• Korean Journal of Plant Resources
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• v.19 no.5
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• pp.628-633
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• 2006

ITS DNA sequences from five individuals, representative of five groups designated according to the degree of leaf teeth and lobes from simple to palmate compound leaf in the Viola albida complex, established and further analysed in order to solve the taxonomic difficulty. A total 702 bp was sequenced at the 5.8S ribosomal DNA and internal transcribed spacer 1 and 2. The 5.8S coding region is 163 bp, and has no sequence variations. The ITS1 and ITS2 noncoding regions have a little bit sequence variations, and those were further analysed by the methods of the analysis of variance (ANOVA), the analysis of sequence divergence and the phylogenetic analysis. The result of ANOVA showed no significant differences among individuals investigated. The analysis of sequence divergence with Kimura 2-parameter distance revealed that in-groups showed much less than 0.05 in absolute value among individuals, while two out groups more than 0.05, V. grypoceras and V. orientalis. This result appeared that the sequence divergence among in-groups was not yet occurred in the species level but situated at somewhere below the species level. In the phylogenetic analysis, two outgroups formed the basal clades in order. Five individuals in-groups formed a clade. The clade was, however, not very robust as around 50% in bootstrap value, suggesting that this result was not meaningful in the phylogenetic point of views.

• Korean Journal of Plant Resources
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• v.24 no.4
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• pp.358-369
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• 2011

The internal transcribed spacer (ITS) regions of nuclear ribosomal DNA from genus Chrysosplenium were sequenced to address phylogenetic relationship. ITS including 5.8S sequence varied in length from 647 bp to 653 bp. Among them, 219 sites were variable sites with parsimony-informative. The aligned sequences were analyzed by maximum parsimony (MP) and neighbor-joining (NJ) methods. In the strict consensus trees of parsimony analysis, the monophyly of Chrysosplenium was supported by 100% bootstrap value. The first clade, C. pseudofauriei was at the basal position of the genus, and others formed two clades with high bootstrap support. The second clade included Ser. Pilosa and Ser. Oppositifolia and third clade included Ser. Alternifolia and Ser. Flagellifera. The NJ trees showed essentially the same topology. Finally, DNA sequences of ITS regions were useful phylogenetic marker in this genus. Based on the ITS and ridge seed morphological results, C. sphaerospermum Maxim. and C. valdepilosum (Ohwi) S.H. Kang & J.W. Han were discussed their scientific names and taxonomic positions.

• Korean Journal of Microbiology
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• v.32 no.4
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• pp.264-270
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• 1994

A gene coding for a novel putative $\sigma$ factor of RNA polymerase has been identified from Streptomyces coelicolor A3(2) using Escherichia coli rpoS gene fragment as a probe. The 486 bp rpoS gene fragment was amplified from E. coli genomic DNA by PCR with two synthetic oligonucleotides, the sequences of which were deduced from the amino acid sequences in the regions 2.3 and 4.2 conserved among various bacterial factors. When E. coli genomic DNA fragments were hybridized with cloned rpoS probe, only one band corresponding to rpoS gene (3.2 kb PvuII fragment or 2.3 kb KpnI fragment) was detected. In S. coelicolor, however, two bands were detected both in PvuII digested DNA and SalI digested DNA. 3.5 kb PvuII fragment which binds the rpoS gene probe was cloned (pMS1) from the sublibrary, and the nucleotide sequences of 1.0 kb BamH'/HincII subclone (pBH2) was partially determined. The nucleotide sequences revealed extensive similarity to other $\sigma$ factor genes of S. coelicolor (hrdA, hrdB, hrdC, hrdD), S. aureofaciens (hrdA, hrdB, hrdC, hrdD), Synechococcus species, Pseudomonas aeruginosa, Stigmatella aurantiaca, and Anabaena species. The nucleotide sequences in regions 1.2 and 4 were compared with the corresponding regions of 5 known ${\sigma}$ factor genes of S. coelicolor by multiple alignment. It turned out that the cloned gene is most closely related to hrdA showing 88% amino acid similarity in region 1.2 and 75% in region 4.

• Applied Biological Chemistry
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• v.47 no.2
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• pp.182-186
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• 2004

Morphological observation of roots and molecular technique were used to investigate the symbiotic relationships between arbuscular mycorrhizal (AM) fungi and ginseng roots. Korean ginseng, Panax ginseng, was collected from 8 sites in Korea. Colonization pattern of AM fungi in ginseng roots was determined as an Arum type under light microscopes. Nested PCR using AM fungal specific primers was employed to amplify a partial region on 18s rDNA of AM fungi from the root extracted mixed DNA. The amplified DNA was cloned and analyzed by random fragment length polymorphism (RFLP) with restriction enzymes, AluI, HinfI and AsuC21. One from each RFLP pattern was selected for sequencing. A total 16 clones were sequenced and identified as 2 species of AM fungi; Paraglomus brasilianum and Glomus spurcum. Paramglomus brasilianum was found from most of the ginseng roots, in this syudy suggesting that this species of AM fungi could have specific relationship with the ginseng root. Possible roles of AM fungal species in ginseng roots are discussed.

• Korean Journal of Soil Science and Fertilizer
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• v.35 no.1
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• pp.12-26
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• 2002

The phylogenetic relationships for 33 strains belonging to the genera Azorhizobium, Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium were conducted by the sequence analyses of the ITS regions. The sequence homologies of these strains showed the high variations(28.0 - 94.9%). According to the phylogenetic analysis of ITS regions. 37 ITS clones from 33 strains of 32 species were classified into four groups. Group I included all strains of the genus Sinorhizobium as core members and R. giardinii as a peripheral member. The genus Rhizobium strains were clustered into group II which was very heterogeneous and the tree toplogy of this group were very unstable. Among the members of group II. the taxonomic position of R. radiobacter and R. rubi was not clearly identified on the basis of ITS I regions. R. undicola and R. vitis were remotely related with other Rhizobium strains including R. leguminosarum, R. galegae, R. gallicum, R. mongolense, R. tropici, R. hainanense, R. rhizogense and R. huautlense of group II were supposed to be loosely related to R. leguminosarum. While the stains of the genera Bradyrhizobium constituted group III with Azorhizobium caulindans, the strains of the genus Mesorhizobium formed group IV on the relatively high sequence homology level.

• Journal of Life Science
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• v.17 no.12
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• pp.1610-1615
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• 2007

Genus Sorbus is a long lived woody species that is primarily distributed throughout Asia and Europe. This species is regarded as very important herbal medicines in Korea and China. Sorbus commixta is primarily distributed throughout Europe. We evaluated a representative sample of the four taxa with nuclear ribosomal DNA internal transcribed spacer sequences (ITS) to estimate genetic relationships within genus. Aligned nucleotide sequences of the length of ITS1 were nearly constant within genus Sorbus varying from 219 in S. aucuparia to 218 in the rest species. Especially, the 5.8S subunit of all taxa of Sorbus was found to constant of 165 bp nucleotides. However, aligned nucleotide sequences of the length of ITS2 vary from 240 in S. sambucifolia var. pseudogrcilisto 245 in S. aucuparia. Total alignment length is 629 positions, of which 35 are parsimony-informative, 32 variable but parsimony-uninformative, and 552 constant characters. The base furtherance showed the difference to the by a total taxon: an average A and T are 17.7% and G and C are 30.4%, 34.2%, respectively. All the four taxa beginning with conserved base paired triplets emerging from single strand regions (domain I). Noteworthy, in the RNA secondary structure proposed for the three Korean Sorbus taxa RNA transcript ITS2, which shows a remarkedly well-conserved folding (domain II). When compared to the European Sorbus (S. aucuparia) of ITS2. ITS analysis may be useful in germ-plasm classification several taxa of genus Sorbus.

• Journal of fish pathology
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• v.26 no.3
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• pp.149-161
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• 2013

Viral haemorrhagic septicaemia virus (VHSV), the causative agent of viral haemorrhagic septicaemia (VHS), is an epidemic virus of cultured olive flounder Paralichthys olivaceus in Korea. In the present study, the entire glycoprotein (G) gene including several hypervariable regions from 36 isolates of diverse geographic and host origin and 8 Korean VHSV isolates from cultured olive flounder were analyzed. Phylogenetic analysis indicated that most of Asian VHSV belong to the genotype IVa group, suggesting that they originated from a common ancestral virus. Comparative sequence analysis of the complete G protein from Korean VHSV isolates revealed 3 Korean strain-specific nucleotide residues (nucleotide number of G-region: A755, T834 and T1221). These results suggest that Korean VHSV originated from a common ancestor, but these regional specific nucleotide sequences suggest that genetic differences of VHSV are more related to geographic areas than to host fish species.

• Korean Journal of Plant Resources
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• v.34 no.1
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• pp.1-16
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• 2021

The phylogenetic relationships among thirty-two strains (P1~P32; including Cordyceps sp., Paecilomyces sp., Beauveria sp., Aranthomyces sp., Isaria sp. and Himenostilbe sp.) in Miryang region located in the southern part of Korea, were investigated based on internal transcribed spacer (ITS) sequences of ribosomal DNA. A fragment of ITS region was amplified by polymerase chain reaction (PCR) using the specific primer pairs ITS1 and ITS4. After obtained same size of PCR products from various strains, we cloned them into a pGEM-T easy vector to determine their sequences. BLAST analyses of the nucleotide sequence ITS1, 5.8S and ITS2 gene fragments revealed the identity and their phylogenetic relationship. Among 32 strains isolated from Miryang region, Cordyceps militaris was shared 100% sequences with Genbank (AY49191, EU825999, AY491992), while some species are not shared perfectly with reported sequences. For example, strain P17 (P. tenuipes in Ulju-gun Gaji Mountain) has some differences among the other strains of P. tenuipes (Miryang-si Jocheon-eup, Miryang-si Gaji Mountain) and those of gene bank. We conclude that ITS analyses with strains in the suburbs of Miryang in this study can be effectively used as a tool for classification, evaluation and collection of the natural eco-type genetic resources.

• Proceedings of the Korean Information Science Society Conference
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• 2003.04a
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• pp.124-126
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• 2003

생물정보학에서 사용되는 많은 프로그램들은 데이터베이스로 부터 방대한 양의 데이터를 검색하고 처리한다. 이러한 환경에서 사용자의 요청마다 데이터베이스를 검색하는 경우 사용자들의 대기 시간이 길어지고 시스템 용량을 초과한다. 이러한 데이터베이스 액세스의 문제점을 해결하기 위하여 카플 기법과 그룹핑 기법이 제안되었다. 본 논문에서는 카플 기법과 그룹핑 기법을 이용하여 유전자 서열 비교 프로그램인 Fasta를 구현하였고 사용자 응답시간을 측정하여 프로그램의 성능을 높일 수 있음을 확인하였다.

• Proceedings of the Korean Information Science Society Conference
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• 2003.10b
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• pp.766-768
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• 2003

인간 및 다른 생물들의 DNA 서열이 밝혀짐에 따라 DNA 서열 정보를 이용할 수 있는 계산적 처리방식에 대한 요구가 늘어나고 있다. 본 논문에서는 DNA의 패턴을 분류할 수 있는 면역계 부정 선택에 기반한 알고리즘을 제안한다. 부정 선택은 면역세포 생성시 자신을 인식하지 않는 항원 인식부를 생성하기 위한 과정이다. 이 항원 인식부를 통해 자기와 비자기를 구별한다. 이것을 n개의 자기 또는 비자기 집단으로 확장하고 n개의 항원 집단을 구성하면 n개의 패턴 분류가 가능하다. 본 논문에서는 부정 선택에 기반한 DNA 염기 레벨에서의 패턴 분류방법과 아미노산 레벨에서의 패턴분류 방법을 제안한다.