydrolase fold family. EH from A. niger LK had 90.6% identity with 3D crystal structure of lqo7 in Protein Data Bank. Sequence comparison with other source EHs suggested that Asp$\^$l92/, Asp$\^$374/ and His$\^$374/ constituted the catalytic triad. Based on the multiple sequence comparison of the functional and structural domain sequence, the phylogenetic tree between relevant epoxide hydrolases from various species were reconstructed by using Neighbor-Joining method. Genetic distances were so far as 1.841-2.682 but characteristic oxyanion hole and catalytic triad were highly conserved, which means they have diverged from a common ancestor.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.10
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• pp.1365-1371
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• 2017

Objective: This study was conducted to investigate the basic information on genetic structure and characteristics of Korean Native chickens (NC) and foreign breeds through the analysis of the pure chicken populations and commercial chicken lines of the Hanhyup Company which are popular in the NC market, using the 20 microsatellite markers. Methods: In this study, the genetic diversity and phylogenetic relationships of 445 NC from five different breeds (NC, Leghorn [LH], Cornish [CS], Rhode Island Red [RIR], and Hanhyup [HH] commercial line) were investigated by performing genotyping using 20 microsatellite markers. Results: The highest genetic distance was observed between RIR and LH (18.9%), whereas the lowest genetic distance was observed between HH and NC (2.7%). In the principal coordinates analysis (PCoA) illustrated by the first component, LH was clearly separated from the other groups. The correspondence analysis showed close relationship among individuals belonging to the NC, CS, and HH lines. From the STRUCTURE program, the presence of 5 clusters was detected and it was found that the proportion of membership in the different clusters was almost comparable among the breeds with the exception of one breed (HH), although it was highest in LH (0.987) and lowest in CS (0.578). For the cluster 1 it was high in HH (0.582) and in CS (0.368), while for the cluster 4 it was relatively higher in HH (0.392) than other breeds. Conclusion: Our study showed useful genetic diversity and phylogenetic relationship data that can be utilized for NC breeding and development by the commercial chicken industry to meet consumer demands.