메뉴 건너뛰기




Volumn 2, Issue 1, 2010, Pages 646-655

Evolutionary dynamics of complete Campylobacter pan-genomes and the bacterial species concept

Author keywords

Lateral gene transfer; Pan and core genome; Prokaryote; Speciation

Indexed keywords

ARTICLE; BACTERIAL GENOME; CAMPYLOBACTER COLI; CAMPYLOBACTER JEJUNI; CHROMOSOME MAP; COMPARATIVE STUDY; GENETICS; HORIZONTAL GENE TRANSFER; MOLECULAR EVOLUTION;

EID: 77958479691     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evq048     Document Type: Article
Times cited : (89)

References (57)
  • 1
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology
    • Ashburner M, et al. 2000. Gene ontology: tool for the unification of biology. Nat Genet. 25:25-29.
    • (2000) Nat. Genet. , vol.25 , pp. 25-29
    • Ashburner, M.1
  • 2
    • 58149187893 scopus 로고    scopus 로고
    • The GOA database in 2009-an integrated gene ontology annotation resource
    • Barrell D, et al. 2009. The GOA database in 2009-an integrated Gene Ontology Annotation resource. Nucleic Acids Res. 37:396-403.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 396-403
    • Barrell, D.1
  • 3
    • 55549089660 scopus 로고    scopus 로고
    • Accurate whole human genome sequencing using reversible terminator chemistry
    • Bentley DR, et al. 2008. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 456:53-59.
    • (2008) Nature , vol.456 , pp. 53-59
    • Bentley, D.R.1
  • 4
    • 12344269924 scopus 로고    scopus 로고
    • GO: Term finder-open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
    • Boyle EI, et al. 2004. GO::TermFinder-open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics. 20:3710-3715.
    • (2004) Bioinformatics , vol.20 , pp. 3710-3715
    • Boyle, E.I.1
  • 5
    • 33646167864 scopus 로고    scopus 로고
    • A simple and robust statistical test for detecting the presence of recombination
    • Bruen TC, Philippe H, Bryant D. 2006. A simple and robust statistical test for detecting the presence of recombination. Genetics. 172:2665-2681.
    • (2006) Genetics , vol.172 , pp. 2665-2681
    • Bruen, T.C.1    Philippe, H.2    Bryant, D.3
  • 6
    • 33644851507 scopus 로고    scopus 로고
    • Sources of Campylobacter spp. colonizing housed broiler flocks during rearing
    • Bull SA, et al. 2006. Sources of Campylobacter spp. colonizing housed broiler flocks during rearing. Appl Environ Microbiol. 72:645-652.
    • (2006) Appl. Environ. Microbiol. , vol.72 , pp. 645-652
    • Bull, S.A.1
  • 7
    • 69949092892 scopus 로고    scopus 로고
    • Genomic insights into the convergence and pathogenicity factors of Campylobacter jejuni and Campylobacter coli species
    • Caro-Quintero A, Rodriguez-Castan̄o GP, Konstantinidis KT. 2009. Genomic insights into the convergence and pathogenicity factors of Campylobacter jejuni and Campylobacter coli species. J Bacteriol. 191:5824-5831.
    • (2009) J. Bacteriol. , vol.191 , pp. 5824-5831
    • Caro-Quintero, A.1    Rodriguez-Castano, G.P.2    Konstantinidis, K.T.3
  • 8
    • 44949108392 scopus 로고    scopus 로고
    • Comparison of Campylobacter populations in wild geese with those in starlings and free-range poultry on the same farm
    • Colles FM, Dingle KE, Cody AJ, Maiden MC. 2008. Comparison of Campylobacter populations in wild geese with those in starlings and free-range poultry on the same farm. Appl Environ Microbiol. 74:3583-3590.
    • (2008) Appl. Environ. Microbiol. , vol.74 , pp. 3583-3590
    • Colles, F.M.1    Dingle, K.E.2    Cody, A.J.3    Maiden, M.C.4
  • 10
    • 0034703744 scopus 로고    scopus 로고
    • Evolutionary implications of the frequent horizontal transfer of mismatch repair genes
    • Denamur E, et al. 2000. Evolutionary implications of the frequent horizontal transfer of mismatch repair genes. Cell. 103:711-721.
    • (2000) Cell. , vol.103 , pp. 711-721
    • Denamur, E.1
  • 11
    • 0023557675 scopus 로고
    • Rythmes saisonniers et composantes stationnelles en milieu aquatique I-Description d'un plan d'observations complet par projection de variables
    • Dolédec S, Chessel D. 1987. Rythmes saisonniers et composantes stationnelles en milieu aquatique I-Description d'un plan d'observations complet par projection de variables. Acta Oecol Oec Gen. 8:403-426.
    • (1987) Acta Oecol Oec Gen. , vol.8 , pp. 403-426
    • Dolédec, S.1    Chessel, D.2
  • 12
    • 37649024043 scopus 로고    scopus 로고
    • The ade4 package: Implementing the duality diagram for ecologists
    • Dray S, Dufour AB. 2007. The ade4 package: implementing the duality diagram for ecologists. J Stat Softw. 22:1-20.
    • (2007) J. Stat. Softw , vol.22 , pp. 1-20
    • Dray, S.1    Dufour, A.B.2
  • 13
    • 0025788069 scopus 로고
    • Recombination in Escherichia coli and the definition of biological species
    • Dykhuizen DE, Green L. 1991. Recombination in Escherichia coli and the definition of biological species. J Bacteriol. 173:7257-7268.
    • (1991) J. Bacteriol. , vol.173 , pp. 7257-7268
    • Dykhuizen, D.E.1    Green, L.2
  • 14
    • 44949157290 scopus 로고    scopus 로고
    • A probabilistic model of local sequence alignment that simplifies statistical significance estimation
    • Eddy SR. 2008. A probabilistic model of local sequence alignment that simplifies statistical significance estimation. PLoS Comput Biol. 4: e1000172.
    • (2008) PLoS Comput. Biol. , vol.4
    • Eddy, S.R.1
  • 15
    • 75549090603 scopus 로고    scopus 로고
    • The Pfam protein families database
    • Finn RD, et al. 2010. The Pfam protein families database. Nucleic Acids Res. 38:211-222.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 211-222
    • Finn, R.D.1
  • 16
    • 0020491327 scopus 로고
    • Codon usage in bacteria: Correlation with gene expressivity
    • Gouy M, Gautier C. 1982. Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res. 10:7055-7074.
    • (1982) Nucleic Acids Res. , vol.10 , pp. 7055-7074
    • Gouy, M.1    Gautier, C.2
  • 17
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696-704.
    • (2003) Syst. Biol. , vol.52 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 18
    • 34347230891 scopus 로고    scopus 로고
    • Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence
    • Gundogdu O, et al. 2007. Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence. BMC Genomics. 8:162.
    • (2007) BMC Genomics , vol.8 , pp. 162
    • Gundogdu, O.1
  • 19
    • 0022376704 scopus 로고
    • Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
    • Hasegawa M, Kishino H, Yano T. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 22:160-174.
    • (1985) J. Mol. Evol. , vol.22 , pp. 160-174
    • Hasegawa, M.1    Kishino, H.2    Yano, T.3
  • 20
    • 58149203231 scopus 로고    scopus 로고
    • Interpro: The integrative protein signature database
    • Hunter S, et al. 2009. Interpro: the integrative protein signature database. Nucleic Acids Res. 37:211-215.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 211-215
    • Hunter, S.1
  • 21
    • 73349119381 scopus 로고    scopus 로고
    • Isolation and characterization of bacteriophages specific for Campylobacter jejuni
    • Hwang S, et al. 2009. Isolation and characterization of bacteriophages specific for Campylobacter jejuni. Microbiol Immunol. 53:559-566.
    • (2009) Microbiol. Immunol. , vol.53 , pp. 559-566
    • Hwang, S.1
  • 22
    • 0029963710 scopus 로고    scopus 로고
    • A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences
    • Jakobsen IB, Easteal S. 1996. A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences. Comput Appl Biosci. 12:291-295.
    • (1996) Comput. Appl. Biosci. , vol.12 , pp. 291-295
    • Jakobsen, I.B.1    Easteal, S.2
  • 23
    • 0031720281 scopus 로고    scopus 로고
    • Codon usages in different gene classes of the Escherichia coli genome
    • Karlin S, Mrázek J, Campbell AM. 1998. Codon usages in different gene classes of the Escherichia coli genome. Mol Microbiol. 29:1341-1355.
    • (1998) Mol. Microbiol. , vol.29 , pp. 1341-1355
    • Karlin, S.1    Mrázek, J.2    Campbell, A.M.3
  • 24
    • 0030635485 scopus 로고    scopus 로고
    • Pathogenesis of enteric infection by Campylobacter
    • Ketley JM. 1997. Pathogenesis of enteric infection by Campylobacter. Microbiology. 143:5-21.
    • (1997) Microbiology , vol.143 , pp. 5-21
    • Ketley, J.M.1
  • 25
    • 76749117156 scopus 로고    scopus 로고
    • Assembly complexity of prokaryotic genomes using short reads
    • Kingsford C, Schatz MC, Pop M. 2010. Assembly complexity of prokaryotic genomes using short reads. BMC Bioinformatics. 11:21.
    • (2010) BMC Bioinformatics , vol.11 , pp. 21
    • Kingsford, C.1    Schatz, M.C.2    Pop, M.3
  • 27
    • 0034283229 scopus 로고    scopus 로고
    • Intraspecies variation in bacterial genomes: The need for a species genome concept
    • Lan R, Reeves PR. 2000. Intraspecies variation in bacterial genomes: the need for a species genome concept. Trends Microbiol. 8:396-401.
    • (2000) Trends Microbiol. , vol.8 , pp. 396-401
    • Lan, R.1    Reeves, P.R.2
  • 28
    • 0035448522 scopus 로고    scopus 로고
    • When does a clone deserve a name? A perspective on bacterial species based on population genetics
    • Lan R, Reeves PR. 2001. When does a clone deserve a name? A perspective on bacterial species based on population genetics. Trends Microbiol. 9:419-424.
    • (2001) Trends Microbiol. , vol.9 , pp. 419-424
    • Lan, R.1    Reeves, P.R.2
  • 29
    • 61349194462 scopus 로고    scopus 로고
    • Estimating the size of the bacterial pangenome
    • Lapierre P, Gogarten JP. 2009. Estimating the size of the bacterial pangenome. Trends Genet. 25:107-110.
    • (2009) Trends Genet. , vol.25 , pp. 107-110
    • Lapierre, P.1    Gogarten, J.P.2
  • 30
    • 65549114090 scopus 로고    scopus 로고
    • The interplay of homologous recombination and horizontal gene transfer in bacterial speciation
    • Lawrence JG, Retchless AC. 2009. The interplay of homologous recombination and horizontal gene transfer in bacterial speciation. Methods Mol Biol. 532:29-53.
    • (2009) Methods Mol. Biol. , vol.532 , pp. 29-53
    • Lawrence, J.G.1    Retchless, A.C.2
  • 31
    • 67650074198 scopus 로고    scopus 로고
    • Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter
    • Lefébure T, Stanhope MJ. 2009. Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter. Genome Res. 19:1224-1232.
    • (2009) Genome Res. , vol.19 , pp. 1224-1232
    • Lefébure, T.1    Stanhope, M.J.2
  • 32
    • 55549097836 scopus 로고    scopus 로고
    • Mapping short DNA sequencing reads and calling variants using mapping quality scores
    • Li H, Ruan J, Durbin R. 2008. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18:1851-1858.
    • (2008) Genome Res. , vol.18 , pp. 1851-1858
    • Li, H.1    Ruan, J.2    Durbin, R.3
  • 33
    • 0033959357 scopus 로고    scopus 로고
    • Barriers to genetic exchange between bacterial species: Streptococcus pneumoniae transformation
    • Majewski J, Zawadzki P, Pickerill P, Cohan FM, Dowson CG. 2000. Barriers to genetic exchange between bacterial species: Streptococcus pneumoniae transformation. J Bacteriol. 182:1016-1023.
    • (2000) J. Bacteriol. , vol.182 , pp. 1016-1023
    • Majewski, J.1    Zawadzki, P.2    Pickerill, P.3    Cohan, F.M.4    Dowson, C.G.5
  • 34
    • 24044455869 scopus 로고    scopus 로고
    • Genome sequencing in microfabricated highdensity picolitre reactors
    • Margulies M, et al. 2005. Genome sequencing in microfabricated highdensity picolitre reactors. Nature. 437:376-380.
    • (2005) Nature , vol.437 , pp. 376-380
    • Margulies, M.1
  • 35
    • 0026708873 scopus 로고
    • Analyzing the mosaic structure of genes
    • Maynard Smith J. 1992. Analyzing the mosaic structure of genes. J Mol Evol. 34:126-129.
    • (1992) J. Mol. Evol. , vol.34 , pp. 126-129
    • Smith, J.M.1
  • 36
    • 33846703734 scopus 로고    scopus 로고
    • Host-associated genetic import in Campylobacter jejuni
    • McCarthy ND, et al. 2007. Host-associated genetic import in Campylobacter jejuni. Emerging Infect Dis. 13:267-272.
    • (2007) Emerging Infect. Dis. , vol.13 , pp. 267-272
    • McCarthy, N.D.1
  • 37
    • 26844544284 scopus 로고    scopus 로고
    • Differentiation of Campylobacter populations as demonstrated by flagellin short variable region sequences
    • Meinersmann RJ, Phillips RW, Hiett KL, Fedorka-Cray P. 2005. Differentiation of Campylobacter populations as demonstrated by flagellin short variable region sequences. Appl Environ Microbiol. 71:6368-6374.
    • (2005) Appl. Environ. Microbiol. , vol.71 , pp. 6368-6374
    • Meinersmann, R.J.1    Phillips, R.W.2    Hiett, K.L.3    Fedorka-Cray, P.4
  • 38
    • 30744442111 scopus 로고    scopus 로고
    • Identification of host-associated alleles by multilocus sequence typing of Campylobacter coli strains from food animals
    • Miller WG, et al. 2006. Identification of host-associated alleles by multilocus sequence typing of Campylobacter coli strains from food animals. Microbiology. 152:245-255.
    • (2006) Microbiology , vol.152 , pp. 245-255
    • Miller, W.G.1
  • 39
    • 14044258713 scopus 로고    scopus 로고
    • Diversity within the Campylobacter jejuni type I restriction-modification loci
    • Miller WG, et al. 2005. Diversity within the Campylobacter jejuni type I restriction-modification loci. Microbiology. 151:337-351.
    • (2005) Microbiology , vol.151 , pp. 337-351
    • Miller, W.G.1
  • 40
    • 0035479142 scopus 로고    scopus 로고
    • Deletional bias and the evolution of bacterial genomes
    • Mira A, Ochman H, Moran NA. 2001. Deletional bias and the evolution of bacterial genomes. Trends Genet. 17:589-596.
    • (2001) Trends Genet. , vol.17 , pp. 589-596
    • Mira, A.1    Ochman, H.2    Moran, N.A.3
  • 41
    • 21044453560 scopus 로고    scopus 로고
    • Campylobacter
    • Moore JE, et al. 2005. Campylobacter. Vet Res. 36:351-382.
    • (2005) Vet. Res. , vol.36 , pp. 351-382
    • Moore, J.E.1
  • 42
    • 0027278850 scopus 로고
    • The effect of DNA sequence divergence on sexual isolation in Bacillus
    • Roberts MS, Cohan FM. 1993. The effect of DNA sequence divergence on sexual isolation in Bacillus. Genetics. 134:401-408.
    • (1993) Genetics , vol.134 , pp. 401-408
    • Roberts, M.S.1    Cohan, F.M.2
  • 43
    • 0021085021 scopus 로고
    • Isolation and characterization of Campylobacter jejuni and Campylobacter coli from domestic and wild mammals in norway
    • Rosef O, Gondrosen B, Kapperud G, Underdal B. 1983. Isolation and characterization of Campylobacter jejuni and Campylobacter coli from domestic and wild mammals in norway. Appl Environ Microbiol. 46:855-859.
    • (1983) Appl. Environ. Microbiol. , vol.46 , pp. 855-859
    • Rosef, O.1    Gondrosen, B.2    Kapperud, G.3    Underdal, B.4
  • 44
    • 42049090179 scopus 로고    scopus 로고
    • Convergence of Campylobacter species: Implications for bacterial evolution
    • Sheppard SK, McCarthy ND, Falush D, Maiden MC. 2008. Convergence of Campylobacter species: implications for bacterial evolution. Science. 320:237-239.
    • (2008) Science , vol.320 , pp. 237-239
    • Sheppard, S.K.1    McCarthy, N.D.2    Falush, D.3    Maiden, M.C.4
  • 45
    • 76149112273 scopus 로고    scopus 로고
    • Investigation of food and environmental exposures relating to the epidemiology of Campylobacter coli in humans in Northwest England
    • Sopwith W, et al. 2010. Investigation of food and environmental exposures relating to the epidemiology of Campylobacter coli in humans in Northwest England. Appl Environ Microbiol. 76:129-135.
    • (2010) Appl. Environ. Microbiol. , vol.76 , pp. 129-135
    • Sopwith, W.1
  • 46
    • 34347388470 scopus 로고    scopus 로고
    • Uniref: Comprehensive and non-redundant uniprot reference clusters
    • Suzek BE, Huang H, McGarvey P, Mazumder R, Wu CH. 2007. Uniref: comprehensive and non-redundant uniprot reference clusters. Bioinformatics. 23:1282-1288.
    • (2007) Bioinformatics , vol.23 , pp. 1282-1288
    • Suzek, B.E.1    Huang, H.2    McGarvey, P.3    Mazumder, R.4    Wu, C.H.5
  • 47
    • 77958465965 scopus 로고    scopus 로고
    • *. 2002
    • Version 4. Sunderland MA: Sinauer Associates
    • * and other methods). Version 4. Sunderland (MA): Sinauer Associates.
    • (2002) * and Other Methods)
    • Swofford, D.L.1
  • 48
    • 25444524604 scopus 로고    scopus 로고
    • Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial pangenome
    • Tettelin H, et al. 2005. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pangenome. Proc Natl Acad Sci U S A. 102:13950-13955.
    • (2005) Proc. Natl. Acad. Sci. U. S. A. , vol.102 , pp. 13950-13955
    • Tettelin, H.1
  • 51
    • 0030924545 scopus 로고    scopus 로고
    • Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in enterobacteria
    • Vulić M, Dionisio F, Taddei F, Radman M. 1997. Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in enterobacteria. Proc Natl Acad Sci U S A. 94:9763-9767.
    • (1997) Proc. Natl. Acad. Sci. U. S. A. , vol.94 , pp. 9763-9767
    • Vulić, M.1    Dionisio, F.2    Taddei, F.3    Radman, M.4
  • 52
    • 0242417584 scopus 로고    scopus 로고
    • Prevalence of Campylobacter jejuni, Campylobacter lari, and Campylobacter coli in different ecological guilds and taxa of migrating birds
    • Waldenström J, et al. 2002. Prevalence of Campylobacter jejuni, Campylobacter lari, and Campylobacter coli in different ecological guilds and taxa of migrating birds. Appl Environ Microbiol. 68:5911-5917.
    • (2002) Appl. Environ. Microbiol. , vol.68 , pp. 5911-5917
    • Waldenström, J.1
  • 53
    • 0346252342 scopus 로고    scopus 로고
    • Variation of the natural transformation frequency of Campylobacter jejuni in liquid shake culture
    • Wilson DL, et al. 2003. Variation of the natural transformation frequency of Campylobacter jejuni in liquid shake culture. Microbiology. 149:3603-3615.
    • (2003) Microbiology , vol.149 , pp. 3603-3615
    • Wilson, D.L.1
  • 54
    • 58449131619 scopus 로고    scopus 로고
    • Rapid evolution and the importance of recombination to the gastroenteric pathogen Campylobacter jejuni
    • Wilson DJ, et al. 2009. Rapid evolution and the importance of recombination to the gastroenteric pathogen Campylobacter jejuni. Mol Biol Evol. 26:385-397.
    • (2009) Mol. Biol. Evol. , vol.26 , pp. 385-397
    • Wilson, D.J.1
  • 55
    • 0029038657 scopus 로고
    • The log-linear relationship between sexual isolation and sequence divergence in Bacillus transformation is robust
    • Zawadzki P, Roberts MS, Cohan FM. 1995. The log-linear relationship between sexual isolation and sequence divergence in Bacillus transformation is robust. Genetics. 140:917-932.
    • (1995) Genetics , vol.140 , pp. 917-932
    • Zawadzki, P.1    Roberts, M.S.2    Cohan, F.M.3
  • 56
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821-829.
    • (2008) Genome Res. , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 57
    • 33748277982 scopus 로고    scopus 로고
    • Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events
    • Zhaxybayeva O, Gogarten JP, Charlebois RL, Doolittle WF, Papke RT. 2006. Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events. Genome Res. 16:1099-1108.
    • (2006) Genome Res. , vol.16 , pp. 1099-1108
    • Zhaxybayeva, O.1    Gogarten, J.P.2    Charlebois, R.L.3    Doolittle, W.F.4    Papke, R.T.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.