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Volumn 91, Issue 6, 2008, Pages 538-543

Ecophysiological significance of scale-dependent patterns in prokaryotic genomes unveiled by a combination of statistic and genometric analyses

Author keywords

Comparative genome analyses; Detrended fluctuation analysis; DNA walk; Genometrics; Long range correlation; Microbial biodiversity, DNA sequence analysis; Microbial ecology; Prokaryote genome

Indexed keywords

DNA;

EID: 44649173628     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2008.03.001     Document Type: Article
Times cited : (9)

References (52)
  • 1
    • 0036205618 scopus 로고    scopus 로고
    • Microheterogeneity in 16S rDNA-defined bacterial populations from a stratified planktonic environment is related to temporal succession and to ecological adaptations
    • Casamayor E.O., Pedrós-Alió C., Muyzer G., and Amann R. Microheterogeneity in 16S rDNA-defined bacterial populations from a stratified planktonic environment is related to temporal succession and to ecological adaptations. Appl. Environ. Microbiol. 68 (2002) 1706-1714
    • (2002) Appl. Environ. Microbiol. , vol.68 , pp. 1706-1714
    • Casamayor, E.O.1    Pedrós-Alió, C.2    Muyzer, G.3    Amann, R.4
  • 2
    • 4344685409 scopus 로고    scopus 로고
    • Microbial population genomics and ecology: the road ahead
    • De Long E.F. Microbial population genomics and ecology: the road ahead. Environ. Microbiol. 6 (2004) 875-878
    • (2004) Environ. Microbiol. , vol.6 , pp. 875-878
    • De Long, E.F.1
  • 3
    • 0348196795 scopus 로고    scopus 로고
    • The future of microbial genomics
    • Nelson K.E. The future of microbial genomics. Environ. Microbiol. 5 (2003) 1223-1225
    • (2003) Environ. Microbiol. , vol.5 , pp. 1223-1225
    • Nelson, K.E.1
  • 4
    • 4644354371 scopus 로고    scopus 로고
    • Metagenomics-the key to the uncultured microbes
    • Streit W.R., and Schmitz R.A. Metagenomics-the key to the uncultured microbes. Curr. Opin. Microbiol. 7 (2004) 492-498
    • (2004) Curr. Opin. Microbiol. , vol.7 , pp. 492-498
    • Streit, W.R.1    Schmitz, R.A.2
  • 5
    • 0013596021 scopus 로고
    • The guanine and cytosine content of genomic DNA and bacterial evolution
    • Muto A., and Osawa S. The guanine and cytosine content of genomic DNA and bacterial evolution. Proc. Natl. Acad. Sci. 84 (1987) 166-169
    • (1987) Proc. Natl. Acad. Sci. , vol.84 , pp. 166-169
    • Muto, A.1    Osawa, S.2
  • 6
    • 0035819839 scopus 로고    scopus 로고
    • High guanine-cytosine content is not an adaptation to high temperature: a comparative analysis amongst prokaryotes
    • Hurst L.D., and Merchant A.R. High guanine-cytosine content is not an adaptation to high temperature: a comparative analysis amongst prokaryotes. Proc. R. Soc. Lond., B Biol. Sci. 268 (2000) 493-497
    • (2000) Proc. R. Soc. Lond., B Biol. Sci. , vol.268 , pp. 493-497
    • Hurst, L.D.1    Merchant, A.R.2
  • 7
    • 7644238105 scopus 로고    scopus 로고
    • Correlations between genomic GC levels and optimal growth temperatures are not 'robust'
    • Marashi S.A., and Ghalanbor Z. Correlations between genomic GC levels and optimal growth temperatures are not 'robust'. Biochem. Biophys. Res. Commun. 325 (2004) 381-383
    • (2004) Biochem. Biophys. Res. Commun. , vol.325 , pp. 381-383
    • Marashi, S.A.1    Ghalanbor, Z.2
  • 8
    • 28544451203 scopus 로고    scopus 로고
    • Environments shape the nucleotide composition of genomes
    • Foerstner K.U., Mering C.V., Hooper S.D., and Bork P. Environments shape the nucleotide composition of genomes. EMBO Rep. 6 (2005) 1208-1213
    • (2005) EMBO Rep. , vol.6 , pp. 1208-1213
    • Foerstner, K.U.1    Mering, C.V.2    Hooper, S.D.3    Bork, P.4
  • 11
    • 0036087165 scopus 로고    scopus 로고
    • Comparative Genometrics (CG): a database dedicated to biometric comparisons of whole genomes
    • Roten C.A.H., Gamba P., Barblan J.L., and Karamata D. Comparative Genometrics (CG): a database dedicated to biometric comparisons of whole genomes. Nucleic Acids Res. 30 (2002) 142-144
    • (2002) Nucleic Acids Res. , vol.30 , pp. 142-144
    • Roten, C.A.H.1    Gamba, P.2    Barblan, J.L.3    Karamata, D.4
  • 17
    • 0025318481 scopus 로고
    • Genetic linkage and complex disease: a comment
    • Elston R.C., and Wilson A.F. Genetic linkage and complex disease: a comment. Genet. Epidemiol. 7 (1990) 17-19
    • (1990) Genet. Epidemiol. , vol.7 , pp. 17-19
    • Elston, R.C.1    Wilson, A.F.2
  • 18
    • 0001045050 scopus 로고    scopus 로고
    • Genomic landscapes
    • Lobry J.R. Genomic landscapes. Microbiol. Today 26 (1999) 164-165
    • (1999) Microbiol. Today , vol.26 , pp. 164-165
    • Lobry, J.R.1
  • 19
    • 84956088098 scopus 로고
    • α spectrum in a non-coding DNA sequence
    • α spectrum in a non-coding DNA sequence. Europhys. Lett. 17 (1992) 655-660
    • (1992) Europhys. Lett. , vol.17 , pp. 655-660
    • Li, W.1    Kaneko, K.2
  • 20
    • 0000428193 scopus 로고
    • Global fractal dimension of human DNA sequences treated as pseudorandom walks
    • Berthelsen C.L., Glazier J.A., and Skolnick M.H. Global fractal dimension of human DNA sequences treated as pseudorandom walks. Phys. Rev., A 45 (1992) 8902-8913
    • (1992) Phys. Rev., A , vol.45 , pp. 8902-8913
    • Berthelsen, C.L.1    Glazier, J.A.2    Skolnick, M.H.3
  • 21
    • 0033232146 scopus 로고    scopus 로고
    • Statistics of DNA sequences: a low-frequency analysis
    • Vieira M.S. Statistics of DNA sequences: a low-frequency analysis. Phys. Rev., E 60 (1999) 5932-5937
    • (1999) Phys. Rev., E , vol.60 , pp. 5932-5937
    • Vieira, M.S.1
  • 22
    • 41349100413 scopus 로고    scopus 로고
    • Recognition of an organism from fragments of its complete genome
    • Anh V.V., Lau K.S., and Yu Z.G. Recognition of an organism from fragments of its complete genome. Phys. Rev., E 66 (2002) 031910
    • (2002) Phys. Rev., E , vol.66 , pp. 031910
    • Anh, V.V.1    Lau, K.S.2    Yu, Z.G.3
  • 23
    • 0142091486 scopus 로고    scopus 로고
    • The genomic tree of living organisms based on a fractal model
    • Yu Z.G., Anh V., Lau K.S., and Chu K.H. The genomic tree of living organisms based on a fractal model. Phys. Lett., A 317 (2003) 293-302
    • (2003) Phys. Lett., A , vol.317 , pp. 293-302
    • Yu, Z.G.1    Anh, V.2    Lau, K.S.3    Chu, K.H.4
  • 26
    • 0000204878 scopus 로고
    • α noise in DNA base sequences
    • α noise in DNA base sequences. Phys. Rev. Lett. 68 (1992) 3805-3808
    • (1992) Phys. Rev. Lett. , vol.68 , pp. 3805-3808
    • Voss, R.F.1
  • 27
    • 84956136196 scopus 로고
    • Crumpled gobule model of the three-dimensional structure of DNA
    • Grosberg A., Rabin Y., Havlin S., and Neer A. Crumpled gobule model of the three-dimensional structure of DNA. Europhys. Lett. 23 (1993) 373-378
    • (1993) Europhys. Lett. , vol.23 , pp. 373-378
    • Grosberg, A.1    Rabin, Y.2    Havlin, S.3    Neer, A.4
  • 28
    • 0034962206 scopus 로고    scopus 로고
    • Evolution of the periodicity and the self-similarity in DNA sequence: a Fourier transform analysis
    • Nagai N., Kuwata K., Hayashi T., Kuwata H., and Era S. Evolution of the periodicity and the self-similarity in DNA sequence: a Fourier transform analysis. Jpn. J. Physiol. 51 (2001) 159-168
    • (2001) Jpn. J. Physiol. , vol.51 , pp. 159-168
    • Nagai, N.1    Kuwata, K.2    Hayashi, T.3    Kuwata, H.4    Era, S.5
  • 30
    • 0031801256 scopus 로고    scopus 로고
    • Molecular characterization of the principal symbiotic bacteria of the weevil Sitophilus oryzae: a peculiar G+C content of an endocytobiotic DNA
    • Heddi A., Charles H., Khatchadourian C., Bonnot G., and Nardon P. Molecular characterization of the principal symbiotic bacteria of the weevil Sitophilus oryzae: a peculiar G+C content of an endocytobiotic DNA. J. Mol. Evol. 47 (1998) 52-61
    • (1998) J. Mol. Evol. , vol.47 , pp. 52-61
    • Heddi, A.1    Charles, H.2    Khatchadourian, C.3    Bonnot, G.4    Nardon, P.5
  • 31
    • 0037040394 scopus 로고    scopus 로고
    • Microbial minimalism: genome reduction in bacterial pathogens
    • Moran N.A. Microbial minimalism: genome reduction in bacterial pathogens. Cell 108 (2002) 583-586
    • (2002) Cell , vol.108 , pp. 583-586
    • Moran, N.A.1
  • 32
    • 0036606915 scopus 로고    scopus 로고
    • Base composition bias might result from competition for metabolic resources
    • Rocha E.P., and Danchin A. Base composition bias might result from competition for metabolic resources. Trends Genet. 18 (2002) 291-294
    • (2002) Trends Genet. , vol.18 , pp. 291-294
    • Rocha, E.P.1    Danchin, A.2
  • 33
    • 0032524384 scopus 로고    scopus 로고
    • Analyzing genomes with cumulative skew diagrams
    • Grigoriev A. Analyzing genomes with cumulative skew diagrams. Nucleic Acids Res. 26 (1998) 2286-2290
    • (1998) Nucleic Acids Res. , vol.26 , pp. 2286-2290
    • Grigoriev, A.1
  • 34
    • 0036709941 scopus 로고    scopus 로고
    • Is there a role for replication fork asymmetry in the distribution of genes in bacterial genomes?
    • Rocha E.P.C. Is there a role for replication fork asymmetry in the distribution of genes in bacterial genomes?. Trends Microbiol. 10 (2000) 393-395
    • (2000) Trends Microbiol. , vol.10 , pp. 393-395
    • Rocha, E.P.C.1
  • 36
    • 43949156767 scopus 로고
    • Understanding long-range correlations in DNA-sequences
    • Li W., Marr T., and Kaneko K. Understanding long-range correlations in DNA-sequences. Physica, D 75 (1994) 392-416
    • (1994) Physica, D , vol.75 , pp. 392-416
    • Li, W.1    Marr, T.2    Kaneko, K.3
  • 38
    • 0032584101 scopus 로고    scopus 로고
    • Strand compositional asymmetry in bacterial and large viral genomes
    • Mrázek J., and Karlin S. Strand compositional asymmetry in bacterial and large viral genomes. Proc. Natl. Acad. Sci. 95 (1997) 3720-3725
    • (1997) Proc. Natl. Acad. Sci. , vol.95 , pp. 3720-3725
    • Mrázek, J.1    Karlin, S.2
  • 39
    • 4444364227 scopus 로고    scopus 로고
    • Multiple origins of replication in archaea
    • Kelman L.M., and Kelman Z. Multiple origins of replication in archaea. Trends Microbiol. 12 (2004) 399-401
    • (2004) Trends Microbiol. , vol.12 , pp. 399-401
    • Kelman, L.M.1    Kelman, Z.2
  • 40
    • 0027278557 scopus 로고
    • Instability and decay of the primary structure of DNA
    • Lindahl T. Instability and decay of the primary structure of DNA. Nature 362 (1993) 709-715
    • (1993) Nature , vol.362 , pp. 709-715
    • Lindahl, T.1
  • 41
    • 0030985997 scopus 로고    scopus 로고
    • Rates of spontaneous mutation in an archaeon from geothermal environments
    • Jacobs K.L., and Grogan D.W. Rates of spontaneous mutation in an archaeon from geothermal environments. J. Bacteriol. 197 (1997) 3298-3303
    • (1997) J. Bacteriol. , vol.197 , pp. 3298-3303
    • Jacobs, K.L.1    Grogan, D.W.2
  • 42
    • 0037315735 scopus 로고    scopus 로고
    • Evolutionary implications of microbial genome tetranucleotide frequency biases
    • Pride D.T., Meinersmann R.J., Wassenaar T.M., and Blaser M.J. Evolutionary implications of microbial genome tetranucleotide frequency biases. Genome Res. 13 (2003) 145-158
    • (2003) Genome Res. , vol.13 , pp. 145-158
    • Pride, D.T.1    Meinersmann, R.J.2    Wassenaar, T.M.3    Blaser, M.J.4
  • 43
    • 4344670204 scopus 로고    scopus 로고
    • Application of tetranucleotide frequencies for the assignment of genomic fragments
    • Teeling H., Meyerdierks A., Bauer M., Amann R., and Glockner F.O. Application of tetranucleotide frequencies for the assignment of genomic fragments. Environ. Microbiol. 6 (2004) 938-947
    • (2004) Environ. Microbiol. , vol.6 , pp. 938-947
    • Teeling, H.1    Meyerdierks, A.2    Bauer, M.3    Amann, R.4    Glockner, F.O.5
  • 45
    • 4344666232 scopus 로고    scopus 로고
    • Correlations between genomic GC levels and optimal growth temperatures in prokaryotes
    • Musto H., Naya H., Zavala A., Romero H., Alvarez-Valín F., and Bernardi G. Correlations between genomic GC levels and optimal growth temperatures in prokaryotes. FEBS Lett. 573 (2004) 73-77
    • (2004) FEBS Lett. , vol.573 , pp. 73-77
    • Musto, H.1    Naya, H.2    Zavala, A.3    Romero, H.4    Alvarez-Valín, F.5    Bernardi, G.6
  • 46
    • 0030900384 scopus 로고    scopus 로고
    • Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes
    • Galtier N., and Lobry J.R. Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes. J. Mol. Evol. 44 (1997) 632-636
    • (1997) J. Mol. Evol. , vol.44 , pp. 632-636
    • Galtier, N.1    Lobry, J.R.2
  • 47
    • 33644622447 scopus 로고    scopus 로고
    • On the correlation between genomic G+C content and optimal growth temperature in prokaryotes: data quality and confounding factors
    • Wang H.C., Susko E., and Roger A.J. On the correlation between genomic G+C content and optimal growth temperature in prokaryotes: data quality and confounding factors. Biochem. Biophys. Res. Commun. 342 (2006) 681-684
    • (2006) Biochem. Biophys. Res. Commun. , vol.342 , pp. 681-684
    • Wang, H.C.1    Susko, E.2    Roger, A.J.3
  • 48
    • 0029805251 scopus 로고    scopus 로고
    • A simple vectorial representation of DNA sequences for the detection of replication origins in bacteria
    • Lobry J.R. A simple vectorial representation of DNA sequences for the detection of replication origins in bacteria. Biochimie 78 (1996) 323-326
    • (1996) Biochimie , vol.78 , pp. 323-326
    • Lobry, J.R.1
  • 51
    • 0000501589 scopus 로고
    • Fractional Brownian motions, fractional noises and applications
    • Mandelbrot B.B., and Van Ness J.W. Fractional Brownian motions, fractional noises and applications. SIAM Rev. 10 (1968) 422-437
    • (1968) SIAM Rev. , vol.10 , pp. 422-437
    • Mandelbrot, B.B.1    Van Ness, J.W.2


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