• Title/Summary/Keyword: Phylogenetic group

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Virulence Differentiation of Eight Turnip mosaic virus Isolates Infecting Cruciferous Crops

  • Choi, Hong-Soo;Sohn, Seong-Han;Yoon, Moo-Kyoung;Cheon, Jeong-Uk;Kim, Jeong-Soo;Were, Hassan Karakacha;Cho, Jang-Kyung;Kim, Kook-Hyung;Takanami, Yoichi
    • The Plant Pathology Journal
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    • v.21 no.4
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    • pp.369-376
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    • 2005
  • Turnip mosaic virus (TuMV) is an infectious viral pathogen on the cruciferous crops, predominantly Chinese cabbage (Brassica campestris subsp. pekinensis) and radish (Raphanus sativus). On the basis of the symptom development in selective differential hosts from indicator host species, Chinese cabbage and Korean radish inbred lines, the representative eight isolates of TuMV were divided into two major groups/or six types. Group I includes Th 1, Ca-ad7, and Cj-ca2-1 isolates, while group II includes the other isolates (rg-pfl, r 9-10, Rhcql-2, Stock and Mustard). According to the molecular phylogenetic analysis, these isolates, however, divided into two groups and two independent isolates. Phylogenetic analysis indicated that four isolates (Tu 1, r9-10, Stock and Rh-cql-2) formed a distinct phylogenetic group, and the other two isolates (Ca-ad7 and Cj-ca2-1) also formed another group. Mustard and rg-pfl isolates did not seem to have any relationship with these two groups. Taken together, these results indicated that virulence differentiation on host plants, molecular phylogenetic analysis of the nucleotide and the deduced amino acid of TuMV coat proteins did not show any relationship. The multi-resistant lines, Wonyae 20026 and BP058 in Chinese cabbage represent valuable genetic materials that can be used for crucifer breeding programs on TuMV resistance, but not in Korean radish.

Molecular Discrimination of Mitis Group Streptococci Isolated from Koreans using RpoB Nucleotide Sequences

  • Park, Soon-Nang;Kook, Joong-Ki
    • International Journal of Oral Biology
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    • v.38 no.1
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    • pp.29-36
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    • 2013
  • Mitis group streptococci (MGS) were classified based on the nucleotide sequences 16S rRNA gene (16S rDNA) and comprised 13 Streptococcus species. However, 16S rDNA homogeneity among MGS was too high to discriminate between clinical strains at the species level, notably between Streptococcus mitis, Streptococcus oralis, Streptococcus pneumoniae, and Streptococcus pseudopneumoniae. The purpose of this study was to discriminate between 37 strains of MGS isolated from Korean oral cavities using phylogenetic analysis of the DNA-dependant RNA polymerase beta-subunit gene (rpoB). 16S rDNA and rpoB from clinical strains of MGS were sequenced using the dideoxy chain termination method and analyzed using MEGA version 5 software. The resulting phylogenetic data showed that the rpoB sequences could delineate clinical strains of MGS at the species level. Phylogenetic analysis of rpoB is therefore a useful approach for identifying MGS at the species level.

Evidence on the Presence of $tRNA^{fMet}$ Group I Intron in the Marine Cyanobacterium Synechococcus elongatus

  • Muralitharan, Gangatharan;Thajuddin, Nooruddin
    • Journal of Microbiology and Biotechnology
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    • v.18 no.1
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    • pp.23-27
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    • 2008
  • Self-splicing group I introns in tRNA anticodon loops have been found in diverse groups of bacteria. In this work, we identified $tRNA^{fMet}$ group I introns in six strains of marine Synechococcus elongatus. Introns with sizes around 280 bp were consistently obtained in all the strains tested. In a phylogenetic analysis using the nucleotide sequence determined in this study with other cyanobacterial $tRNA^{fMet}$ and $tRNA^{Leu}$ intron sequences, the Synechococcus sequence was grouped together with the sequences from other unicellular cyanobacterial strains. Interestingly, the phylogenetic tree inferred from the intronic sequences clearly separates the different tRNA introns, suggesting that each family has its own evolutionary history.

Phylogenetic Analysis of Reticulitermes speratus using the Mitochondrial Cytochrome C Oxidase Subunit I Gene

  • Cho, Moon-Jung;Shin, Keum;Kim, Young-Kyoon;Kim, Yeong-Suk;Kim, Tae-Jong
    • Journal of the Korean Wood Science and Technology
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    • v.38 no.2
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    • pp.135-139
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    • 2010
  • Reticulitermes speratus is commonly found in Asia, including Korea and Japan. We recently analyzed the 5' region of mitochondrial cytochrome c oxidase subunit I to perform a phylogenetic analysis of R. speratus KMT1, isolated in Seoul, Korea. Our results, using COXI, suggest that the taxonomy of R. speratus should be reconsidered with regard to the subgenus group. A similar phylogenetic analysis by COXI and COXII demonstrated the reliability of COXI genetic information in a molecular phylogenetic analysis of termites.

Phylogenetic Relationships of the Fireflies Co-occurring in Korean and Japanese Territories Analyzed by Luciferase and Mitochondrial DNA Sequences

  • Kim, Iksoo;Kim, Jong Gill;Jin, Byung Rae
    • International Journal of Industrial Entomology and Biomaterials
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    • v.9 no.2
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    • pp.155-165
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    • 2004
  • In Korean Peninsula including neighboring islands and Japanese Islands identical firefly species or the species belonging to same genera occur together in both territories. These geographic firefly species, nonetheless, have never been subject to taxonomic consideration together until recently, lacking clear species status and phylogenetic relationships. A recent serial study of these fireflies using luciferase gene and/or portions of mitochondrial DNA sequences provided some insight into these populations in terms of validity of species name, phylogenetic relationships, and speciation event. In this article, thus, we have reviewed the recent progress on phylogenetic and/or population genetic aspects of these species, i.e., Hotaria-group fireflies, Luciola lateralis, and Pyrocoelia rufa to better understand the firefly species in these regions.

Correlation Between Sorangium cellulosum Subgroups and Their Potential for Secondary Metabolite Production

  • Lee, Chayul;An, Dongju;Lee, Hanbit;Cho, Kyungyun
    • Journal of Microbiology and Biotechnology
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    • v.23 no.3
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    • pp.297-303
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    • 2013
  • Phylogenetic analysis of the groEL1 and xynB1 gene sequences from Sorangium cellulosum strains isolated in Korea previously revealed the existence of at least 5 subgroups (A-E). In the present study, we used sequence analysis of polymerase chain reaction-amplified biosynthetic genes of strains from the 5 subgroups to indicate correlations between S. cellulosum subgroups and their secondary metabolic gene categories. We detected putative biosynthetic genes for disorazol, epothilone, ambruticin, and soraphen in group A, group C, group D, and group E strains, respectively. With the exception of KYC3204, culture extracts from group A, group B, and group C strains exhibited no noticeable antimicrobial inhibitory activities. By contrast, culture extracts from group D strains inhibited the growth of Candida albicans, whereas culture extracts from group E strains inhibited the growth of C. albicans and Staphylococcus aureus. High performance liquid chromatography analysis of the culture extracts from the strains of each subgroup revealed unique peak patterns. Our findings indicate the existence of at least 5 subgroups of S. cellulosum strains, each of which has the potential to produce a unique set of secondary metabolites.

Molecular Systematics of Tephritidae (Insecta : Diptera): Testing Phylogenetic Position of Korean Acidiella spp. (Trypetini) Using Mitochondrial 16S rDNA Sequences

  • Han, Ho-Yeon;Ro, Kyung-Eui
    • Animal cells and systems
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    • v.6 no.1
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    • pp.13-18
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    • 2002
  • Phylogenetic relationships of Korean Acidiella species were tested using mitochondrial 16S ribosomal RNA gene sequences. We used 16 published sequences as outgroup, and 10 new sequences for nine Korean Acidiella species as ingroup. The number of aligned sites was 1,281 bp, but 1,135 bp were used for the analysis after excluding sites with missing data or gaps. Among these 1,135 sites, 464 sites were variable and 340 were informative for parsimony analysis. Phylogenetic information was extracted from this data set using neighbor-joining, maximum likelihood and maximum parsimony methods and compared to a morphology-based phylogenetic hypothesis. Our molecular data suggest that: (1) the tribe Trypetini appears to be monophyletic even when the nine additional Acidiella species are added to our previous phylogenetic analysis; (2) all the Korean Acidiella species belong to the Trypeta group, but the genus Acidiella is not supported as monophyletic; (3) the close relationship of A. circumvaga, A. issikii, and A. sapporensis is supported; (4) the close relationship of A. pachypogon and two additional new Acidiella species is strongly supported; and (5) the possible presence of two or more cryptic species among the specimens previously identified as A. obscuripennis is suggested. Sequence data from the mitochondrial 16S rDNA allowed us to better understand the systematic status of Korean Acidiella species. They indicated that the current concept about the genus Acidiella is insufficient and needs to be refined further. This study also showed a few interesting relationships, that had not been recognized by morphological study alone. Based on this study, we were able to plan further experiments to analyze relationships within the Trypeta Group.

Comparison of O-serogroups, Virulence Factors and Phylogenetic Groups of Uropathogenic Escherichia coli Isolated from Patients with Urinary Tract Infections between 2 Time Periods of 1989 and 2010-2014 at Gangwon Province in Korea

  • Park, Min;Kim, Seong-Mi
    • Biomedical Science Letters
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    • v.28 no.2
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    • pp.127-136
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    • 2022
  • Uropathogenic Escherichia coli (UPEC) is main causative agent of urinary tract infections. They are classified based on various types of O antigen. UPEC strains commonly possess many genes encoding virulece-associated factors. E. coli strains are generally divided into four main phylogenetic groups. The virulence factor (VF) profiles of UPEC are related with their O-serogroups in each strains. A total of 681 strains of UPEC clinical isolates were collected from Korean healthcare facility (1989: 123 strains and 2010-2014: 558 strains). The UPEC clinical isolates were analyzed by polymerase chain reaction (PCR) methods. A total of 14 O-serotypes (O1, O2, O4, O6, O7, O8, O15, O16, O18, O21, O22, O25, O75 and O83), 6 virulence factors (papC, fimG/H, sfaD/E, hly1, cnf1 and usp) and phylogenetic groups were identified. The most prevalent O-serogroups were O6 (11.1%) in 1989 UPEC strains and O25 (21.0%) in 2010-2014 UPEC strains. The identified VFs, phylogenetic groups in 1989 UPEC strains and 2010-2014 UPEC strains were fimG/H and B2 group. In this study, O6 serotype was revealed the close relationships with VFs. Also, the distribution of prevalence O-serogroups of UPEC has been changed from O6 to O25 and virulence of UPEC strains was increased during past twenty-one years.

Molecular Authentication and Phylogenetic Analysis of Plant Species for Breeae and Cirsii Herba based on DNA barcodes (DNA 바코드 분석을 통한 소계(小薊) 및 대계(大薊) 기원식물 감별과 종간 유연관계 분석)

  • Moon, Byeong Cheol;Lee, Young Mi;Ji, Yunui;Choi, Goya;Chun, Jin Mi;Kim, Ho Kyoung
    • The Korea Journal of Herbology
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    • v.28 no.3
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    • pp.75-84
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    • 2013
  • Objectives : The origin of Breeae Herba (So-gye) and Cirsii Herba (Dae-gye) is differently prescribed in Korean and Chinese modern pharmacopoeia. Since the similar morphological characteristics and chaotic plant names, moreover, the aerial part of Carduus crispus have been used as the Cirsii Herba. To develop a reliable method for correct identification of these herbal medicines and to evaluate the genetic relationship of these closely related plant species, we analyzed sequences of DNA barcode regions. Methods : Thirty-one samples of 6 medicinal plants (B. segeta, B. setosa, C. japonicum var. maackii, C. setidens, C. chanroenicum, and C. crispus) were collected from different habitate and nucleotide sequences of DNA barcode regions (rDNA-ITS, matK, and rbcL) were analyzed after amplification using appropriate primers reported in previous studies. The nucleotides of species-specific authentic marker and phylogenetic relations were estimated based on the entire sequences of DNA barcodes by the analysis of ClastalW and UPGMA, respectively. Results : In comparative analysis of DNA barcode sequences, we obtained specific nucleotides to discriminate the medicinal plant of Breeae/Cirsii Herba in species level and evaluated the phylogenetic relationship of these species. Futhermore, we identified distinct marker nucleotides enough to authenticate respective species. These sequence differences at corresponding positions were avaliable genetic markers to determine the botanical origins of Breeae Herbal as well as Cirsii Herba. Conclusions : These marker nucleotides would be useful to identify the official herbal medicines by providing of definitive information that can identify each plant species and distinguish from unauthentic adulterants and substitutes.

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.