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Volumn 86, Issue 4, 2005, Pages 462-475

A comparative categorization of gene flux in diverse microbial species

Author keywords

COG database; Gene flux; Genomic islands; Horizontal gene transfer; Lateral gene transfer; Xenologous genes

Indexed keywords

ARTICLE; ESCHERICHIA; GENE TRANSFER; GENETIC CODE; GENOME; GENOME ANALYSIS; GENOMIC ISLAND; HORIZONTAL GENE TRANSFER; LISTERIA; METHANOSARCINA; MICROBIAL GENETICS; PRIORITY JOURNAL; RHIZOBIALES; THERMOPHILIC BACTERIUM; THERMUS THERMOPHILUS;

EID: 33644502889     PISSN: 08887543     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ygeno.2005.05.014     Document Type: Article
Times cited : (12)

References (56)
  • 1
    • 0030994798 scopus 로고    scopus 로고
    • Amelioration of bacterial genomes: Rates of change and exchange
    • J.G. Lawrence, and H. Ochman Amelioration of bacterial genomes: rates of change and exchange J. Mol. Evol. 44 1997 383 397
    • (1997) J. Mol. Evol. , vol.44 , pp. 383-397
    • Lawrence, J.G.1    Ochman, H.2
  • 2
    • 0033603539 scopus 로고    scopus 로고
    • Phylogenetic classification and the universal tree
    • W.F. Doolittle Phylogenetic classification and the universal tree Science 284 1999 2124 2129
    • (1999) Science , vol.284 , pp. 2124-2129
    • Doolittle, W.F.1
  • 3
    • 0036143446 scopus 로고    scopus 로고
    • Genomes in flux: The evolution of archaeal and proteobacterial gene content
    • B. Snel, P. Bork, and M.A. Huynen Genomes in flux: the evolution of archaeal and proteobacterial gene content Genome Res. 12 2002 17 25
    • (2002) Genome Res. , vol.12 , pp. 17-25
    • Snel, B.1    Bork, P.2    Huynen, M.A.3
  • 5
    • 0035943134 scopus 로고    scopus 로고
    • On surrogate methods for detecting lateral gene transfer
    • M.A. Ragan On surrogate methods for detecting lateral gene transfer FEMS Microbiol. Lett. 201 2001 187 191
    • (2001) FEMS Microbiol. Lett. , vol.201 , pp. 187-191
    • Ragan, M.A.1
  • 7
    • 0035546223 scopus 로고    scopus 로고
    • Detection of lateral gene transfer among microbial genomes
    • M.A. Ragan Detection of lateral gene transfer among microbial genomes Curr. Opin. Genet. Dev. 11 2001 620 626
    • (2001) Curr. Opin. Genet. Dev. , vol.11 , pp. 620-626
    • Ragan, M.A.1
  • 8
    • 0028069540 scopus 로고
    • Excision of large DNA regions termed pathogenicity islands from tRNA-specific loci in the chromosome of an Escherichia coli wild-type pathogen
    • G. Blum, M. Ott, A. Lischewski, A. Ritter, H. Imrich, and H. Tschape Excision of large DNA regions termed pathogenicity islands from tRNA-specific loci in the chromosome of an Escherichia coli wild-type pathogen Infect. Immun. 62 1994 606 614
    • (1994) Infect. Immun. , vol.62 , pp. 606-614
    • Blum, G.1    Ott, M.2    Lischewski, A.3    Ritter, A.4    Imrich, H.5    Tschape, H.6
  • 10
    • 0033758756 scopus 로고    scopus 로고
    • Pathogenicity islands and the evolution of microbes
    • J. Hacker, and J.B. Kaper Pathogenicity islands and the evolution of microbes Annu. Rev. Microbiol. 54 2000 641 679
    • (2000) Annu. Rev. Microbiol. , vol.54 , pp. 641-679
    • Hacker, J.1    Kaper, J.B.2
  • 11
    • 3042849253 scopus 로고    scopus 로고
    • Biased biological functions of horizontally transferred genes in prokaryotic genomes
    • Y. Nakamura, T. Itoh, H. Matsuda, and T. Gojobori Biased biological functions of horizontally transferred genes in prokaryotic genomes Nat. Genet. 36 2004 760 766
    • (2004) Nat. Genet. , vol.36 , pp. 760-766
    • Nakamura, Y.1    Itoh, T.2    Matsuda, H.3    Gojobori, T.4
  • 12
    • 0033616714 scopus 로고    scopus 로고
    • Horizontal gene transfer among genomes: The complexity hypothesis
    • R. Jain, M.C. Rivera, and J.A. Lake Horizontal gene transfer among genomes: the complexity hypothesis Proc. Natl. Acad. Sci. U. S. A. 96 1999 3801 3806
    • (1999) Proc. Natl. Acad. Sci. U. S. A. , vol.96 , pp. 3801-3806
    • Jain, R.1    Rivera, M.C.2    Lake, J.A.3
  • 13
    • 0033609333 scopus 로고    scopus 로고
    • Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima
    • K.E. Nelson, R.A. Clayton, S.R. Gill, M.L. Gwinn, R.J. Dodson, and D.H. Haft Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima Nature 399 1999 323 329
    • (1999) Nature , vol.399 , pp. 323-329
    • Nelson, K.E.1    Clayton, R.A.2    Gill, S.R.3    Gwinn, M.L.4    Dodson, R.J.5    Haft, D.H.6
  • 14
    • 0030660581 scopus 로고    scopus 로고
    • A genomic perspective on protein families
    • R.L. Tatusov, E.V. Koonin, and D.J. Lipman A genomic perspective on protein families Science 278 1997 631 637
    • (1997) Science , vol.278 , pp. 631-637
    • Tatusov, R.L.1    Koonin, E.V.2    Lipman, D.J.3
  • 16
    • 2942519433 scopus 로고    scopus 로고
    • SIGI: Score-based identification of genomic islands
    • R. Merkl SIGI: Score-based identification of genomic islands BMC Bioinformatics 5 2004 22
    • (2004) BMC Bioinformatics , vol.5 , pp. 22
    • Merkl, R.1
  • 23
    • 0038648028 scopus 로고    scopus 로고
    • Quantifying the species-specificity in genomic signatures, synonymous codon choice, amino acid usage and G+C content
    • R. Sandberg, C.I. Bränden, I. Ernberg, and J. Cöster Quantifying the species-specificity in genomic signatures, synonymous codon choice, amino acid usage and G+C content Gene 311 2003 35 42
    • (2003) Gene , vol.311 , pp. 35-42
    • Sandberg, R.1    Bränden, C.I.2    Ernberg, I.3    Cöster, J.4
  • 24
    • 0035961748 scopus 로고    scopus 로고
    • Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12
    • T. Hayashi, K. Makino, M. Ohnishi, K. Kurokawa, K. Ishii, and K. Yokoyama Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12 DNA Res. 8 2001 11 22
    • (2001) DNA Res. , vol.8 , pp. 11-22
    • Hayashi, T.1    Makino, K.2    Ohnishi, M.3    Kurokawa, K.4    Ishii, K.5    Yokoyama, K.6
  • 27
  • 29
    • 0034739881 scopus 로고    scopus 로고
    • Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti
    • T. Kaneko, Y. Nakamura, S. Sato, E. Asamizu, T. Kato, and S. Sasamoto Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti DNA Res. 7 2000 331 338
    • (2000) DNA Res. , vol.7 , pp. 331-338
    • Kaneko, T.1    Nakamura, Y.2    Sato, S.3    Asamizu, E.4    Kato, T.5    Sasamoto, S.6
  • 30
    • 0035958746 scopus 로고    scopus 로고
    • The composite genome of the legume symbiont Sinorhizobium meliloti
    • F. Galibert, T.M. Finan, S.R. Long, A. Pühler, P. Abola, and F. Ampe The composite genome of the legume symbiont Sinorhizobium meliloti Science 293 2001 668 672
    • (2001) Science , vol.293 , pp. 668-672
    • Galibert, F.1    Finan, T.M.2    Long, S.R.3    Pühler, A.4    Abola, P.5    Ampe, F.6
  • 31
    • 0032574728 scopus 로고    scopus 로고
    • Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene
    • J.T. Sullivan, and C.W. Ronson Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene Proc. Natl. Acad. Sci. U. S. A. 95 1998 5145 5149
    • (1998) Proc. Natl. Acad. Sci. U. S. A. , vol.95 , pp. 5145-5149
    • Sullivan, J.T.1    Ronson, C.W.2
  • 33
    • 0022448655 scopus 로고
    • Genetic transformation of the extreme thermophile Thermus thermophilus and of other Thermus spp
    • Y. Koyama, T. Hoshino, N. Tomizuka, and K. Furukawa Genetic transformation of the extreme thermophile Thermus thermophilus and of other Thermus spp J. Bacteriol. 166 1986 338 340
    • (1986) J. Bacteriol. , vol.166 , pp. 338-340
    • Koyama, Y.1    Hoshino, T.2    Tomizuka, N.3    Furukawa, K.4
  • 34
    • 0036151806 scopus 로고    scopus 로고
    • Molecular analyses of the natural transformation machinery and identification of pilus structures in the extremely thermophilic bacterium Thermus thermophilus strain HB27
    • A. Friedrich, C. Prust, T. Hartsch, A. Henne, and B. Averhoff Molecular analyses of the natural transformation machinery and identification of pilus structures in the extremely thermophilic bacterium Thermus thermophilus strain HB27 Appl. Environ. Microbiol. 68 2002 745 755
    • (2002) Appl. Environ. Microbiol. , vol.68 , pp. 745-755
    • Friedrich, A.1    Prust, C.2    Hartsch, T.3    Henne, A.4    Averhoff, B.5
  • 35
    • 0032482924 scopus 로고    scopus 로고
    • Molecular archaeology of the Escherichia coli genome
    • J.G. Lawrence, and H. Ochman Molecular archaeology of the Escherichia coli genome Proc. Natl. Acad. Sci. U. S. A. 95 1998 9413 9417
    • (1998) Proc. Natl. Acad. Sci. U. S. A. , vol.95 , pp. 9413-9417
    • Lawrence, J.G.1    Ochman, H.2
  • 36
    • 0035399931 scopus 로고    scopus 로고
    • Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes
    • S. Karlin Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes Trends Microbiol. 9 2001 335 343
    • (2001) Trends Microbiol. , vol.9 , pp. 335-343
    • Karlin, S.1
  • 37
    • 0035040364 scopus 로고    scopus 로고
    • Analysis of codon usage patterns of bacterial genomes using the self-organizing map
    • H.C. Wang, J. Badger, P. Kearney, and M. Li Analysis of codon usage patterns of bacterial genomes using the self-organizing map Mol. Biol. Evol. 18 2001 792 800
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 792-800
    • Wang, H.C.1    Badger, J.2    Kearney, P.3    Li, M.4
  • 38
    • 0142093984 scopus 로고    scopus 로고
    • Detecting pathogenicity islands and anomalous gene clusters by iterative discriminant analysis
    • Q. Tu, and D. Ding Detecting pathogenicity islands and anomalous gene clusters by iterative discriminant analysis FEMS Microbiol. Lett. 221 2003 269 275
    • (2003) FEMS Microbiol. Lett. , vol.221 , pp. 269-275
    • Tu, Q.1    Ding, D.2
  • 40
  • 41
    • 0035106010 scopus 로고    scopus 로고
    • Phylogenetic analyses of two "archaeal" genes in Thermotoga maritima reveal multiple transfers between Archaea and Bacteria
    • C.L. Nesbø, S. L'Haridon, K.O. Stetter, and W.F. Doolittle Phylogenetic analyses of two "archaeal" genes in Thermotoga maritima reveal multiple transfers between Archaea and Bacteria Mol. Biol. Evol. 18 2001 362 375
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 362-375
    • Nesbø, C.L.1    L'Haridon, S.2    Stetter, K.O.3    Doolittle, W.F.4
  • 42
    • 0033670249 scopus 로고    scopus 로고
    • Horizontal gene transfer in bacterial and archaeal complete genomes
    • S. Garcia-Vallvé, A. Romeu, and J. Palau Horizontal gene transfer in bacterial and archaeal complete genomes Genome Res. 10 2000 1719 1725
    • (2000) Genome Res. , vol.10 , pp. 1719-1725
    • Garcia-Vallvé, S.1    Romeu, A.2    Palau, J.3
  • 43
    • 0242424342 scopus 로고    scopus 로고
    • Targeting clusters of transferred genes in Thermotoga maritima
    • C.L. Nesbø, and W.F. Doolittle Targeting clusters of transferred genes in Thermotoga maritima Environ. Microbiol. 5 2003 1144 1154
    • (2003) Environ. Microbiol. , vol.5 , pp. 1144-1154
    • Nesbø, C.L.1    Doolittle, W.F.2
  • 44
    • 0642312312 scopus 로고    scopus 로고
    • The source of laterally transferred genes in bacterial genomes
    • V. Daubin, E. Lerat, and G. Perrière The source of laterally transferred genes in bacterial genomes Genome Biol. 4 2003 R57
    • (2003) Genome Biol. , vol.4 , pp. 57
    • Daubin, V.1    Lerat, E.2    Perrière, G.3
  • 45
    • 0034163439 scopus 로고    scopus 로고
    • Horizontal gene transfer and the origin of species: Lessons from bacteria
    • F. de la Cruz, and J. Davies Horizontal gene transfer and the origin of species: lessons from bacteria Trends Microbiol. 8 2000 128 133
    • (2000) Trends Microbiol. , vol.8 , pp. 128-133
    • De La Cruz, F.1    Davies, J.2
  • 46
    • 2042507722 scopus 로고    scopus 로고
    • Have archaeal genes contributed to bacterial virulence?
    • U. Gophna, R.L. Charlebois, and W.F. Doolittle Have archaeal genes contributed to bacterial virulence? Trends Microbiol. 12 2004 213 219
    • (2004) Trends Microbiol. , vol.12 , pp. 213-219
    • Gophna, U.1    Charlebois, R.L.2    Doolittle, W.F.3
  • 47
    • 2042421069 scopus 로고    scopus 로고
    • Lateral gene transfer (LGT) between Archaea and Escherichia coli is a contributor to the emergence of novel infectious disease
    • D.M. Faguy Lateral gene transfer (LGT) between Archaea and Escherichia coli is a contributor to the emergence of novel infectious disease BMC Infect. Dis. 3 2003 13
    • (2003) BMC Infect. Dis. , vol.3 , pp. 13
    • Faguy, D.M.1
  • 48
    • 1542327668 scopus 로고    scopus 로고
    • Trends between gene content and genome size in prokaryotic species with larger genomes
    • K.T. Konstantinidis, and J.M. Tiedje Trends between gene content and genome size in prokaryotic species with larger genomes Proc. Natl. Acad. Sci. U. S. A. 101 2004 3160 3165
    • (2004) Proc. Natl. Acad. Sci. U. S. A. , vol.101 , pp. 3160-3165
    • Konstantinidis, K.T.1    Tiedje, J.M.2
  • 49
    • 0031945225 scopus 로고    scopus 로고
    • Cell wall polymers in Archaea (Archaebacteria)
    • O. Kandler, and H. König Cell wall polymers in Archaea (Archaebacteria) Cell. Mol. Life Sci. 54 1998 305 308
    • (1998) Cell. Mol. Life Sci. , vol.54 , pp. 305-308
    • Kandler, O.1    König, H.2
  • 50
    • 0032766490 scopus 로고    scopus 로고
    • Comparative genomics of the Archaea (Euryarchaeota): Evolution of conserved protein families, the stable core, and the variable shell
    • K.S. Makarova, L. Aravind, M.Y. Galperin, N.V. Grishin, R.L. Tatusov, and Y.I. Wolf Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell Genome Res. 9 1999 608 628
    • (1999) Genome Res. , vol.9 , pp. 608-628
    • Makarova, K.S.1    Aravind, L.2    Galperin, M.Y.3    Grishin, N.V.4    Tatusov, R.L.5    Wolf, Y.I.6
  • 51
    • 0015598484 scopus 로고
    • Aerobic bacteria occurring in the hind-gut of the cockroach, Blatta orientalis
    • N.R. Burgess, S.N. McDermott, and J. Whiting Aerobic bacteria occurring in the hind-gut of the cockroach, Blatta orientalis J. Hyg. (Lond.) 71 1973 1 7
    • (1973) J. Hyg. (Lond.) , vol.71 , pp. 1-7
    • Burgess, N.R.1    McDermott, S.N.2    Whiting, J.3
  • 52
    • 0032777154 scopus 로고    scopus 로고
    • Insights into the evolutionary process of genome degradation
    • J.O. Andersson, and S.G. Andersson Insights into the evolutionary process of genome degradation Curr. Opin. Genet. Dev. 9 1999 664 671
    • (1999) Curr. Opin. Genet. Dev. , vol.9 , pp. 664-671
    • Andersson, J.O.1    Andersson, S.G.2
  • 54
    • 0035479142 scopus 로고    scopus 로고
    • Deletional bias and the evolution of bacterial genomes
    • A. Mira, H. Ochman, and N.A. Moran Deletional bias and the evolution of bacterial genomes Trends Genet. 17 2001 589 596
    • (2001) Trends Genet. , vol.17 , pp. 589-596
    • Mira, A.1    Ochman, H.2    Moran, N.A.3
  • 55
    • 0038486918 scopus 로고    scopus 로고
    • The balance of driving forces during genome evolution in prokaryotes
    • V. Kunin, and C.A. Ouzounis The balance of driving forces during genome evolution in prokaryotes Genome Res. 13 2003 1589 1594
    • (2003) Genome Res. , vol.13 , pp. 1589-1594
    • Kunin, V.1    Ouzounis, C.A.2
  • 56
    • 0028027521 scopus 로고
    • Hyperrecombination in the terminus region of the Escherichia coli chromosome: Possible relation to nucleoid organization
    • J. Louarn, F. Cornet, V. Francois, J. Patte, and J.M. Louarn Hyperrecombination in the terminus region of the Escherichia coli chromosome: possible relation to nucleoid organization J. Bacteriol. 176 1994 7524 7531
    • (1994) J. Bacteriol. , vol.176 , pp. 7524-7531
    • Louarn, J.1    Cornet, F.2    Francois, V.3    Patte, J.4    Louarn, J.M.5


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