• 생명과학회지
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• 제22권8호
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• pp.1120-1125
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• 2012

국내에 자생 중인 큰엉겅퀴(Cirsium pendulum)를 강원도의 홍천, 원주, 평창, 양양 및 경기도 가평과 충청북도의 충주에서 채취하고, 고려엉겅퀴(Cirsium setidens)를 강원도의 태백 및 경상북도의 봉화에서 채취하였다. 채취된 식물들의 genomic DNA를 분리하여서 18S rDNA, ITS1, 5.8S rDNA, ITS2 및 28S rDNA의 일부를 증폭하고, 그 염기서열을 분석하였다. 이렇게 얻어진 염기서열을 GenBank에 등록하고, 서로 비교해 보았다. 그 결과 큰엉겅퀴는 6개체 모두에서 18S rDNA 및 5.8S rDNA의 염기서열은 서로 완전히 일치하고 있으나, ITS1과 ITS2의 염기서열에서는 약간의 차이를 보였다. 고려엉겅퀴의 경우에는 18S rDNA, ITS1 및 ITS2에서 2개체가 서로 비교적 큰 차이를 보였다. 일본의 홋카이도에서 채취된 큰엉겅퀴와 중국의 안휘성에서 채취된 엉겅퀴(Cirsium japonicum)를 포함하여서 ITS1과 ITS2 염기서열을 비교한 결과, 엉겅퀴, 큰엉겅퀴, 고려엉겅퀴는 확연하게 서로 다른 그룹을 형성하는 것으로 나타났다. 또한 채취된 큰엉겅퀴 및 고려엉겅퀴들의 silymarin 함량을 분석해 본 결과, 모두에서 그 함량이 2 mg/ml가 넘는 것으로 나타났다. 따라서 엉겅퀴뿐만 아니라 큰엉겅퀴나 고려엉겅퀴도 여러 가지 약리작용을 가진 것으로 보고된 silymarin을 상당히 높은 농도로 함유하고 있는 것으로 나타났다.

• Fisheries and Aquatic Sciences
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• 제15권2호
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• pp.125-135
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• 2012

This study was carried out to understand the correlation between phylogenetic relationships based on 18S rDNA sequences and growth by salinity of Chlorella-like species. The 18S rDNA sequences of 71 Chlorella-like species which were mainly collected from Korean waters were analyzed. The 18S rDNA sequences of Chlorella-like species were divided into three groups (group A, B and C) and group B was further divided into three subgroups (subgroup B-1, B-2 and B-3). Thirty-seven Chlorella-like species in group A grew well at high salinity (32 psu) but the other groups grew well in freshwater. The sequence identities of the species in group A and B were 97.2-99.5%, but those of 6 species in group C ("Chlorella" saccharophila), which contained group I intron sequences region were 75.0-75.4%. Two representative species of each group were cultured at different salinities (0, 16 and 32 psu) to examine the correlation between the molecular phylogenetic groups and the phenotypic characteristics on cell growth and size by different salinities. The size of cell cultured at different salinities varied according to the species of each molecular phylogenetic group. The size of "Chlorella" saccharophila in group C was bigger and more obviously elliptical rather than that of the other Chlorella-like species. Considering the results on molecular and phenotypic characteristics, the group A and B belonged to Chlorellaceae, but group C was distinctly different from them.

• Animal cells and systems
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• 제4권3호
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• pp.257-261
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• 2000

To elucidate phylogenetic relationships among poecilostome families 18S rDNA sequence data were generated for seven poecilostome and one cyclopoid copopods by PCR cloning and sequencing techmiques. Phylogenetic trees were constructed by maximum parsimony, neighbor joining, and maximum likelihood methods using cyclopoid sequence as an outgroup. The results from three different analyses showed that the seven poecilostome families were eiridel into two groups: Clausidiidae-Myicolidae-Synaptiphillidae-bomolochidae and Lichomologidae-Chondracanthidae-Ergasilidae. The molecular phylogenies were consistent with those from the morphological characters. Therefore, these analyses porvide further evidence for the utility of 18S rDNA sequences in addressing phylogenetic relationships among poecilostome families.

• 한국산학기술학회논문지
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• 제18권12호
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• pp.466-472
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• 2017

본 연구의 목적은 곰팡이 28S rDNA 염기서열의 메타분석을 통하여 반추위 곰팡이의 다양성을 조사하는데 있다. 'rumen'과 'ruminal'이 반추위 곰팡이 유래 염기서열들을 회수하기 위한 검색어로 사용되었다. 2016년 9월부로 모든 28S rDNA 염기서열이 보관되어 있는 Ribosomal Database Project(RDP, http://rdp.cme.msu.edu) 데이터베이스에서 반추위 곰팡이 유래 28S rDNA 유전자 염기서열(n=165)을 획득하였다. 총 165개의 염기서열은 분류학상의 '문(phylum)'인 Ascomycota, Neocallimastigomycota 및 Basidiomycota로 분류되었고, 165개의 염기서열 중에서 각각 109개, 48개, 8개의 염기서열을 차지하였다. Ascomycota 염기서열은 식물병원성곰팡이나 마이코톡신을 생성하는 곰팡이를 포함하고 있는 '속(genus)' Pseudonectria, Magnaporthe, Alternaria, Cochliobolus, Cladosporium 및 Davidiella로 분류되었다. 또한, Basidiomycota 염기서열은 식물병원성곰팡이를 포함하고 있는 '속(genus)' Thanatephorus와 Cryptococcus로 분류되었다. 뿐만 아니라, Neocallimastigomycota 염기서열의 경우 섭취된 조사료의 주요 구조탄수화물을 분해하는 '속(genus)' Cyllamyces, Neocallimastix, Anaeromyces, Caecomyces, Orpinomyces, Piromyces로 분류되었다. 본 연구는 처음으로 28S rDNA 염기서열의 메타분석을 통해 반추위 곰팡이 다양성에 대한 정보를 통합적으로 제공하였다. 본 연구의 결과는 향후 반추위 곰팡이 연구에 대한 방향을 제공할 것이고, 새로운 분석도구 개발에 응용될 수 있을 것이다.

• ALGAE
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• 제35권3호
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• pp.293-301
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• 2020

The applications of DNA barcoding have a wide range of uses, such as in taxonomic studies to help elucidate cryptic species and phylogenetic relationships and analyzing environmental samples for biodiversity monitoring and conservation assessments of species. After obtaining the DNA barcode sequences, sequence similarity-based homology analysis is commonly used. This means that the obtained barcode sequences are compared to the DNA barcode reference databases. This bioinformatic analysis necessarily implies that the overall quantity and quality of the reference databases must be stringently monitored to not have an adverse impact on the accuracy of species identification. With the development of next-generation sequencing techniques, a noticeably large number of DNA barcode sequences have been produced and are stored in online databases, but their degree of validity, accuracy, and reliability have not been extensively investigated. In this study, we investigated the extent to which the amount and types of erroneous barcode sequences were deposited in publicly accessible databases. Over 4.1 million sequences were investigated in three largescale DNA barcode databases (NCBI GenBank, Barcode of Life Data System [BOLD], and Protist Ribosomal Reference database [PR2]) for four major DNA barcodes (cytochrome c oxidase subunit 1 [COI], internal transcribed spacer [ITS], ribulose bisphosphate carboxylase large chain [rbcL], and 18S ribosomal RNA [18S rRNA]); approximately 2% of erroneous barcode sequences were found and their taxonomic distributions were uneven. Consequently, our present findings provide compelling evidence of data quality problems along with insufficient and unreliable annotation of taxonomic data in DNA barcode databases. Therefore, we suggest that if ambiguous taxa are presented during barcoding analysis, further validation with other DNA barcode loci or morphological characters should be mandated.

• ALGAE
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• 제24권4호
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• pp.205-212
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• 2009

Molecular genetic tools are widely used to learn more about the identical characterization of obscure microalgal strains. At the Korea Marine Microalgae Culture Center (KMMCC), the authors deduced the genetic relationship of 41 strains of the genus Tetraselmis by analysing a small subunit ribosomal DNA (18S rDNA) sequences. Forty-one strains were seperated into five groups, which showed over a 98-99% similarity to Tetraselmis striata or Tetraselmis sp. Tsbre. Also, 13 strains among them had an identical genotype to Tetraselmis striata while 5 strains had with Tetraselmis sp. Tsbre, respectively. The mean size of each strain generally showed the tendency of different variation according to the groups.

• Journal of Microbiology
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• 제35권2호
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• pp.79-86
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• 1997

For the phylogenetic study of the genus Trichaptum, nuclear ribosomal DNA sequences from eight strains of four Trichaptium species were examined. Phylogenetic trees were constructed using molecular data on 18 rDNA and 5.8S rDNA and thei ITSs. Parsimony analyses of the Trichaptum species showed that T. biforme and T. laricinum made a monophyletic group respectively, suggesting that each species is phylogenetically independent. However, T. abietum represented a polyphyletic group and T. fusco-violaceum formed a polytomous group, suggesting that these species could be in the process of evolutionary differentiation. Examination of base substitutions of the 18S rRNA gene reveals that the C-T transition is most predominant and that there is a stronger transition bias between closely related organisms rather than between distantly related ones.

• Parasites, Hosts and Diseases
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• 제44권2호
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• pp.117-125
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• 2006

Genetic diversity of 18 Acanthamoeba isolates from ocean sediments was evaluated by comparing mitochondrial (mt) DNA RFLP, 18S rDNA sequences and by examining their cytopathic effects on human corneal epithelial cells versus reference strains. All isolates belonged to morphologic group II. Total of 16 restriction phenotypes of mtDNA from 18 isolates demonstrated the genetic diversity of Acanthamoeba in ocean sediments. Phylogenetic analysis using 18s rDNA sequences revealed that the 18 isolates were distinct from morphological groups I and III. Fifteen isolates showed close relatedness with 17 clinical isolates and A. castellanii Castellani and formed a lineage equivalent to T4 genotype of Byers' group. Two reference strains from ocean sediment, A. hatchetti BH-2 and A. griffini S-7 clustered unequivocally with these 15 isolates. Diversity among isolates was also evident from their cytopathic effects on human corneal cells. This is the first time describing Acanthamoeba diversity in ocean sediments in Korea.

• Animal Systematics, Evolution and Diversity
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• 제38권3호
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• pp.144-147
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• 2022

The polychaete Scolelepis (Scolelepis) sagittaria was originally described from Japanese waters and subsequently reported from Korean waters. In this study, we determined for the first time the mitochondrial cytochrome c oxidase subunit I (COI), 16S ribosomal DNA (16S rDNA), and nuclear 18S ribosomal DNA (18S rDNA) sequences of Korean specimens of S. (S.) sagittaria. We also assessed intraspecific variation in the shape of the prostomium of this species based on an examination of 247 individuals. All materials were collected from intertidal sandy beaches of the Korea Strait. The molecular data and morphological observations reported herein will contribute to gaining a better understanding of the taxonomic relationships among members of the genus Scolelepis.

• Animal Systematics, Evolution and Diversity
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• 제37권4호
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• pp.349-353
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• 2021

Scolelepis (Parascolelepis) papillosa (Okuda, 1937), originally described from a single incomplete individual from Jeju Island in Korea, was collected from the intertidal sandflats of Soan Island (Jeollanam-do province) in Korea. The examined specimens of S. (P.) papillosa agree well with the original description in having the papillae on the basal sheath of the palps, presence of occipital antenna, absence of notochaetae in chaetiger 1, branchiae completely fused with notopodial postchaetal lamellae at the anterior chaetigers, and neuropodial hooded hooks appearing from chaetiger 16. In this study, the sequences of partial mitochondrial cytochrome c oxidase subunit I (COI), 16S ribosomal DNA (16S rDNA), and the nuclear 18S ribosomal DNA (18S rDNA) of the species were determined. We also provide the detailed description and illustrations on this species based on the complete specimens newly collected in this study.