메뉴 건너뛰기




Volumn 57, Issue 2, 2007, Pages 276-286

Congruence of evolutionary relationships inside the Leuconostoc-Oenococcus-Wiessella clade assessed by phylogenetic analysis of the 16S rRNA gene, dnaA, gyrB, rpoC and dnaK

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; DNA DIRECTED DNA POLYMERASE BETA; DNA TOPOISOMERASE (ATP HYDROLYSING) B; PROTEIN DNAK; REPLICATION INITIATOR PROTEIN DNAA; RNA 16S;

EID: 33847198333     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.64468-0     Document Type: Article
Times cited : (55)

References (39)
  • 1
    • 9744231340 scopus 로고    scopus 로고
    • Dissection of phylogenetic relationships among 19 rapidly growing Mycobacterium species by 16S rRNA, hsp65, sodA, recA and rpoB gene sequencing
    • Adékambi, T. & Drancourt, M. (2004). Dissection of phylogenetic relationships among 19 rapidly growing Mycobacterium species by 16S rRNA, hsp65, sodA, recA and rpoB gene sequencing. Int J Syst Evol Microbiol 54, 2095-2105.
    • (2004) Int J Syst Evol Microbiol , vol.54 , pp. 2095-2105
    • Adékambi, T.1    Drancourt, M.2
  • 2
    • 0037329391 scopus 로고    scopus 로고
    • Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence
    • Alfaro, M. E., Zoller, S. & Lutzoni, F. (2003). Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol Biol Evol 20, 255-266.
    • (2003) Mol Biol Evol , vol.20 , pp. 255-266
    • Alfaro, M.E.1    Zoller, S.2    Lutzoni, F.3
  • 3
    • 0036206183 scopus 로고    scopus 로고
    • Leuconostoc ficulneum sp. nov., a novel lactic acid bacterium isolated from a ripe fig, and reclassification of Lactobacillus fructosus as Leuconostoc fructosum comb. nov
    • Antunes, A., Rainey, F. A., Nobre, M. F., Schumann, P., Ferreira, A. M., Ramos, A., Santos, H. & da Costa, M. S. (2002). Leuconostoc ficulneum sp. nov., a novel lactic acid bacterium isolated from a ripe fig, and reclassification of Lactobacillus fructosus as Leuconostoc fructosum comb. nov. Int J Syst Evol Microbiol 52, 647-655.
    • (2002) Int J Syst Evol Microbiol , vol.52 , pp. 647-655
    • Antunes, A.1    Rainey, F.A.2    Nobre, M.F.3    Schumann, P.4    Ferreira, A.M.5    Ramos, A.6    Santos, H.7    da Costa, M.S.8
  • 4
    • 9944255059 scopus 로고    scopus 로고
    • Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards
    • Brandley, M. C., Schmitz, A. & Reeder, T. W. (2005). Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards. Syst Biol 54, 373-390.
    • (2005) Syst Biol , vol.54 , pp. 373-390
    • Brandley, M.C.1    Schmitz, A.2    Reeder, T.W.3
  • 6
    • 3242695950 scopus 로고    scopus 로고
    • Data partitions and complex models in Bayesian analysis: The phylogeny of gymnophtalmid lizards
    • Castoe, T. A., Doan, T. M. & Parkinson, C. L. (2004). Data partitions and complex models in Bayesian analysis: the phylogeny of gymnophtalmid lizards. Syst Biol 53, 448-469.
    • (2004) Syst Biol , vol.53 , pp. 448-469
    • Castoe, T.A.1    Doan, T.M.2    Parkinson, C.L.3
  • 7
    • 0026010926 scopus 로고
    • Phylogenetic analysis of the genus Lactobacillus and related lactic acid bacteria as determined by reverse transcriptase sequencing of 16S rRNA
    • Collins, M. D., Rodrigues, U., Aguirre, M., Farrow, J., Martinez-Murcia, A., Phillips, B., Williams, A. & Wallbanks, S. (1991). Phylogenetic analysis of the genus Lactobacillus and related lactic acid bacteria as determined by reverse transcriptase sequencing of 16S rRNA. FEMS Microbiol Lett 77, 5-12.
    • (1991) FEMS Microbiol Lett , vol.77 , pp. 5-12
    • Collins, M.D.1    Rodrigues, U.2    Aguirre, M.3    Farrow, J.4    Martinez-Murcia, A.5    Phillips, B.6    Williams, A.7    Wallbanks, S.8
  • 8
    • 0027768689 scopus 로고
    • Taxonomic studies on some leuconostoc-like organisms from fermented sausages: Description of a new genus Weissella for the Leuconostoc paramesenteroides group of species
    • Collins, M. D., Samells, J., Metaxopoulos, J. & Wallbanks, S. (1993). Taxonomic studies on some leuconostoc-like organisms from fermented sausages: description of a new genus Weissella for the Leuconostoc paramesenteroides group of species. J Appl Bacteriol 75, 595-603.
    • (1993) J Appl Bacteriol , vol.75 , pp. 595-603
    • Collins, M.D.1    Samells, J.2    Metaxopoulos, J.3    Wallbanks, S.4
  • 9
    • 0028936112 scopus 로고
    • Proposal to reclassify Leuconostoc oenos as Oenococcus oeni gen. nov., comb. nov
    • Dicks, L. M. T., Dellaglio, F. E. & Collins, M. D. (1995). Proposal to reclassify Leuconostoc oenos as Oenococcus oeni gen. nov., comb. nov. Int J Syst Bacteriol 45, 395-397.
    • (1995) Int J Syst Bacteriol , vol.45 , pp. 395-397
    • Dicks, L.M.T.1    Dellaglio, F.E.2    Collins, M.D.3
  • 10
    • 84959798530 scopus 로고
    • Cases in which parsimony or compatibility methods will be positively misleading
    • Felsenstein, J. (1978). Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 27, 401-410.
    • (1978) Syst Zool , vol.27 , pp. 401-410
    • Felsenstein, J.1
  • 11
    • 0003437299 scopus 로고    scopus 로고
    • PHYLIP (phylogenetic inference package), version 3.6a
    • Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA
    • Felsenstein, J. (2002). PHYLIP (phylogenetic inference package), version 3.6a. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
    • (2002)
    • Felsenstein, J.1
  • 12
    • 0017143034 scopus 로고
    • Hybridization between the deoxyribonucleic acids of some strains of heterofermentative lactic acid bacteria
    • Garvie, E. I. (1976). Hybridization between the deoxyribonucleic acids of some strains of heterofermentative lactic acid bacteria. Int J Syst Bacteriol 26, 116-122.
    • (1976) Int J Syst Bacteriol , vol.26 , pp. 116-122
    • Garvie, E.I.1
  • 13
    • 0019770522 scopus 로고
    • Sub-divisions within the genus Leuconostoc as shown by RNA/DNA hybridization
    • Garvie, E. I. (1981). Sub-divisions within the genus Leuconostoc as shown by RNA/DNA hybridization. J Gen Microbiol 127, 209-212.
    • (1981) J Gen Microbiol , vol.127 , pp. 209-212
    • Garvie, E.I.1
  • 14
    • 0034351387 scopus 로고    scopus 로고
    • Likelihood-based tests of topologies in phylogenetics
    • Goldman, N., Anderson, J. P. & Rodrigo, A. G. (2000). Likelihood-based tests of topologies in phylogenetics. Syst Biol 49, 652-670.
    • (2000) Syst Biol , vol.49 , pp. 652-670
    • Goldman, N.1    Anderson, J.P.2    Rodrigo, A.G.3
  • 16
    • 0029113744 scopus 로고
    • The robustness of two phylogenetic methods: Four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining
    • Huelsenbeck, J. P. (1995). The robustness of two phylogenetic methods: four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining. Mol Biol Evol 12, 843-849.
    • (1995) Mol Biol Evol , vol.12 , pp. 843-849
    • Huelsenbeck, J.P.1
  • 17
    • 12044255023 scopus 로고
    • Success of phylogenetic methods in the four-taxon case
    • Huelsenbeck, J. P. & Hillis, D. M. (1993). Success of phylogenetic methods in the four-taxon case. Syst Biol 42, 247-264.
    • (1993) Syst Biol , vol.42 , pp. 247-264
    • Huelsenbeck, J.P.1    Hillis, D.M.2
  • 18
    • 0034849408 scopus 로고    scopus 로고
    • MrBayes: Bayesian inference of phylogenetic trees
    • Huelsenbeck, J. P. & Ronquist F. R. (2001). MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754-755.
    • (2001) Bioinformatics , vol.17 , pp. 754-755
    • Huelsenbeck, J.P.1    Ronquist, F.R.2
  • 19
    • 0000219186 scopus 로고
    • Regular, nonsporing gram-positive rods
    • In Edited by P. H. A. Sneath, N. S. Mair, M. E. Sharpe & J. G. Holt. Baltimore: Williams & Wilkins
    • Kandler, O. & Weiss, N. (1986). Regular, nonsporing gram-positive rods. In Bergey's Manual of Systematic Bacteriology, vol. 2, pp. 1208-1234. Edited by P. H. A. Sneath, N. S. Mair, M. E. Sharpe & J. G. Holt. Baltimore: Williams & Wilkins.
    • (1986) Bergey's Manual of Systematic Bacteriology , vol.2 , pp. 1208-1234
    • Kandler, O.1    Weiss, N.2
  • 20
    • 24944587193 scopus 로고    scopus 로고
    • Towards a genome-based taxonomy for prokaryotes
    • Konstantinidis, K. T. & Tiedje, J. M. (2005). Towards a genome-based taxonomy for prokaryotes. J Bacteriol 187, 6258-6264.
    • (2005) J Bacteriol , vol.187 , pp. 6258-6264
    • Konstantinidis, K.T.1    Tiedje, J.M.2
  • 21
    • 0021277009 scopus 로고
    • A new method for calculating evolutionary substitution rates
    • Lanave, C., Preparata, G., Saccone, C. & Serio, G. (1984). A new method for calculating evolutionary substitution rates. J Mol Evol 20, 86-93.
    • (1984) J Mol Evol , vol.20 , pp. 86-93
    • Lanave, C.1    Preparata, G.2    Saccone, C.3    Serio, G.4
  • 22
    • 0025982062 scopus 로고
    • Construction of T-vectors, a rapid and general system for direct cloning of unmodified PCR products
    • Marchuk, D., Drumm, M., Saulino, A. & Collins, F. (1991). Construction of T-vectors, a rapid and general system for direct cloning of unmodified PCR products. Nucleic Acids Res 19, 1154.
    • (1991) Nucleic Acids Res , vol.19 , pp. 1154
    • Marchuk, D.1    Drumm, M.2    Saulino, A.3    Collins, F.4
  • 23
    • 0025707918 scopus 로고
    • A phylogenetic analysis of the genus Leuconostoc based on reverse transcriptase sequencing of 16S rRNA
    • Martinez-Murcia, A. J. & Collins, M. D. (1990). A phylogenetic analysis of the genus Leuconostoc based on reverse transcriptase sequencing of 16S rRNA. FEMS Microbiol Lett 70, 73-84.
    • (1990) FEMS Microbiol Lett , vol.70 , pp. 73-84
    • Martinez-Murcia, A.J.1    Collins, M.D.2
  • 24
    • 0027300577 scopus 로고
    • Phylogenetic analysis of some leuconostocs and related organisms as determined from large-subunit rRNA gene sequences: Assessment of congruence of small- and large-subunit rRNA derived trees
    • Martinez-Murcia, A. J., Harland, N. M. & Collins, M. D. (1993). Phylogenetic analysis of some leuconostocs and related organisms as determined from large-subunit rRNA gene sequences: assessment of congruence of small- and large-subunit rRNA derived trees. J Appl Bacteriol 74, 532-541.
    • (1993) J Appl Bacteriol , vol.74 , pp. 532-541
    • Martinez-Murcia, A.J.1    Harland, N.M.2    Collins, M.D.3
  • 25
    • 23944514505 scopus 로고    scopus 로고
    • Genomic analysis of Oenococcus oeni PSU-1 and its relevance to winemaking
    • Mills, D. A., Rawsthorne, H., Parker, C., Tamir, D. & Makarova, K. (2005). Genomic analysis of Oenococcus oeni PSU-1 and its relevance to winemaking. FEMS Microbiol Rev 29, 465-475.
    • (2005) FEMS Microbiol Rev , vol.29 , pp. 465-475
    • Mills, D.A.1    Rawsthorne, H.2    Parker, C.3    Tamir, D.4    Makarova, K.5
  • 26
    • 0029798105 scopus 로고    scopus 로고
    • Analysis of the beta subunit of DNA-dependent RNA polymerase does not support the hypothesis inferred from 16S rRNA analysis that Oenococcus oeni (formerly Leuconostoc oenos) is a tachytelic (fast-evolving) bacterium
    • Morse, R., Collins, M. D., O'Hanlon, K., Wallbanks, S. & Richardson, P. T. (1996). Analysis of the beta subunit of DNA-dependent RNA polymerase does not support the hypothesis inferred from 16S rRNA analysis that Oenococcus oeni (formerly Leuconostoc oenos) is a tachytelic (fast-evolving) bacterium. Int J Syst Bacteriol 46, 1004-1009.
    • (1996) Int J Syst Bacteriol , vol.46 , pp. 1004-1009
    • Morse, R.1    Collins, M.D.2    O'Hanlon, K.3    Wallbanks, S.4    Richardson, P.T.5
  • 27
    • 0036739151 scopus 로고    scopus 로고
    • Phylogenetic, amino acid content and indel analyses of the β subunit of DNA-dependent RNA polymerase of Gram-positive and Gram-negative bacteria
    • Morse, R., O'Hanlon, K. & Collins, M. D. (2002). Phylogenetic, amino acid content and indel analyses of the β subunit of DNA-dependent RNA polymerase of Gram-positive and Gram-negative bacteria. Int J Syst Evol Microbiol 52, 1477-1484.
    • (2002) Int J Syst Evol Microbiol , vol.52 , pp. 1477-1484
    • Morse, R.1    O'Hanlon, K.2    Collins, M.D.3
  • 29
    • 0024553747 scopus 로고
    • Rapid extraction of bacterial genomic DNA with guanidium thiocyanate
    • Pitcher, D. G., Sanders, N. A. & Owen, R. J. (1989). Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett Appl Microbiol 8, 151-156.
    • (1989) Lett Appl Microbiol , vol.8 , pp. 151-156
    • Pitcher, D.G.1    Sanders, N.A.2    Owen, R.J.3
  • 30
    • 0031773680 scopus 로고    scopus 로고
    • Modeltest: Testing the model of DNA substitution
    • Posada, D. & Crandall, K. A. (1998). Modeltest: testing the model of DNA substitution. Bioinfiormatics 14, 817-818.
    • (1998) Bioinfiormatics , vol.14 , pp. 817-818
    • Posada, D.1    Crandall, K.A.2
  • 31
    • 0032766857 scopus 로고    scopus 로고
    • Multiple comparisons of log-likelihoods with applications to phylogenetic: Inference
    • Shimodaira, H. & Hasegawa, M. (1999). Multiple comparisons of log-likelihoods with applications to phylogenetic: inference. Mol Biol Evol 16, 1114-1116.
    • (1999) Mol Biol Evol , vol.16 , pp. 1114-1116
    • Shimodaira, H.1    Hasegawa, M.2
  • 34
    • 0027157960 scopus 로고
    • Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees
    • Tamura, K. & Nei, M. (1993). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10, 512-526.
    • (1993) Mol Biol Evol , vol.10 , pp. 512-526
    • Tamura, K.1    Nei, M.2
  • 35
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673-4680.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 36
    • 0028948030 scopus 로고
    • PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains
    • Yamamoto, S. & Harayama, S. (1995). PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains. Appl Environ Microbiol 61, 1104-1109.
    • (1995) Appl Environ Microbiol , vol.61 , pp. 1104-1109
    • Yamamoto, S.1    Harayama, S.2
  • 37
    • 0031827993 scopus 로고    scopus 로고
    • Phylogenetic relationships of Pseudomonas putida strains deduced from the nucleotide sequences of gyrB, rpoD and 16S rRNA genes
    • Yamamoto, S. & Harayama, S. (1998). Phylogenetic relationships of Pseudomonas putida strains deduced from the nucleotide sequences of gyrB, rpoD and 16S rRNA genes. Int J Syst Bacteriol 48, 813-819.
    • (1998) Int J Syst Bacteriol , vol.48 , pp. 813-819
    • Yamamoto, S.1    Harayama, S.2
  • 38
    • 0029970097 scopus 로고    scopus 로고
    • Maximum-likelihood models for combined analyses of multiple sequence data
    • Yang, Z. (1996). Maximum-likelihood models for combined analyses of multiple sequence data. J Mol Evol 42, 587-596.
    • (1996) J Mol Evol , vol.42 , pp. 587-596
    • Yang, Z.1
  • 39
    • 0024322776 scopus 로고
    • Phylogenetic structure of the "leuconostocs": An interesting case of a rapidly evolving organism
    • Yang, D. & Woese, C. R. (1989). Phylogenetic structure of the "leuconostocs": an interesting case of a rapidly evolving organism. Syst Appl Microbiol 12, 145-149.
    • (1989) Syst Appl Microbiol , vol.12 , pp. 145-149
    • Yang, D.1    Woese, C.R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.