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Volumn 13, Issue 2, 2003, Pages 145-156

Evolutionary implications of microbial genome tetranucleotide frequency biases

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S; ARCHAEAL DNA; ARCHAEAL RNA; BACTERIAL DNA; BACTERIAL RNA; MICROSATELLITE DNA;

EID: 0037315735     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.335003     Document Type: Article
Times cited : (212)

References (46)
  • 1
    • 0021109593 scopus 로고
    • A Markov analysis of DNA sequences
    • Almagor, H. 1983. A Markov analysis of DNA sequences. J. Theor. Biol. 104: 633-645.
    • (1983) J. Theor. Biol. , vol.104 , pp. 633-645
    • Almagor, H.1
  • 2
    • 0026552754 scopus 로고
    • DNA mismatch correction by very short patch repair may have altered the abundance of oligonucleotides in the E. coli genome
    • Bhagwat, A.S. and McClelland, M. 1992. DNA mismatch correction by very short patch repair may have altered the abundance of oligonucleotides in the E. coli genome. Nucleic Acids Res. 20: 1663-1668.
    • (1992) Nucleic Acids Res. , vol.20 , pp. 1663-1668
    • Bhagwat, A.S.1    McClelland, M.2
  • 3
    • 0026502711 scopus 로고
    • Over- And under-representation of short oligonucleotides in DNA sequences
    • Burge, C., Campbell, A.M., and Karlin, S. 1992. Over- and under-representation of short oligonucleotides in DNA sequences. Proc. Natl. Acad. Sci. 89: 1358-1362.
    • (1992) Proc. Natl. Acad. Sci. , vol.89 , pp. 1358-1362
    • Burge, C.1    Campbell, A.M.2    Karlin, S.3
  • 4
    • 0028028028 scopus 로고
    • Computational DNA sequence analysis
    • Cardon, L.R. and Karlin, S. 1994. Computational DNA sequence analysis. Annu. Rev. Microbiol. 48: 619-654.
    • (1994) Annu. Rev. Microbiol. , vol.48 , pp. 619-654
    • Cardon, L.R.1    Karlin, S.2
  • 5
    • 0033603539 scopus 로고    scopus 로고
    • Phylogenetic classification and the universal tree
    • Doolittle, W.F. 1999. Phylogenetic classification and the universal tree. Science 284: 2124-2128.
    • (1999) Science , vol.284 , pp. 2124-2128
    • Doolittle, W.F.1
  • 6
    • 0033783996 scopus 로고    scopus 로고
    • Assessing evolutionary relationships among microbes from whole-genome analysis
    • Eisen, J.A. 2000a. Assessing evolutionary relationships among microbes from whole-genome analysis. Curr. Opin. Microbiol. 3: 475-480.
    • (2000) Curr. Opin. Microbiol. , vol.3 , pp. 475-480
    • Eisen, J.A.1
  • 7
    • 0033669672 scopus 로고    scopus 로고
    • Horizontal gene transfer among microbial genomes: New insights from complete genome analysis
    • Eisen, J.A. 2000b. Horizontal gene transfer among microbial genomes: New insights from complete genome analysis. Curr. Opin. Genet. Dev. 10: 606-611.
    • (2000) Curr. Opin. Genet. Dev. , vol.10 , pp. 606-611
    • Eisen, J.A.1
  • 10
    • 0033231209 scopus 로고    scopus 로고
    • Whole-genome based phylogenetic analysis of free-living microorganisms
    • Fitz-Gibbon, S.T. and House, C.H. 1999. Whole-genome based phylogenetic analysis of free-living microorganisms. Nucleic Acids Res. 27: 4218-4222.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 4218-4222
    • Fitz-Gibbon, S.T.1    House, C.H.2
  • 11
    • 0030740993 scopus 로고    scopus 로고
    • Avoidance of palindromic words in bacterial and archaeal genome: A close connection with restriction enzymes
    • Gelfand, M.S. and Koonin, E.V. 1997. Avoidance of palindromic words in bacterial and archaeal genome: A close connection with restriction enzymes. Nucleic Acids Res. 25: 2430-2439.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 2430-2439
    • Gelfand, M.S.1    Koonin, E.V.2
  • 13
    • 0020363515 scopus 로고
    • Preferential codon usage in prokaryotic genes: The optimal codon-anti-codon interaction energy and the selective codon usage in efficiently expressed genes
    • Grosjean, H. and Freirs, W. 1982. Preferential codon usage in prokaryotic genes: The optimal codon-anti-codon interaction energy and the selective codon usage in efficiently expressed genes. Gene 18: 199-209.
    • (1982) Gene , vol.18 , pp. 199-209
    • Grosjean, H.1    Freirs, W.2
  • 15
    • 0343586537 scopus 로고    scopus 로고
    • Uneven distribution of GATC motifs in the Escherichia coli chromosome, its plasmids and its phages
    • Henaut, A., Rouxel, T., Gleizes, A., Moszer, I., and Danchin, A. 1996. Uneven distribution of GATC motifs in the Escherichia coli chromosome, its plasmids and its phages. J. Mol. Biol. 257: 574-585.
    • (1996) J. Mol. Biol. , vol.257 , pp. 574-585
    • Henaut, A.1    Rouxel, T.2    Gleizes, A.3    Moszer, I.4    Danchin, A.5
  • 16
    • 0033053213 scopus 로고    scopus 로고
    • The influence of recombination on the population structure and evolution of the human pathogen Neisseria meningitides
    • Holmes, E.C., Urwin, R., and Maiden, M.C.J. 1999. The influence of recombination on the population structure and evolution of the human pathogen Neisseria meningitides. Mol. Biol. Evol. 16: 741-749.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 741-749
    • Holmes, E.C.1    Urwin, R.2    Maiden, M.C.J.3
  • 17
    • 1842332701 scopus 로고    scopus 로고
    • Compositional biases of bacterial genomes and evolutionary implications
    • Karlin S., Mrazek, J., and Campbell, A.M. 1997. Compositional biases of bacterial genomes and evolutionary implications. J. Bacteriol. 179: 3899-3913.
    • (1997) J. Bacteriol. , vol.179 , pp. 3899-3913
    • Karlin, S.1    Mrazek, J.2    Campbell, A.M.3
  • 18
    • 0032426005 scopus 로고    scopus 로고
    • Comparative DNA analysis across diverse genomes
    • Karlin, S., Campbell, A.M., and Mrazek, J. 1998. Comparative DNA analysis across diverse genomes. Annu. Rev. Genet. 32: 185-225.
    • (1998) Annu. Rev. Genet. , vol.32 , pp. 185-225
    • Karlin, S.1    Campbell, A.M.2    Mrazek, J.3
  • 19
    • 0034625235 scopus 로고    scopus 로고
    • The impact of comparative genomics on our understanding of evolution
    • Koonin, E.V., Aravind, L., and Kondrashov, A.S. 2000. The impact of comparative genomics on our understanding of evolution. Cell 101: 573-576.
    • (2000) Cell , vol.101 , pp. 573-576
    • Koonin, E.V.1    Aravind, L.2    Kondrashov, A.S.3
  • 20
    • 0034284411 scopus 로고    scopus 로고
    • Functional analysis of putative restriction-modification system genes in the Helicobacter pylori J99 genome
    • Kong, H., Lin, L.-F., Porter, N., Stickel, S., Byrd, D., Posfai, J., and Roberts, R.J. 2000. Functional analysis of putative restriction-modification system genes in the Helicobacter pylori J99 genome. Nucleic Acids Res. 28: 3216-3223.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 3216-3223
    • Kong, H.1    Lin, L.-F.2    Porter, N.3    Stickel, S.4    Byrd, D.5    Posfai, J.6    Roberts, R.J.7
  • 21
    • 0030994798 scopus 로고    scopus 로고
    • Amelioration of bacterial genomes: Rates of change and exchange
    • Lawrence, J.G. and Ochman, H. 1997. Amelioration of bacterial genomes: Rates of change and exchange. J. Mol. Evol. 44: 383-397.
    • (1997) J. Mol. Evol. , vol.44 , pp. 383-397
    • Lawrence, J.G.1    Ochman, H.2
  • 22
    • 0029795578 scopus 로고    scopus 로고
    • Over- and underrepresentation of short DNA words in herpesvirus genomes
    • Leung, M.Y., Marsh, G.M., and Speed, T.P. 1996. Over- and underrepresentation of short DNA words in herpesvirus genomes. J. Comp. Biol. 3: 345-360.
    • (1996) J. Comp. Biol. , vol.3 , pp. 345-360
    • Leung, M.Y.1    Marsh, G.M.2    Speed, T.P.3
  • 23
    • 0035956977 scopus 로고    scopus 로고
    • Comparative genomics of the restriction-modification systems in Helicobacter pylori
    • Lin, L.-F., Posfai, J., Roberts, R. J., and Kong, H. 2001. Comparative genomics of the restriction-modification systems in Helicobacter pylori. Proc. Natl. Acad. Sci. 98: 2740-2745.
    • (2001) Proc. Natl. Acad. Sci. , vol.98 , pp. 2740-2745
    • Lin, L.-F.1    Posfai, J.2    Roberts, R.J.3    Kong, H.4
  • 25
    • 0031897789 scopus 로고    scopus 로고
    • Detecting recombination from gene trees
    • Maynard Smith, J. and Smith, N.H. 1998. Detecting recombination from gene trees. Mol. Biol. Evol. 15: 590-599.
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 590-599
    • Maynard Smith, J.1    Smith, N.H.2
  • 26
    • 0013596021 scopus 로고
    • The guanine and cytosine content of genomic DNA and bacterial-evolution
    • Muto, A. and Osawa, S. 1987. The guanine and cytosine content of genomic DNA and bacterial-evolution. Proc. Natl. Acad. Sci. 84: 166-169.
    • (1987) Proc. Natl. Acad. Sci. , vol.84 , pp. 166-169
    • Muto, A.1    Osawa, S.2
  • 28
    • 0028055018 scopus 로고
    • The winds of (evolutionary) change: Breathing new life into microbiology
    • Olsen, G.J., Woese, C.R., and Overbeek, R. 1994. The winds of (evolutionary) change: Breathing new life into microbiology. J. Bacteriol. 176: 1-6.
    • (1994) J. Bacteriol. , vol.176 , pp. 1-6
    • Olsen, G.J.1    Woese, C.R.2    Overbeek, R.3
  • 29
    • 0030982247 scopus 로고    scopus 로고
    • A molecular view of microbial diversity and the biosphere
    • Pace, N.R. 1997. A molecular view of microbial diversity and the biosphere. Science 276: 734-740.
    • (1997) Science , vol.276 , pp. 734-740
    • Pace, N.R.1
  • 30
    • 0030203863 scopus 로고    scopus 로고
    • TREEVIEW: An application to display phylogenetic trees on personal computers
    • Page, R.D.M. 1996. TREEVIEW: An application to display phylogenetic trees on personal computers. Comp. Appl. Biosci. 12: 357-458.
    • (1996) Comp. Appl. Biosci. , vol.12 , pp. 357-458
    • Page, R.D.M.1
  • 32
    • 0002393841 scopus 로고
    • The use of tree comparison metrics
    • Penny, D. and Hendy, M.D. 1985. The use of tree comparison metrics. Systematic Zoology 34: 75-82.
    • (1985) Systematic Zoology , vol.34 , pp. 75-82
    • Penny, D.1    Hendy, M.D.2
  • 34
    • 0002576679 scopus 로고    scopus 로고
    • Identification of horizontally acquired genetic elements in Helicobacter pylori and other prokaryotes using oligonucleotide difference analysis
    • Pride, D.T. and Blaser, MJ. 2002. Identification of horizontally acquired genetic elements in Helicobacter pylori and other prokaryotes using oligonucleotide difference analysis. Genome Letters 1: 2-15.
    • (2002) Genome Letters , vol.1 , pp. 2-15
    • Pride, D.T.1    Blaser, M.J.2
  • 35
    • 0032526323 scopus 로고    scopus 로고
    • Oligonucleotide bias in Bacillus subtilis: General trends and taxonomic comparisons
    • Rocha, E.P.C., Viari, A., and Danchin, A. 1998. Oligonucleotide bias in Bacillus subtilis: General trends and taxonomic comparisons. Nucleic Acids Res. 26: 2971-2980.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 2971-2980
    • Rocha, E.P.C.1    Viari, A.2    Danchin, A.3
  • 36
    • 0026680446 scopus 로고
    • Gene order comparisons for phylogenetic inference: Evolution of the mitochondrial genome
    • Sankoff, D., Leduc, G., Antoine, N., Paquin, B., Lang, B.F., and Cedergren, R. 1992. Gene order comparisons for phylogenetic inference: Evolution of the mitochondrial genome. Proc. Natl. Acad. Sci. 89: 6575-6579.
    • (1992) Proc. Natl. Acad. Sci. , vol.89 , pp. 6575-6579
    • Sankoff, D.1    Leduc, G.2    Antoine, N.3    Paquin, B.4    Lang, B.F.5    Cedergren, R.6
  • 37
    • 0029365207 scopus 로고
    • Exceptional motifs in different Markov chain models for a statistical analysis of DNA sequences
    • Schbath, S., Prum, B., and de Turckheim, E. 1995. Exceptional motifs in different Markov chain models for a statistical analysis of DNA sequences. J. Comp. Biol. 2: 417-437.
    • (1995) J. Comp. Biol. , vol.2 , pp. 417-437
    • Schbath, S.1    Prum, B.2    de Turckheim, E.3
  • 38
    • 0027715731 scopus 로고
    • Codon usage: Mutational bias, translational selection, or both?
    • Sharp, P.M., Stenico, M., Peden, J.F., and Lloyd, A.T. 1993. Codon usage: Mutational bias, translational selection, or both? Biochem. Soc. Trans. 21: 835-841.
    • (1993) Biochem. Soc. Trans. , vol.21 , pp. 835-841
    • Sharp, P.M.1    Stenico, M.2    Peden, J.F.3    Lloyd, A.T.4
  • 39
    • 0032900532 scopus 로고    scopus 로고
    • Genome phylogeny based on gene content
    • Snel, B., Bork, P., and Huynen, M.A. 1999. Genome phylogeny based on gene content. Nature Genetics 21: 108-110.
    • (1999) Nature Genetics , vol.21 , pp. 108-110
    • Snel, B.1    Bork, P.2    Huynen, M.A.3
  • 40
    • 0023991945 scopus 로고
    • Directional mutation pressure and neutral molecular evolution
    • Suoeka, N. 1988. Directional mutation pressure and neutral molecular evolution. Proc. Natl. Acad. Sci. 85: 2653-2657.
    • (1988) Proc. Natl. Acad. Sci. , vol.85 , pp. 2653-2657
    • Suoeka, N.1
  • 41
    • 0004248459 scopus 로고    scopus 로고
    • Paup 4.0b2. Phylogenetic analysis using parsimony (* and other methods)
    • Version 4. Sinauer Associates, Sunderland, Massachusetts
    • Swofford, D.L. 1998. Paup 4.0b2. Phylogenetic analysis using parsimony (* and other methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.
    • (1998)
    • Swofford, D.L.1
  • 44
    • 0001271789 scopus 로고
    • Phylogenetic structure of the prokaryotic domain: The primary kingdoms
    • Woese, C.R. and Fox, G.E. 1977. Phylogenetic structure of the prokaryotic domain: The primary kingdoms. Proc. Natl. Acad. Sci. 74:5088-5090.
    • (1977) Proc. Natl. Acad. Sci. , vol.74 , pp. 5088-5090
    • Woese, C.R.1    Fox, G.E.2
  • 45
    • 0025300402 scopus 로고
    • Towards a natural system of organisms: Proposal for the domains archaea, bacteria, and eukarya
    • Woese, C.R., Kandler, O., and Wheelis, M.L. 1990. Towards a natural system of organisms: Proposal for the domains archaea, bacteria, and eukarya. Proc. Natl. Acad. Sci. 87: 4576-4579.
    • (1990) Proc. Natl. Acad. Sci. , vol.87 , pp. 4576-4579
    • Woese, C.R.1    Kandler, O.2    Wheelis, M.L.3
  • 46
    • 0034662923 scopus 로고    scopus 로고
    • Identification of type II restriction and modification systems in Helicobacter pylori reveals their substantial diversity among strains
    • Xu, Q., Morgan, R.D., Roberts, R.J., and Blaser, M.J. 2000. Identification of type II restriction and modification systems in Helicobacter pylori reveals their substantial diversity among strains. Proc. Natl. Acad. Sci. 97: 9671-9676.
    • (2000) Proc. Natl. Acad. Sci. , vol.97 , pp. 9671-9676
    • Xu, Q.1    Morgan, R.D.2    Roberts, R.J.3    Blaser, M.J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.