• Title, Summary, Keyword: 16S rDNA

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Mixed Infection of 16S rDNA I and V Groups of Phytoplasma in a Single Jujube Tree

  • Lee, Sang-Hun;Han, Sang-Sub;Cha, Byeong-Jin
    • The Plant Pathology Journal
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    • v.25 no.1
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    • pp.21-25
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    • 2009
  • Jujube trees infected with phytoplasma exhibit symptoms of typical witches' broom, such as yellowing, abnormally small leaves, short internodes and proliferation of shoots. A 1.2 kb fragment of the 16S rDNA from jujube phytoplasma was generated by R16F2n/R16R2 primer pair from earlier amplified P1/P7 PCR products of cloned jujube witches' broom phytoplasmas. Enzymatic restriction fragment length polymorphism (RFLP) and sequence analysis of 16S rDNA revealed that the jujube tree was infected with 16S rDNA I and V groups of phytoplasmas. Extensive comparative analyses of restriction enzyme profiles from Alu I, Hha I, Msp I, and Rsa I clearly classified the two into different phytoplasma groups. The phylogenie analyses based on 16S rDNA showed that the similarity of the two different clones was 87.5%. This is the first report of a mixed phytoplasmal infection in a single jujube tree.

Application of rDNA-PCR Amplification and DGGE Fingerprinting for Detection of Microbial Diversity in a Malaysian Crude Oil

  • Liew, Pauline Woan Ying;Jong, Bor Chyan
    • Journal of Microbiology and Biotechnology
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    • v.18 no.5
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    • pp.815-820
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    • 2008
  • Two culture-independent methods, namely ribosomal DNA libraries and denaturing gradient gel electrophoresis (DGGE), were adopted to examine the microbial community of a Malaysian light crude oil. In this study, both 16S and 18S rDNAs were PCR-amplified from bulk DNA of crude oil samples, cloned, and sequenced. Analyses of restriction fragment length polymorphism (RFLP) and phylogenetics clustered the 16S and 18S rDNA sequences into seven and six groups, respectively. The ribosomal DNA sequences obtained showed sequence similarity between 90 to 100% to those available in the GenBank database. The closest relatives documented for the 16S rDNAs include member species of Thermoincola and Rhodopseudomonas, whereas the closest fungal relatives include Acremonium, Ceriporiopsis, Xeromyces, Lecythophora, and Candida. Others were affiliated to uncultured bacteria and uncultured ascomycete. The 16S rDNA library demonstrated predomination by a single uncultured bacterial type by >80% relative abundance. The predomination was confirmed by DGGE analysis.

Using Reverse Dot Hybridization Method and 16S rRNA Gene (16S rDNA) for Identifying the Food Poisoning Microorganism in Foods (Reverse dot hybridization 방법과 16S rRNA gene(16S rDNA)을 이용한 식품에서 식중독균의 탐색)

  • Kim, Min-Seong;Shin, Kyu-Chul;Lee, Hyung-Gu;Han, Myung-Soo;Min, Byung-Re;Choi, Yong-Keel
    • Korean Journal of Food Science and Technology
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    • v.35 no.3
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    • pp.470-474
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    • 2003
  • DNA sequence information on small-subunit rRNA gene (16S rDNA) obtained from food-poisoning bacterial culture was used to investigate the presence of bacterial pathogens in food. By reverse dot blot detection method, presence of food-poisoning bacteria could be confirmed on hybridization of digoxigenin-labeled 16S rDNA Polymerase Chain Reaction (PCR) primer product and biotin-labeled specific oligonucleotide probe. Escherichia coli, Bacillus cereus. and Salmonella sp. were used as the representative food-poisoning bacterial microorganisms. An oligonucleotide probe, based on the variable region of 16S rRNA gene, was used as the specific probe. These tools may be more useful than classic biochemical method for rapid identification of contaminated food.

Species Identification of Five Penaeid Shrimps Using PCR-RFLP and SSCP Analyses of 16S Ribosomal DNA

  • Khamnamtong, Bavornlak;Klinbunga, Sirawut;Menasveta, Piamsak
    • BMB Reports
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    • v.38 no.4
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    • pp.491-499
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    • 2005
  • DNA-based molecular markers for differentiation of five penaeid shrimps (Penaeus monodon, P. semisulcatus, Feneropenaeus merguiensis, Litopenaeus vannamei and Marsupenaeus japonicus) were developed based on polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and single-stranded conformation polymorphism (SSCP) of 16S ribosomal (r) DNA. Differentiation of P. monodon, P. semisulcatus and L. vannamei can be unambiguously carried out by PCR-RFLP of 16S $rDNA_{560}$ whereas P. semisulcatus and M. japonicus shared a BABB mitotype. These shrimps were successfully discriminated by SSCP analysis of 16S $rDNA_{560}$. Nevertheless, the amplification success for L. vannamei and F. merguiensis was not consistent when tested against larger sample sizes. As a result, 16S $rDNA_{560}$ of an individual representing the most common mitotype of each species was cloned and sequenced. The new primer pair was designed and tested against the large sample sizes (312 bp product, N = 185). The amplification success was consistent across all species. PCR-RFLP of 16S $rDNA_{312}$ was as effective as that of 16S $rDNA_{560}$. Differentiation of all shrimp species were successfully carried out by SSCP analysis.

Molecular Systematics of the Tephritoidea (Insecta: Diptera): Phylogenetic Signal in 16S and 28S rDNAs for Inferring Relationships Among Families

  • Han, Ho-Yeon;Ro, Kyung-Eui;Choi, Deuk-Soo;Kim, Sam-Kyu
    • Animal cells and systems
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    • v.6 no.2
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    • pp.145-151
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    • 2002
  • Phylogenetic signal present in the mitochondrial 16S ribosomal RNA gene (16S rDNA) and the nuclear large subunit ribosomal RNA gene (28S rDNA) was explored to assess their utility in resolving family level relationships of the superfamily Tephritoidea. These two genes were chosen because they appear to evolve at different rates, and might contribute to resolve both shallow and deeper phylogenetic branches within a highly diversified group. For the 16S rDNA data set, the number of aligned sites was 1,258 bp, but 1,204 bp were used for analysis after excluding sites of ambiguous alignment. Among these 1,204 sites, 662 sites were variable and 450 sites were informative for parsimony analysis. For the 28S rDNA data set, the number of aligned sites was 1,102 bp, but 1,000 bp were used for analysis after excluding sites of ambiguous alignment. Among these 1000 sites, 235 sites were variable and 95 sites were informative for parsimony analysis. Our analyses suggest that: (1) while 16S rDNA is useful for resolving more recent phylogenetic divergences, 28S rDNA can be used to define much deeper phylogenetic branches; (2) the combined analysis of the 16S and 28S rDNAs enhances the overall resolution without losing phylogenetic signal from either single gene analysis; and (3) additional genes that evolve at intermediate rates between the 16S and 28S rDNAs are needed to further resolve relationships among the tephritoid families.

Molecular Identification of Anginosus Group Streptococci Isolated from Korean Oral Cavities

  • Park, Soon-Nang;Choi, Mi-Hwa;Kook, Joong-Ki
    • 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.

Differentiation of Major Rice-Seedborne Bacteria by PCR-Amplified Polymorphism of Spacer Region Between 16S and 23S Ribosomal DNA (PCR로 증폭된 16S와 23S rDNA 사이 Spacer 부위의 다형성에 의한 주요 벼종자전염성 세균의 구별)

  • 김형무;송완엽
    • Korean Journal Plant Pathology
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    • v.12 no.1
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    • pp.11-20
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    • 1996
  • 한 쌍의 R16-1과 R23-2R primer를 이용한 PCR에 의해 증폭된 16S와 23S rDNA 사이의 rDNA spacer 부위의 다형성들이 Pseudomonas avenae, P. glumae, P. fuscovaginae, P. syringae pv. syrngae, Xanthomonas oryzae pv. oryzae, X. oryzae, Xanthomonas herbicola 등 벼 종자전염성 51개 균주의 구분을 위하여 적용되었다. 증폭산물은 820∼950bp의 크기였으며, 각각의 종에 특이적이었고 구분이 가능하였다. Pseudomonas species의 증폭산물은 P. avenae는 950bp, P. glumae는 850bp, P. fuscovaginae는 770pb 및 P. syringae pv. syringae는 1,240, 1,100 및 820bp로 특이적이었다. P. avenae와 P. glumae의 국내균주들은 다형성에 있어 종내 변이는 없었다. X. oryzae pv. oryzae의 860bp와 X. oryzae pv. oryzicola의 890, 440 및 370bp의 이차산물에서 Xanthomonas species의 종내에서 균주에 관련없이 단일화된 다형성을 보였다. CXO 211을 제외한 모든 국내 균주는 a형에 속한 반면 하나의 국내 균주를 포함하여 4개 균주는 b형이었다. E. herbicola의 spacer 부위 증폭은 여러 개의 band를 보였으며, 증폭상은 각각 동일하였고, strain간의 종내 변이는 없었다. 본 실험 결과에 의하여 16S와 23S rDNAdp R16-1과 R23-2R primer를 이용하여 PCR 증폭된 spacer 다형성의 구별은 종자전염성 세균의 신속한 구별에 이용될 수 있을것이다.

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Detection and Molecular Characterization of a Stolbur Phytoplasma in Lilium Oriental Hybrids

  • Chung, Bong-Nam;Jeong, Myeong-Il
    • The Plant Pathology Journal
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    • v.19 no.2
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    • pp.106-110
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    • 2003
  • Stolbur Phytoplasma was detected from Lilium Oriental hybrids showing flattened stem and flower clustering. The presence of phytoplasma was demonstrated using polymerase chain reaction(PCR) assays with phyto-plasma-universal(P1/P6)and stolbur phytoplasma-specific 16F1/R1-S primer pairs amplifying phytoplasma 16S rDNA regions. Nucleotide suquences of the phytoplasma 16S rDNA were determined. Nucleic acid extracted from lily amplified 1.5 kb DNA with a phytoplasma universal primer pair. In nested PCR, 1.1 kb PCR product was obtained using specific primer pair, indicating an isolate of stolbur phytoplasma. Nucleotide sequence of phytoplasma 16S rDNA reported in this study showed 99.5% and 99.1% identities with two known stolbur phytoplamas (16Sr XII-A). Also, it exhibited a sequence homology of 98.0% with phormium yellow leaf (16Sr XII-B), and 97.9% with Australian grapevine yellows (16Sr XII-B). Meanwhile, it showed 98.1% identity with strawberry green petal phytoplama, (16Sr1-C), and 94.7 % with American aster yellows (16Sr1-B). Homology percentage of the 16S rDNA nucleotide sequence suggests that this phytoplama could be classified into the stolbur phytoplasma, subgroup A (16Sr XII-A), as a type strain stolbur.

Phylogenetic Relationship Among Four Species of Korean Oysters Based on Mitochondrial 16S rDNA and COI Gene (미토콘드리아 16S rDNA와 COI유전자에 근거한 한국산 굴류 4종의 유연관계)

  • 이상엽;박두원;안혜숙;김상해
    • Animal Systematics, Evolution and Diversity
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    • v.16 no.2
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    • pp.203-211
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    • 2000
  • Partial mitochondrial 16S rDNA and COI gene were amplified using PCR and sequenced for four species of oysters in Korea. Phylogenetic relationships among them were inferred from their aligned sequences by neighbor-joining method. The sequence comparison data of two mitochondrial genes showed that the genetic distinction between two oyster genera (Crassostreo and Ostrea) was obvious. Phylogenetic analysis based on the nucleotide sequences and A+T percentage of two genes indicates that C. gigas and C. nippona strongly formed a sister group and then C. ariakensis was clustered with the clade although that based on amino acid sequences of COI gene by neighbor-joining method represented different phylogenetic tree.

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Identification of Bacteria Causing Fermentation of Oriental Melon in Korea (참외 발효과를 유발하는 세균의 동정)

  • Choi, Jae-Eul;Cha, Sun-Kyung;Kim, Jin-Hee;Yuk, Jin-Ah;Hwang, Yong-Soo;Kwon, Soon-Wo
    • Research in Plant Disease
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    • v.9 no.4
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    • pp.189-195
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    • 2003
  • Bacteria causing fermentation in Oriental melon were identified as three independent groups on the basis of 16S rDNA sequence analysis. The 16S rDNA sequence of the strain CM2105 showed the highest identity (99.6%) with that of Microbacterium phyllosphaerae, and also indicated high sequence identity to that of M. holiorum (99.5%). The 16S rDNA sequences of the strain CM2101 and CM2121 matched at the high sequence similarity (98.9%, 98.8, respectively), to that of Pseudomonas pavonacea, and the DNA sequence of CM2126 showed high sequence identity to that of P. costantinii (99.5%), and P. grimontii (99.0%). The 16S rDNA sequence of the strain CM2113 showed the highest identity (99.7%) with that of Enterobacter cloacae. The 16S rDNA sequences, the physiological and biochemical analysis suggested that the strain CM2105 belonged to Microbacterium phyllosphaerae, CM2101, CM2121 and CM2126 to Pseudomonas spp., CM2113 to Enterobacter cloacae.