• Korean Journal of Microbiology
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• v.49 no.4
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• pp.383-390
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• 2013

Lateral gene transfer (LGT) of genes from other bacteria into Vibrio cholerae is expectable because of the pronounced natural competence of the bacterium. In this study, quantitative aspects of LGT among the three species of Vibrio pathogenic to humans were characterized. Genome sequences of V. cholerae N16961, V. parahaemolyticus RIMD2210633, V. vulnificus CMCP6, and Escherichia coli K12 substrain MG1655 were analyzed to determine orthologous quartets of protein coding genes present in all four genomes. Phylogenetic analyses on the quartets were conducted to resolve vertical versus lateral patterns of gene polymorphisms based on congruence versus incongruence of phylogenetic trees. About 70% of the quartets could be resolved as either cohesive topology (75%) or LGT tree topologies (25%). The amount of LGT genes in Vibrio spp. appeared to be abnormally high for a genus and comparable to those of families. Patched distributions of LGT from different donors were observed on a chromosome. In the small chromosome of V. cholerae, physical linkages among LGT loci spanned half the length of the chromosome. Either accumulative selection for the donor alleles in LGT or presence of large-scale LGT events was hypothesized. These findings warrant further studies on the nature of donor-specificity of LGT alleles and its influence on evolution of Vibrio virulence to humans.

• Korean Journal of Medicinal Crop Science
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• v.16 no.1
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• pp.20-26
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• 2008

Anemarrhena asphodeloides (Korean name "Ji-Mo") has been used for oriental medicinal purposes in Korea, China and Japan. In this study, 29 A. asphodeloides samples were collected including 3 certified A. asphodeloides plants and many commercially marketed A. asphodeloides products. Chloroplast trnL-F regions of the "Ji-Mo" samples were sequenced and used to identify whether the samples were genuine A. asphodeloides or not. As the result, the trnL-F sequences of all the "Ji-Mo" samples were shown to be identical and it was proven that commercially available medicinal products "Ji-Mo" are genuine A. asphodeloides. Phylogenetic tree of. A. asphodeloides using the trnL-F sequences was constructed and compared with phylogenetic tree using rubisco large subunit (rbcL) gene sequences. In these tree, A. asphodeloides was affiliated in the family Agavaceae in the order Asparagales. It is proven that trnL-F phylogenetic tree is useful to study taxonomic position of A. asphodeloides.

• Animal Systematics, Evolution and Diversity
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• v.1 no.1_2
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• pp.3-20
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• 1985

혹무늬 톡토기과의 56개 아과들에서 20개 형질복합을 추추랗여 형질평가방법과 Wagner algorithm의 형질 비평가방법을 사용하여 계통수를 작성, 비교하였다. 전자의 방법을 이해 진화적 형질순서와 극성을 결정하고 고등급의 파생공유 형질을 토대로한 단계통군과 자매군을 확인하여 계통분화를 추적하였다. 이 두가지 방법에 의한 계통수에서 분지 방식은 매우 다르게 나타났으나 나열순서는 유사했고, 단지 마지막의 2개 아과가 후자에서는 반대로 나타났다. 그 원인은 후자의 방법으로는 파생혈질수가 많은 분류군에서의 형질상태가 Wagner algorithm에서 누적효과를 일으킨 때문인 것으로 생각되며, 아울러 1, 10 및 20 번 형질의 적응이동(adaptive shift) 상 나타낼 중요한 의의를 적절히 평가 반영할 수 없는 것으로 추정된다.

• Journal of Life Science
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• v.26 no.6
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• pp.711-720
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• 2016

To determine the degree of common genes and the phylogenetic relationships among genome-sequenced 680 prokaryotes, the similarities among 4,631 clusters of orthologous groups of protein (COGs)’ presence/ absence and gene content trees were analyzed. The number of COGs was in the range of 103–2,199 (mean 1377.1) among 680 prokaryotes. Candidatus Nasuia deltocephalinicola str. NAS-ALF, an obligate symbiont with insects, showed the minimum COG, while Pseudomonas aeruginosa PAO1, an opportunistic pathogen, represented the maximum COG. The similarities between two prokaryotes were 49.30–99.78 % (mean 72.65%). Methanocaldococcus jannaschii DSM 2661 (hyperthermophilic and autotrophic, Euryarchaeota phylum) and Mesorhizobium loti MAFF303099 (mesophilic and symbiotic, alpha-Proteobacteria class) had the minimum amount of similarities. As gene content may represent the potential for an organism to adapt to each habitat, this may represent the history of prokaryotic evolution or the range of prokaryotic habitats at present on earth. COG content trees represented the following. First, two members of Chloroflexi phylum (Dehalogenimonas lykanthroporepellens BL-DC-9 and Dehalococcoides mccartyi 195) showed a greater relationship with Archaea than other Eubacteria. Second, members of the same phylum or class in the 16S rRNA gene were separated in the COG content tree. Finally, delta- and epsilon-Proteobacteria were in different lineages with other Proteobacteria classes in neighbor-joining (NJ) and maximum likelihood (ML) trees. The results of this study would be valuable to identifying the origins of organisms, functional relationships, and useful genes.

• Korean Journal of Plant Taxonomy
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• v.36 no.3
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• pp.189-207
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• 2006

Goodyera rosulacea, which is morphologically similar to G. repens, is described recently as a new species based on its distinct morphological characters such as rosette-formed leaves, short rhizome and habitat. To verify the taxonomic identity of G. rosulacea and its taxonomic relationship within Korean Goodyera taxa, sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA and the trnL region of cpDNA from 24 accessions including 1 outgroup accession were analyzed. Aligned sequences were analyzed using maximum parsimony and distance method, and the taxonomic identity and the taxonomic relationships among the related taxa were estimated by the existence of private marker gene and the phylogenetic tree of the aligned sequences. Molecular data indicate that G. rosulacea gas several private marker genes and shows monophyly in phylogenetic trees of both ITS and trnL sequences. the pairwise distance between G. rosulacea and the orher taxa of Korean Goodyera was 3.49-6.68% for ITS region and 5.05-9.53% for trnL region, indicating that G. rosulacea could be treated as an independent species. Therefore, our molecular data support the taxonomic of G. rosulacea as a distinct species of Korea. In phylogenetic trees, G. rosulacea formed same clade with G. repens, which has similar morphological characters with G. rosulacea, and showed the lowest pairwise distance with G. repens among Korean Goodyera taxa. These molecular data sugguested that G. rosulacea and G. repens are closely related taxa.

• Research in Plant Disease
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• v.21 no.3
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• pp.235-242
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• 2015

A 2014 nationwide survey in radish fields investigated the distribution of common viruses and possible emerging viruses. Radish leaves with virus-like symptoms were collected and 108 samples assayed by RT-PCR using specific primers for Radish mosaic virus (RaMV), Cucumber mosaic virus (CMV), and Turnip mosaic virus (TuMV); 47 samples were TuMV positive, and RaMV and CMV were detected in 3 and 2 samples, respectively. No samples showed double infection of TuMV/RaMV, or RaMV/CMV, but two double infections of TuMV/CMV were detected. TuMV isolates were sorted by symptom severity, and three isolates (R007-mild; R041 and R065-severe) selected for BLAST and phylogenetic analysis, which indicated that the coat protein (CP) of these isolates (R007, R041, and R065) have approx. 98-99% homology to a previously reported TuMV isolate. RaMV CP showed approx. 99% homology to a previously reported isolate, and the CMV CP is identical to a previously reported Korean isolate (GenBank : GU327368). Three isolates of TuMV showing different pathogenicity (degree of symptom severity) will be valuable to study determinants of pathogenicity.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.5 no.2
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• pp.157-168
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• 2000

Sea urchin S. intermedius occurring in the Korean east coast is a cold water species that belongs to the family Strongylocentrotidae of Echinoidea. Although it is known that there are nine species in the family, species identification criteria, phylogenetic relationships, time and process of evolution of the family members have not been uncovered clearly. In the present study, I tried to find some clues to such problems for S. intermedius by means of DNA sequences. For this, cytochrome c oxidase subunit I (COI), one of the mitochondrial genes that evolve fast and follow maternal inheritance was analyzed. DNA was extracted from the female gonad of S. intermedius, a segment of COI gene amplified by polymerase chain reaction (PCR), and finally a total of 1077 base pair sequence of COI obtained by cloning and sequencing the PCR product. The sequence was compared with homologous genes of other sea urchins and echinoderm species. Phylogenetic trees of the COI gene segment revealed that S. intenedius is a sister species of S. purpuratus which lives along the east coast of the Paciflc. With reference to the fossil records of sea urchins and genetic distances in the molecular phylogenies, it is estimated that the two species were separated about 0.89 million years ago when the earth temperature fluctuated significantly. The current disjunct distribution patterns of the two species and the climate change of the earth at the time of separation suggest that speciation might have occurred by vicariance. The COI gene sequence obtained here now can be used as a molecular character which discerns S. intermedius from the other sea urchin species of Strongylocentrotidae.

• Korean Journal of Plant Taxonomy
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• v.46 no.1
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• pp.1-12
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• 2016

DNA sequences of nrITS regions obtained from 49 accessions representing 12 species and one variety within the section Adonanthe of the genus Adonis were analyzed to test the previous intra-sectional classification system and to determine their phylogenetic relationships. The results showed that the seven accessions of A. amurensis Regel et Radde included in the present study did not form a monophyletic group, as some of the accessions showed a close relationship with the Japanese endemic species A. ramosa Franch., which implies that the current species delimitation and identification of A. amurensis is problematic. Adonis pseudoamurensis W. T. Wang, which is frequently misidentified as A. ramosa in Korea, formed a segregated group, which suggests that they should not be considered as conspecific taxa. Accessions from A. shikokuensis Nishikawa et Koji Ito, A. multiflora Nishikawa et Koji Ito, and A. pseudoamurensis formed a clade, but monophyly of each species was not evident. The nrITS data did not support the classification system proposed by Wang, who classified sect. Adonanthe into four series, as most of these were found to be either polyphyletic or paraphyletic.

• KSBB Journal
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• v.20 no.5 s.94
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• pp.387-391
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• 2005

Totally 16,299 conservative genes, commonly found in 13 thermophilic and hyperthermophilic bacteria, were analyzed. All genes were belong to W 67 COGs (clusters of orthologous groups of proteins). COGs related to protein metabolism were 80 among 167 COGs. Conservative genes were not limited only thermophiles and hyperthermophiles, meaning thermal stability is independent of specific protein. However reverse gyrase was only found in all hyperthermophilic archaebacteria and eubacteria, meaning DNA stability is important in hyperthermophiles. Hyperthermophilic eubacteria and thermophilic archaebacteria had different position between phylogenetic tree of gene content and 165 rRNA gene. Thermophilic archaebacteria hyperthermophilic eubacteria and archaebacteria had similar values by the statistical analysis of distance values with 167 COGs in each organism.

• Proceedings of the Korean Institute of Intelligent Systems Conference
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• 2006.11a
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• pp.75-78
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• 2006

계통발생학적 분석은 바이오인포메틱스에서 분류 단위의 진화적인 관계를 추정하는데 있어서 중요한 문제 중 하나이다. 계통발생학적 분석에서 사용되는 계통수는 분류 단위들 사이의 진화 거리에 대한 정보를 표현하기에는 부족하다. 이 논문은 진화거리 표현을 위해 3차윈 공간으로 분류 단위가 표현되기 위한 방법을 제안하고, 2차원 트리 뷰와 함께 3차원 공간에서 분류 단위들을 시각화하기 위한 도구를 개발하였다.