메뉴 건너뛰기




Volumn 7, Issue 11, 2012, Pages 1283-1296

Developing insights into the mechanisms of evolution of bacterial pathogens from whole-genome sequences

Author keywords

bacteria; evolution; genome sequencing; horizontal gene transfer; mutation; recombination; selection

Indexed keywords

ANTIBIOTIC RESISTANCE; BACTERIAL GENOME; BACTERIAL VIRULENCE; GENE DELETION; GENE INSERTION; GENE TRANSFER; GENETIC MARKER; MUTAGENESIS; NONHUMAN; POINT MUTATION; PRIORITY JOURNAL; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 84867729107     PISSN: 17460913     EISSN: 17460921     Source Type: Journal    
DOI: 10.2217/fmb.12.108     Document Type: Review
Times cited : (80)

References (99)
  • 1
    • 0029653518 scopus 로고
    • Whole-genome random sequencing and assembly of Haemophilus influenzae Rd
    • Fleischmann RD, Adams MD, White O et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269(5223), 496-512 (1995).
    • (1995) Science , vol.269 , Issue.5223 , pp. 496-512
    • Fleischmann, R.D.1    Adams, M.D.2    White, O.3
  • 2
    • 0028829125 scopus 로고
    • The minimal gene complement of Mycoplasma genitalium
    • Fraser CM, Gocayne JD, White O et al. The minimal gene complement of Mycoplasma genitalium. Science 270(5235), 397-403 (1995).
    • (1995) Science , vol.270 , Issue.5235 , pp. 397-403
    • Fraser, C.M.1    Gocayne, J.D.2    White, O.3
  • 3
    • 0035838557 scopus 로고    scopus 로고
    • Bacterial virulence:Can we draw the line
    • Wassenaar TM, Gaastra W. Bacterial virulence:Can we draw the line? FEMS Microbiol. Lett. 201(1), 1-7 (2001).
    • (2001) FEMS Microbiol. Lett , vol.201 , Issue.1 , pp. 1-7
    • Wassenaar, T.M.1    Gaastra, W.2
  • 4
    • 84860557378 scopus 로고    scopus 로고
    • Whole-genome sequencing of Sordaria macrospora mutants identifies developmental genes
    • Nowrousian M, Teichert I, Masloff S, Kück U. Whole-genome sequencing of Sordaria macrospora mutants identifies developmental genes. G3 (Bethesda) 2(2), 261-270 (2012).
    • (2012) G3 Bethesda , vol.2 , Issue.2 , pp. 261-270
    • Nowrousian, M.1    Teichert, I.2    Masloff, S.3    Kück, U.4
  • 5
    • 79959577368 scopus 로고    scopus 로고
    • Whole genome sequencing and complete genetic analysis reveals novel pathways to glycopeptide resistance in Staphylococcus aureus
    • Renzoni A, Andrey DO, Jousselin A et al. Whole genome sequencing and complete genetic analysis reveals novel pathways to glycopeptide resistance in Staphylococcus aureus. Plos One 6(6), e21577 (2011).
    • (2011) Plos One , vol.6 , Issue.6
    • Renzoni, A.1    Andrey, D.O.2    Jousselin, A.3
  • 6
    • 84555209977 scopus 로고    scopus 로고
    • Whole-genome sequencing of rifampicinresistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes
    • Comas I, Borrell S, Roetzer A et al. Whole-genome sequencing of rifampicinresistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes. Nat. Genet. 44(1), 106-110 (2011).
    • (2011) Nat. Genet , vol.44 , Issue.1 , pp. 106-110
    • Comas, I.1    Borrell, S.2    Roetzer, A.3
  • 7
    • 33745615117 scopus 로고    scopus 로고
    • The competitive cost of antibiotic resistance in Mycobacterium tuberculosis
    • Gagneux S, Long CD, Small PM, Van T, Schoolnik GK, Bohannan BJ. The competitive cost of antibiotic resistance in Mycobacterium tuberculosis. Science 312(5782), 1944-1946 (2006).
    • (2006) Science , vol.312 , Issue.5782 , pp. 1944-1946
    • Gagneux, S.1    Long, C.D.2    Small, P.M.3    Van T Schoolnik, G.K.4    Bohannan, B.J.5
  • 8
    • 0346726023 scopus 로고    scopus 로고
    • Neutral mutations and neutral substitutions in bacterial genomes
    • Ochman H. Neutral mutations and neutral substitutions in bacterial genomes. Mol. Biol. Evol. 20(12), 2091-2096 (2003).
    • (2003) Mol. Biol. Evol , vol.20 , Issue.12 , pp. 2091-2096
    • Ochman, H.1
  • 9
    • 0345549815 scopus 로고
    • A set of lacZ mutations in Escherichia coli that allow rapid detection of each of the six base substitutions
    • Cupples CG, Miller JH. A set of lacZ mutations in Escherichia coli that allow rapid detection of each of the six base substitutions. Proc. Natl Acad. Sci. USA 86(14), 5345-5349 (1989).
    • (1989) Proc. Natl Acad. Sci. USA , vol.86 , Issue.14 , pp. 5345-5349
    • Cupples, C.G.1    Miller, J.H.2
  • 11
    • 0023274170 scopus 로고
    • The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias
    • Sharp PM, Li WH. The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias. Mol. Biol. Evol. 4(3), 222-230 (1987).
    • (1987) Mol. Biol. Evol , vol.4 , Issue.3 , pp. 222-230
    • Sharp, P.M.1    Li, W.H.2
  • 12
    • 75649084906 scopus 로고    scopus 로고
    • Evolution of MRSA during hospital transmission and intercontinental spread
    • Harris SR, Feil EJ, Holden MT et al. Evolution of MRSA during hospital transmission and intercontinental spread. Science 327(5964), 469-474 (2010
    • (2010) Science , vol.327 , Issue.5964 , pp. 469-474
    • Harris, S.R.1    Feil, E.J.2    Holden, M.T.3
  • 14
    • 77952326903 scopus 로고    scopus 로고
    • The population dynamics and control of tuberculosis
    • Dye C, Williams BG. The population dynamics and control of tuberculosis. Science 328(5980), 856-861 (2010).
    • (2010) Science , vol.328 , Issue.5980 , pp. 856-861
    • Dye, C.1    Williams, B.G.2
  • 15
    • 79955460244 scopus 로고    scopus 로고
    • Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection
    • Ford CB, Lin PL, Chase MR et al. Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection. Nat. Genet. 43(5), 482-486 (2011).
    • (2011) Nat. Genet , vol.43 , Issue.5 , pp. 482-486
    • Ford, C.B.1    Lin, P.L.2    Chase, M.R.3
  • 16
    • 33744814106 scopus 로고    scopus 로고
    • Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients
    • Smith EE, Buckley DG, Wu Z et al. Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients. Proc. Natl Acad. Sci. USA 103(22), 8487-8492 (2006).
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , Issue.22 , pp. 8487-8492
    • Smith, E.E.1    Buckley, D.G.2    Wu, Z.3
  • 17
    • 79251544864 scopus 로고    scopus 로고
    • Rapid pneumococcal evolution in response to clinical interventions
    • Croucher NJ, Harris SR, Fraser C et al. Rapid pneumococcal evolution in response to clinical interventions. Science 331(6016), 430-434 (2011).
    • (2011) Science , vol.331 , Issue.6016 , pp. 430-434
    • Croucher, N.J.1    Harris, S.R.2    Fraser, C.3
  • 18
    • 78049445172 scopus 로고    scopus 로고
    • Evidence that mutation is universally biased towards AT in bacteria
    • Hershberg R, Petrov DA. Evidence that mutation is universally biased towards AT in bacteria. Plos Genet. 6(9), e1001115 (2010).
    • (2010) Plos Genet , vol.6 , Issue.9
    • Hershberg, R.1    Petrov, D.A.2
  • 19
    • 28544451203 scopus 로고    scopus 로고
    • Environments shape the nucleotide composition of genomes
    • Foerstner KU, Von Mering C, Hooper SD, Bork P. Environments shape the nucleotide composition of genomes. EMBO Rep. 6(12), 1208-1213 (2005).
    • (2005) EMBO Rep , vol.6 , Issue.12 , pp. 1208-1213
    • Foerstner, K.U.1    Von Mering, C.2    Hooper, S.D.3    Bork, P.4
  • 20
    • 73949105846 scopus 로고    scopus 로고
    • Use of high throughput sequencing to observe genome dynamics at a single cell level
    • Parkhomchuk D, Amstislavskiy V, Soldatov A, Ogryzko V. Use of high throughput sequencing to observe genome dynamics at a single cell level. Proc. Natl Acad. Sci. USA 106(49), 20830-20835 (2009).
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , Issue.49 , pp. 20830-20835
    • Parkhomchuk, D.1    Amstislavskiy, V.2    Soldatov, A.3    Ogryzko, V.4
  • 21
    • 56649099178 scopus 로고    scopus 로고
    • Whole-genome mutational biases in bacteria
    • Lind PA, Andersson DI. Whole-genome mutational biases in bacteria. Proc. Natl Acad. Sci. USA 105(46), 17878-17883 (2008).
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , Issue.46 , pp. 17878-17883
    • Lind, P.A.1    Andersson, D.I.2
  • 22
    • 79954672317 scopus 로고    scopus 로고
    • Genome structural variation discovery and genotyping
    • Alkan C, Coe BP, Eichler EE. Genome structural variation discovery and genotyping. Nat. Rev. Genet. 12(5), 363-376 (2011).
    • (2011) Nat. Rev. Genet , vol.12 , Issue.5 , pp. 363-376
    • Alkan, C.1    Coe, B.P.2    Eichler, E.E.3
  • 23
    • 70449704529 scopus 로고    scopus 로고
    • Computational methods for discovering structural variation with next-generation sequencing
    • Medvedev P, Stanciu M, Brudno M. Computational methods for discovering structural variation with next-generation sequencing. Nat. Methods 6(11 Suppl.), S13-S20 (2009).
    • (2009) Nat. Methods , vol.6 , Issue.11 SUPPL.
    • Medvedev, P.1    Stanciu, M.2    Brudno, M.3
  • 24
    • 77953478153 scopus 로고    scopus 로고
    • The phage-related chromosomal islands of Gram-positive bacteria
    • Novick RP, Christie GE, Penades Jr. The phage-related chromosomal islands of Gram-positive bacteria. Nat. Rev. Microbiol. 8(8), 541-551 (2010).
    • (2010) Nat. Rev. Microbiol , vol.8 , Issue.8 , pp. 541-551
    • Novick, R.P.1    Christie, G.E.2    Penades, J.R.3
  • 25
    • 80053133499 scopus 로고    scopus 로고
    • Evidence for several waves of global transmission in the seventh cholera pandemic
    • Mutreja A, Kim DW, Thomson NR et al. Evidence for several waves of global transmission in the seventh cholera pandemic. Nature 477(7365), 462-465 (2011).
    • (2011) Nature , vol.477 , Issue.7365 , pp. 462-465
    • Mutreja, A.1    Kim, D.W.2    Thomson, N.R.3
  • 26
    • 67650658074 scopus 로고    scopus 로고
    • Rapid evolution of virulence and drug resistance in the emerging zoonotic pathogen Streptococcus suis
    • Holden MT, Hauser H, Sanders M et al. Rapid evolution of virulence and drug resistance in the emerging zoonotic pathogen Streptococcus suis. Plos One 4(7), e6072 (2009).
    • (2009) Plos One , vol.4 , Issue.7
    • Holden, M.T.1    Hauser, H.2    Sanders, M.3
  • 28
    • 0025962238 scopus 로고
    • Natural transfer of conjugative transposon Tn916 between Gram-positive and Gram-negative bacteria
    • Bertram J, Stratz M, Durre P. Natural transfer of conjugative transposon Tn916 between Gram-positive and Gram-negative bacteria. J. Bacteriol. 173(2), 443-448 (1991).
    • (1991) J. Bacteriol , vol.173 , Issue.2 , pp. 443-448
    • Bertram, J.1    Stratz, M.2    Durre, P.3
  • 29
    • 67349179001 scopus 로고    scopus 로고
    • Molecular diversity and transferability of the tetracycline resistance gene tet(M), carried on Tn916-1545 family transposons, in enterococci from a total food chain
    • Rizzotti L, La Gioia F, Dellaglio F, Torriani S. Molecular diversity and transferability of the tetracycline resistance gene tet(M), carried on Tn916-1545 family transposons, in enterococci from a total food chain. Antonie Van Leeuwenhoek 96(1), 43-52 (2009).
    • (2009) Antonie Van Leeuwenhoek , vol.96 , Issue.1 , pp. 43-52
    • Rizzotti, L.1    La Gioia, F.2    Dellaglio, F.3    Torriani, S.4
  • 30
    • 33645834530 scopus 로고    scopus 로고
    • Identification of Tn5397-like and Tn916-like transposons and diversity of the tetracycline resistance gene tet (M) in enterococci from humans, pigs and poultry
    • Agerso Y, Pedersen AG, Aarestrup FM. Identification of Tn5397-like and Tn916-like transposons and diversity of the tetracycline resistance gene tet(M) in enterococci from humans, pigs and poultry. J. Antimicrob. Chemother. 57(5), 832-839 (2006).
    • (2006) J. Antimicrob. Chemother , vol.57 , Issue.5 , pp. 832-839
    • Agerso, Y.1    Pedersen, A.G.2    Aarestrup, F.M.3
  • 31
    • 69049084639 scopus 로고    scopus 로고
    • Diversity of the tetracycline resistance gene tet(M) and identification of Tn916- And Tn5801-like (Tn6014) transposons in Staphylococcus aureus from humans and animals
    • De Vries LE, Christensen H, Skov RL, Aarestrup FM, Agerso Y. Diversity of the tetracycline resistance gene tet(M) and identification of Tn916- And Tn5801-like (Tn6014) transposons in Staphylococcus aureus from humans and animals. J. Antimicrob. Chemother. 64(3), 490-500 (2009).
    • (2009) J. Antimicrob. Chemother , vol.64 , Issue.3 , pp. 490-500
    • De Vries, L.E.1    Christensen, H.2    Skov, R.L.3    Aarestrup, F.M.4    Agerso, Y.5
  • 32
    • 84861154088 scopus 로고    scopus 로고
    • Behaviour and target site selection of the conjugative transposon Tn916 in two different strains of toxigenic Clostridium difficile
    • Mullany P, Williams R, Langridge GC et al. Behaviour and target site selection of the conjugative transposon Tn916 in two different strains of toxigenic Clostridium difficile. Appl. Environ. Microbiol. 78(7), 2147-2153, (2012).
    • (2012) Appl. Environ. Microbiol , vol.78 , Issue.7 , pp. 2147-2153
    • Mullany, P.1    Williams, R.2    Langridge, G.C.3
  • 34
    • 80052860715 scopus 로고    scopus 로고
    • Genetic diversity of Tn916-related transposons among drugresistant Streptococcus pneumoniae isolates colonizing healthy children in Venezuela
    • Quintero B, Araque M, Van Der Gaast-De Jongh C, Hermans PW. Genetic diversity of Tn916-related transposons among drugresistant Streptococcus pneumoniae isolates colonizing healthy children in Venezuela. Antimicrob. Agents Chemother. 55(10), 4930-4932 (2011).
    • (2011) Antimicrob. Agents Chemother , vol.55 , Issue.10 , pp. 4930-4932
    • Quintero, B.1    Araque, M.2    Van Der Gaast-De Jongh, C.3    Hermans, P.W.4
  • 35
    • 79953187260 scopus 로고    scopus 로고
    • Heterogeneity of Tn5253-like composite elements in clinical Streptococcus pneumoniae isolates
    • Mingoia M, Tili E, Manso E, Varaldo PE, Montanari MP. Heterogeneity of Tn5253-like composite elements in clinical Streptococcus pneumoniae isolates. Antimicrob. Agents Chemother. 55(4), 1453-1459 (2011).
    • (2011) Antimicrob. Agents Chemother , vol.55 , Issue.4 , pp. 1453-1459
    • Mingoia, M.1    Tili, E.2    Manso, E.3    Varaldo, P.E.4    Montanari, M.P.5
  • 36
    • 80052896564 scopus 로고    scopus 로고
    • Antibiotic and antiseptic resistance genes are linked on a novel mobile genetic element: Tn6087
    • Ciric L, Mullany P, Roberts AP. Antibiotic and antiseptic resistance genes are linked on a novel mobile genetic element: Tn6087. J. Antimicrob. Chemother. 66(10), 2235-2239 (2011).
    • (2011) J. Antimicrob. Chemother , vol.66 , Issue.10 , pp. 2235-2239
    • Ciric, L.1    Mullany, P.2    Roberts, A.P.3
  • 37
    • 80052236025 scopus 로고    scopus 로고
    • Molecular mechanisms of tetracycline and macrolide resistance and emm characterization of Streptococcus pyogenes isolates in Tunisia
    • Hraoui M, Boutiba-Ben Boubaker I, Doloy A, Ben Redjeb S, Bouvet A. Molecular mechanisms of tetracycline and macrolide resistance and emm characterization of Streptococcus pyogenes isolates in Tunisia. Microb. Drug Resist. 17(3), 377-382 (2011).
    • (2011) Microb. Drug Resist , vol.17 , Issue.3 , pp. 377-382
    • Hraoui, M.1    Boutiba-Ben Boubaker, I.2    Doloy, A.3    Ben Redjeb, S.4    Bouvet, A.5
  • 38
    • 78650384735 scopus 로고    scopus 로고
    • Diversity and mobility of integrative and conjugative elements in bovine isolates of Streptococcus agalactiae S. dysgalactiae subsp. dysgalactiae, and S. uberis
    • Haenni M, Saras E, Bertin S, Leblond P, Madec JY, Payot S. Diversity and mobility of integrative and conjugative elements in bovine isolates of Streptococcus agalactiae, S. dysgalactiae subsp. dysgalactiae, and S. uberis. Appl. Environ. Microbiol. 76(24), 7957-7965 (2010).
    • (2010) Appl. Environ. Microbiol , vol.76 , Issue.24 , pp. 7957-7965
    • Haenni, M.1    Saras, E.2    Bertin, S.3    Leblond, P.4    Madec, J.Y.5    Payot, S.6
  • 39
    • 84857052296 scopus 로고    scopus 로고
    • Enterococcus faecalis from patients with chronic periodontitis: Virulence and antimicrobial resistance traits and determinants
    • Sun J, Sundsfjord A, Song X. Enterococcus faecalis from patients with chronic periodontitis: Virulence and antimicrobial resistance traits and determinants. Eur. J. Clin. Microbiol. Infect. Dis. 31(3), 267-272 (2011).
    • (2011) Eur. J. Clin. Microbiol. Infect. Dis , vol.31 , Issue.3 , pp. 267-272
    • Sun, J.1    Sundsfjord, A.2    Song, X.3
  • 40
    • 0042355274 scopus 로고    scopus 로고
    • Comparative analysis of the genome sequences of Bordetella pertussis Bordetella parapertussis and Bordetella bronchiseptica
    • Parkhill J, Sebaihia M, Preston A et al. Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Nat. Genet. 35(1), 32-40 (2003).
    • (2003) Nat. Genet , vol.35 , Issue.1 , pp. 32-40
    • Parkhill, J.1    Sebaihia, M.2    Preston, A.3
  • 41
    • 84867696163 scopus 로고    scopus 로고
    • 3rd Edition). Blackwell Publishing UK
    • Bemis DA. Bordetella (3rd Edition). Blackwell Publishing, UK, 259-272 (2004).
    • (2004) Bordetella , pp. 259-272
    • Bemis, D.A.1
  • 42
    • 77954054691 scopus 로고    scopus 로고
    • The early stage of bacterial genome-reductive evolution in the host
    • Song H, Hwang J, Yi H et al. The early stage of bacterial genome-reductive evolution in the host. Plos Pathog. 6(5), e1000922 (2010).
    • (2010) Plos Pathog , vol.6 , Issue.5
    • Song, H.1    Hwang, J.2    Yi, H.3
  • 43
    • 79955753012 scopus 로고    scopus 로고
    • Citrobacter rodentium is an unstable pathogen showing evidence of significant genomic flux
    • Petty NK, Feltwell T, Pickard D et al. Citrobacter rodentium is an unstable pathogen showing evidence of significant genomic flux. Plos Pathog. 7(4), e1002018 (2011).
    • (2011) Plos Pathog , vol.7 , Issue.4
    • Petty, N.K.1    Feltwell, T.2    Pickard, D.3
  • 44
    • 79960063903 scopus 로고    scopus 로고
    • The genome sequence of Brucella pinnipedialis B2/94 sheds light on the evolutionary history of the genus Brucella
    • Audic S, Lescot M, Claverie JM, Cloeckaert A, Zygmunt MS. The genome sequence of Brucella pinnipedialis B2/94 sheds light on the evolutionary history of the genus Brucella. BMC Evol. Biol. 11, 200 (2011).
    • (2011) BMC Evol. Biol , vol.11 , pp. 200
    • Audic, S.1    Lescot, M.2    Claverie, J.M.3    Cloeckaert, A.4    Zygmunt, M.S.5
  • 45
    • 73249130761 scopus 로고    scopus 로고
    • Simultaneous assay of every Salmonella typhi gene using one million transposon mutants
    • Langridge GC, Phan MD, Turner DJ et al. Simultaneous assay of every Salmonella typhi gene using one million transposon mutants. Genome Res. 19(12), 2308-2316 (2009).
    • (2009) Genome Res , vol.19 , Issue.12 , pp. 2308-2316
    • Langridge, G.C.1    Phan, M.D.2    Turner, D.J.3
  • 46
    • 70349510646 scopus 로고    scopus 로고
    • Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lung
    • Gawronski JD, Wong SM, Giannoukos G, Ward DV, Akerley BJ. Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lung. Proc. Natl Acad. Sci. USA 106(38), 16422-16427 (2009).
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , Issue.38 , pp. 16422-16427
    • Gawronski, J.D.1    Wong, S.M.2    Giannoukos, G.3    Ward, D.V.4    Akerley, B.J.5
  • 47
    • 79955079817 scopus 로고    scopus 로고
    • Genome-scale identification of resistance functions in Pseudomonas aeruginosa using Tn-seq
    • Gallagher LA, Shendure J, Manoil C. Genome-scale identification of resistance functions in Pseudomonas aeruginosa using Tn-seq. MBio 2(1), e00315-10 (2011).
    • (2011) MBio , vol.2 , Issue.1
    • Gallagher, L.A.1    Shendure, J.2    Manoil, C.3
  • 48
    • 77955796409 scopus 로고    scopus 로고
    • A universal TagModule collection for parallel genetic analysis of microorganisms
    • Oh J, Fung E, Price MN et al. A universal TagModule collection for parallel genetic analysis of microorganisms. Nucleic Acids Res. 38(14), e146 (2010).
    • (2010) Nucleic Acids Res , vol.38 , Issue.14
    • Oh, J.1    Fung, E.2    Price, M.N.3
  • 49
    • 80052337291 scopus 로고    scopus 로고
    • Salmonella bongori provides insights into the evolution of the Salmonellae
    • Fookes M, Schroeder GN, Langridge GC et al. Salmonella bongori provides insights into the evolution of the Salmonellae. Plos Pathog. 7(8), e1002191 (2011).
    • (2011) Plos Pathog , vol.7 , Issue.8
    • Fookes, M.1    Schroeder, G.N.2    Langridge, G.C.3
  • 50
    • 73649127936 scopus 로고    scopus 로고
    • Short-term signatures of evolutionary change in the Salmonella enterica serovar typhimurium 14028 genome
    • Jarvik T, Smillie C, Groisman EA, Ochman H. Short-term signatures of evolutionary change in the Salmonella enterica serovar typhimurium 14028 genome. J. Bacteriol. 192(2), 560-567 (2010).
    • (2010) J. Bacteriol , vol.192 , Issue.2 , pp. 560-567
    • Jarvik, T.1    Smillie, C.2    Groisman, E.A.3    Ochman, H.4
  • 51
    • 0037609037 scopus 로고    scopus 로고
    • Flagellar phase variation in Salmonella enterica is mediated by a posttranscriptional control mechanism
    • Bonifield HR, Hughes KT. Flagellar phase variation in Salmonella enterica is mediated by a posttranscriptional control mechanism. J. Bacteriol. 185(12), 3567-3574 (2003).
    • (2003) J. Bacteriol , vol.185 , Issue.12 , pp. 3567-3574
    • Bonifield, H.R.1    Hughes, K.T.2
  • 52
    • 84861568496 scopus 로고    scopus 로고
    • A novel nonhomologous recombination-mediated mechanism for Escherichia coli unilateral flagellar phase variation
    • Liu B, Hu B, Zhou Z et al. A novel nonhomologous recombination-mediated mechanism for Escherichia coli unilateral flagellar phase variation. Nucleic Acids Res. 40(10), 4530-4538 (2012).
    • (2012) Nucleic Acids Res , vol.40 , Issue.10 , pp. 4530-4538
    • Liu, B.1    Hu, B.2    Zhou, Z.3
  • 53
    • 0035479142 scopus 로고    scopus 로고
    • Deletional bias and the evolution of bacterial genomes
    • Mira A, Ochman H, Moran NA. Deletional bias and the evolution of bacterial genomes. Trends Genet. 17(10), 589-596 (2001).
    • (2001) Trends Genet , vol.17 , Issue.10 , pp. 589-596
    • Mira, A.1    Ochman, H.2    Moran, N.A.3
  • 54
    • 0037040394 scopus 로고    scopus 로고
    • Microbial minimalism: Genome reduction in bacterial pathogens
    • Moran NA. Microbial minimalism: Genome reduction in bacterial pathogens. Cell 108(5), 583-586 (2002).
    • (2002) Cell , vol.108 , Issue.5 , pp. 583-586
    • Moran, N.A.1
  • 55
    • 77953809752 scopus 로고    scopus 로고
    • Evolutionary microbial genomics: Insights into bacterial host adaptation
    • Toft C, Andersson SG. Evolutionary microbial genomics: Insights into bacterial host adaptation. Nat. Rev. Genet. 11(7), 465-475 (2010).
    • (2010) Nat. Rev. Genet , vol.11 , Issue.7 , pp. 465-475
    • Toft, C.1    Andersson, S.G.2
  • 56
    • 77955709379 scopus 로고    scopus 로고
    • Continuing evolution of Burkholderia mallei through genome reduction and large-scale rearrangements
    • Losada L, Ronning CM, Deshazer D et al. Continuing evolution of Burkholderia mallei through genome reduction and large-scale rearrangements. Genome Biol. Evol. 2, 102-116 (2010).
    • (2010) Genome Biol. Evol , vol.2 , pp. 102-116
    • Losada, L.1    Ronning, C.M.2    Deshazer, D.3
  • 57
    • 81155131410 scopus 로고    scopus 로고
    • Gene decay in Shigella as an incipient stage of hostadaptation
    • Feng Y, Chen Z, Liu SL. Gene decay in Shigella as an incipient stage of hostadaptation. Plos One 6(11), e27754 (2011).
    • (2011) Plos One 6 , vol.6 , Issue.11
    • Feng, Y.1    Chen, Z.2    Liu, S.L.3
  • 58
    • 78649565669 scopus 로고    scopus 로고
    • Comparative genomics of the bacterial genus listeria genome evolution is characterized by limited gene acquisition and limited gene loss
    • Den Bakker HC, Cummings CA, Ferreira V et al. Comparative genomics of the bacterial genus Listeria. Genome evolution is characterized by limited gene acquisition and limited gene loss. BMC Genomics 11, 688 (2010).
    • (2010) BMC Genomics , vol.11 , pp. 688
    • Den Bakker, H.C.1    Cummings, C.A.2    Ferreira, V.3
  • 59
    • 83855165105 scopus 로고    scopus 로고
    • Repetitive DNA and next-generation sequencing:Computational challenges and solutions
    • Treangen TJ, Salzberg SL. Repetitive DNA and next-generation sequencing:Computational challenges and solutions. Nat. Rev. Genet. 13(1), 36-46 (2012).
    • (2012) Nat. Rev. Genet , vol.13 , Issue.1 , pp. 36-46
    • Treangen, T.J.1    Salzberg, S.L.2
  • 60
    • 78650909427 scopus 로고    scopus 로고
    • Limitations of next-generation genome sequence assembly
    • Alkan C, Sajjadian S, Eichler EE. Limitations of next-generation genome sequence assembly. Nat. Methods 8(1), 61-65 (2011).
    • (2011) Nat. Methods , vol.8 , Issue.1 , pp. 61-65
    • Alkan, C.1    Sajjadian, S.2    Eichler, E.E.3
  • 61
    • 45549109750 scopus 로고    scopus 로고
    • Genome assembly forensics: Finding the elusive mis-assembly
    • Phillippy AM, Schatz MC, Pop M. Genome assembly forensics: Finding the elusive mis-assembly. Genome Biol. 9(3), R55 (2008).
    • (2008) Genome Biol , vol.9 , Issue.3
    • Phillippy, A.M.1    Schatz, M.C.2    Pop, M.3
  • 62
    • 79953854485 scopus 로고    scopus 로고
    • Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies
    • Wetzel J, Kingsford C, Pop M. Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies. BMC Bioinformatics 12, 95 (2011).
    • (2011) BMC Bioinformatics , vol.12 , Issue.95
    • Wetzel, J.1    Kingsford, C.2    Pop, M.3
  • 63
    • 0023600057 scopus 로고
    • Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product
    • Ishino Y, Shinagawa H, Makino K, Amemura M, Nakata A. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J. Bacteriol. 169(12), 5429-5433 (1987).
    • (1987) J. Bacteriol , vol.169 , Issue.12 , pp. 5429-5433
    • Ishino, Y.1    Shinagawa, H.2    Makino, K.3    Amemura, M.4    Nakata, A.5
  • 64
    • 34250662138 scopus 로고    scopus 로고
    • The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats
    • Grissa I, Vergnaud G, Pourcel C. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics 8, 172 (2007).
    • (2007) BMC Bioinformatics , vol.8 , pp. 172
    • Grissa, I.1    Vergnaud, G.2    Pourcel, C.3
  • 65
    • 84856264333 scopus 로고    scopus 로고
    • Impact of small repeat sequences on bacterial genome evolution
    • Delihas N. Impact of small repeat sequences on bacterial genome evolution. Genome Biol. Evol. 3, 959-973 (2011).
    • (2011) Genome Biol. Evol , vol.3 , pp. 959-973
    • Delihas, N.1
  • 66
    • 77249170201 scopus 로고    scopus 로고
    • CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea
    • Marraffini LA, Sontheimer EJ. CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nat. Rev. Genet. 11(3), 181-190 (2010).
    • (2010) Nat. Rev. Genet , vol.11 , Issue.3 , pp. 181-190
    • Marraffini, L.A.1    Sontheimer, E.J.2
  • 67
    • 74249095519 scopus 로고    scopus 로고
    • CRISPR/Cas, the immune system of bacteria and archaea
    • Horvath P, Barrangou R. CRISPR/Cas, the immune system of bacteria and archaea. Science 327(5962), 167-170 (2010).
    • (2010) Science , vol.327 , Issue.5962 , pp. 167-170
    • Horvath, P.1    Barrangou, R.2
  • 68
    • 73649130281 scopus 로고    scopus 로고
    • The CRISPR system: Small RNA-guided defense in bacteria and archaea
    • Karginov FV, Hannon GJ. The CRISPR system: Small RNA-guided defense in bacteria and archaea. Mol. Cell 37(1), 7-19 (2010).
    • (2010) Mol. Cell , vol.37 , Issue.1 , pp. 7-19
    • Karginov, F.V.1    Hannon, G.J.2
  • 69
    • 73149087453 scopus 로고    scopus 로고
    • Transcription profile of Thermus thermophilus CRISPR systems after phage infection
    • Agari Y, Sakamoto K, Tamakoshi M, Oshima T, Kuramitsu S, Shinkai A. Transcription profile of Thermus thermophilus CRISPR systems after phage infection. J. Mol. Biol. 395(2), 270-281 (2010).
    • (2010) J. Mol. Biol , vol.395 , Issue.2 , pp. 270-281
    • Agari, Y.1    Sakamoto, K.2    Tamakoshi, M.3    Oshima, T.4    Kuramitsu, S.5    Shinkai, A.6
  • 71
    • 80054971915 scopus 로고    scopus 로고
    • Targeted bacterial immunity buffers phage diversity
    • Haerter JO, Trusina A, Sneppen K. Targeted bacterial immunity buffers phage diversity. J. Virol. 85(20), 10554-10560 (2011).
    • (2011) J. Virol , vol.85 , Issue.20 , pp. 10554-10560
    • Haerter, J.O.1    Trusina, A.2    Sneppen, K.3
  • 72
    • 33947375199 scopus 로고    scopus 로고
    • New functional identity for the DNA uptake sequence in transformation and its presence in transcriptional terminators
    • Ambur OH, Frye SA, Tonjum T. New functional identity for the DNA uptake sequence in transformation and its presence in transcriptional terminators. J. Bacteriol. 189(5), 2077-2085 (2007).
    • (2007) J. Bacteriol , vol.189 , Issue.5 , pp. 2077-2085
    • Ambur, O.H.1    Frye, S.A.2    Tonjum, T.3
  • 73
    • 45549105909 scopus 로고    scopus 로고
    • The impact of the neisserial DNA uptake sequences on genome evolution and stability
    • Treangen TJ, Ambur OH, Tonjum T, Rocha EP. The impact of the neisserial DNA uptake sequences on genome evolution and stability. Genome Biol. 9(3), R60 (2008).
    • (2008) Genome Biol , vol.9 , Issue.3
    • Treangen, T.J.1    Ambur, O.H.2    Tonjum, T.3    Rocha, E.P.4
  • 74
    • 67349123357 scopus 로고    scopus 로고
    • Genome flexibility in Neisseria meningitidis
    • Schoen C, Tettelin H, Parkhill J, Frosch M. Genome flexibility in Neisseria meningitidis. Vaccine 27(Suppl. 2), B103-B111 (2009).
    • (2009) Vaccine , vol.27 , Issue.SUPPL. 2
    • Schoen, C.1    Tettelin, H.2    Parkhill, J.3    Frosch, M.4
  • 76
    • 79951566871 scopus 로고    scopus 로고
    • Identification, variation and transcription of pneumococcal repeat sequences
    • Croucher NJ, Vernikos GS, Parkhill J, Bentley SD. Identification, variation and transcription of pneumococcal repeat sequences. BMC Genomics 12, 120 (2011).
    • (2011) BMC Genomics , vol.12 , Issue.120
    • Croucher, N.J.1    Vernikos, G.S.2    Parkhill, J.3    Bentley, S.D.4
  • 77
    • 33646721216 scopus 로고
    • The need for recombination to prevent genetic deterioration
    • Muller HJ. The need for recombination to prevent genetic deterioration. Genetics 48, 903-903 (1964).
    • (1964) Genetics , vol.48 , pp. 903-903
    • Muller, H.J.1
  • 78
    • 0029866448 scopus 로고    scopus 로고
    • Accelerated evolution and Muller's rachet in endosymbiotic bacteria
    • Moran NA. Accelerated evolution and Muller's rachet in endosymbiotic bacteria. Proc. Natl Acad. Sci. USA 93(7), 2873-2878 (1996).
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , Issue.7 , pp. 2873-2878
    • Moran, N.A.1
  • 80
    • 67149119196 scopus 로고    scopus 로고
    • Hyper-recombination, diversity, and antibiotic resistance in pneumococcus
    • Hanage WP, Fraser C, Tang J, Connor TR, Corander J. Hyper-recombination, diversity, and antibiotic resistance in pneumococcus. Science 324(5933), 1454-1457 (2009).
    • (2009) Science , vol.324 , Issue.5933 , pp. 1454-1457
    • Hanage, W.P.1    Fraser, C.2    Tang, J.3    Connor, T.R.4    Corander, J.5
  • 81
    • 84863596741 scopus 로고    scopus 로고
    • Population structure in the Neisseria, and the biological significance of fuzzy species
    • Corander J, Connor TR, O'Dwyer CA, Kroll JS, Hanage WP. Population structure in the Neisseria, and the biological significance of fuzzy species. J. R. Soc. Interface 9(71), 1208-1215, (2011).
    • (2011) J. R. Soc. Interface , vol.9 , Issue.71 , pp. 1208-1215
    • Corander, J.1    Connor, T.R.2    O'Dwyer, C.A.3    Kroll, J.S.4    Hanage, W.P.5
  • 82
    • 71049152453 scopus 로고    scopus 로고
    • Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer
    • Pearson T, Giffard P, Beckstrom-Sternberg S et al. Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer. BMC Biol. 7, 78 (2009).
    • (2009) BMC Biol , vol.7 , pp. 78
    • Pearson, T.1    Giffard, P.2    Beckstrom-Sternberg, S.3
  • 83
    • 79960935954 scopus 로고    scopus 로고
    • Recombination and population structure in Salmonella enterica
    • Didelot X, Bowden R, Street T et al. Recombination and population structure in Salmonella enterica. Plos Genet. 7(7), e1002191 (2011).
    • (2011) Plos Genet , vol.7 , Issue.7
    • Didelot, X.1    Bowden, R.2    Street, T.3
  • 84
    • 84855261123 scopus 로고    scopus 로고
    • Detection of recombination events in bacterial genomes from large population samples
    • Marttinen P, Hanage WP, Croucher NJ et al. Detection of recombination events in bacterial genomes from large population samples. Nucleic Acids Res. 40(1), e6 (2012).
    • (2012) Nucleic Acids Res , vol.40 , Issue.1
    • Marttinen, P.1    Hanage, W.P.2    Croucher, N.J.3
  • 85
    • 84859499489 scopus 로고    scopus 로고
    • Population genomics of early events in the ecological differentiation of bacteria
    • Shapiro BJ, Friedman J, Cordero OX et al. Population genomics of early events in the ecological differentiation of bacteria. Science 336(6077), 48-51 (2012
    • (2012) Science , vol.336 , Issue.6077 , pp. 48-51
    • Shapiro, B.J.1    Friedman, J.2    Cordero, O.X.3
  • 86
    • 82255186689 scopus 로고    scopus 로고
    • Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes
    • Lieberman TD, Michel JB, Aingaran M et al. Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes. Nat. Genet. 43(12), 1275-1280 (2011).
    • (2011) Nat. Genet , vol.43 , Issue.12 , pp. 1275-1280
    • Lieberman, T.D.1    Michel, J.B.2    Aingaran, M.3
  • 88
    • 33644630612 scopus 로고    scopus 로고
    • Comparisons of dN/dS are time dependent for closely related bacterial genomes
    • Rocha EP, Smith JM, Hurst LD et al. Comparisons of dN/dS are time dependent for closely related bacterial genomes. J. Theor. Biol. 239(2), 226-235 (2006).
    • (2006) J. Theor. Biol , vol.239 , Issue.2 , pp. 226-235
    • Rocha, E.P.1    Smith, J.M.2    Hurst, L.D.3
  • 89
    • 77952168929 scopus 로고    scopus 로고
    • Evolutionary dynamics of Clostridium difficile over short and long time scales
    • He M, Sebaihia M, Lawley TD et al. Evolutionary dynamics of Clostridium difficile over short and long time scales. Proc. Natl Acad. Sci. USA 107(16), 7527-7532 (2010).
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , Issue.16 , pp. 7527-7532
    • He, M.1    Sebaihia, M.2    Lawley, T.D.3
  • 90
    • 80052578549 scopus 로고    scopus 로고
    • Selection in coastal Synechococcus (cyanobacteria) populations evaluated from environmental metagenomes
    • Tai V, Poon AF, Paulsen IT, Palenik B. Selection in coastal Synechococcus (cyanobacteria) populations evaluated from environmental metagenomes. Plos One 6(9), e24249 (2011).
    • (2011) Plos One , vol.6 , Issue.9
    • Tai, V.1    Poon, A.F.2    Paulsen, I.T.3    Palenik, B.4
  • 91
    • 35348821456 scopus 로고    scopus 로고
    • Phylogenomic analysis of natural selection pressure in Streptococcus genomes
    • Anisimova M, Bielawski J, Dunn K, Yang Z. Phylogenomic analysis of natural selection pressure in Streptococcus genomes. BMC Evol. Biol. 7, 154 (2007).
    • (2007) BMC Evol. Biol , vol.7 , pp. 154
    • Anisimova, M.1    Bielawski, J.2    Dunn, K.3    Yang, Z.4
  • 92
    • 68949148715 scopus 로고    scopus 로고
    • Rapidly evolving genes in pathogens: Methods for detecting positive selection and examples among fungi, bacteria, viruses and protists
    • Aguileta G, Refregier G, Yockteng R, Fournier E, Giraud T. Rapidly evolving genes in pathogens: Methods for detecting positive selection and examples among fungi, bacteria, viruses and protists. Infect. Genet. Evol. 9(4), 656-670 (2009).
    • (2009) Infect. Genet. Evol , vol.9 , Issue.4 , pp. 656-670
    • Aguileta, G.1    Refregier, G.2    Yockteng, R.3    Fournier, E.4    Giraud, T.5
  • 93
    • 79952965476 scopus 로고    scopus 로고
    • Evolution in action: A 50,000-generation salute to charles darwin
    • Lenski RE. Evolution in action: A 50,000-generation salute to Charles Darwin. Microbe 6, 30-33 (2011
    • (2011) Microbe , vol.6 , pp. 30-33
    • Lenski, R.E.1
  • 94
    • 79952793415 scopus 로고    scopus 로고
    • Second-order selection for evolvability in a large Escherichia coli population
    • Woods RJ, Barrick JE, Cooper TF, Shrestha U, Kauth MR, Lenski RE. Second-order selection for evolvability in a large Escherichia coli population. Science 331(6023), 1433-1436 (2011).
    • (2011) Science , vol.331 , Issue.6023 , pp. 1433-1436
    • Woods, R.J.1    Barrick, J.E.2    Cooper, T.F.3    Shrestha, U.4    Kauth, M.R.5    Lenski, R.E.6
  • 95
    • 84555171441 scopus 로고    scopus 로고
    • Evolutionary paths to antibiotic resistance under dynamically sustained drug selection
    • Toprak E, Veres A, Michel JB, Chait R, Hartl DL, Kishony R. Evolutionary paths to antibiotic resistance under dynamically sustained drug selection. Nat. Genet. 44(1), 101-105 (2011).
    • (2011) Nat. Genet , vol.44 , Issue.1 , pp. 101-105
    • Toprak, E.1    Veres, A.2    Michel, J.B.3    Chait, R.4    Hartl, D.L.5    Kishony, R.6
  • 96
    • 0016169589 scopus 로고
    • Molecular evolution as predicted by natural selection
    • Van Valen L. Molecular evolution as predicted by natural selection. J. Mol. Evol. 3(2), 89-101 (1974).
    • (1974) J. Mol. Evol , vol.3 , Issue.2 , pp. 89-101
    • Van Valen, L.1
  • 97
    • 77949423965 scopus 로고    scopus 로고
    • Antagonistic coevolution accelerates molecular evolution
    • Paterson S, Vogwill T, Buckling A et al. Antagonistic coevolution accelerates molecular evolution. Nature 464(7286), 275-278 (2010).
    • (2010) Nature , vol.464 , Issue.7286 , pp. 275-278
    • Paterson, S.1    Vogwill, T.2    Buckling, A.3
  • 98
    • 77954975104 scopus 로고    scopus 로고
    • Next-generation sequencing: Adjusting to data overload
    • Baker M. Next-generation sequencing: Adjusting to data overload. Nat. Methods 7(7), 495-499 (2010).
    • (2010) Nat. Methods , vol.7 , Issue.7 , pp. 495-499
    • Baker, M.1
  • 99
    • 67649114038 scopus 로고    scopus 로고
    • Co-evolution of genomes and plasmids within Chlamydia trachomatis and the emergence in Sweden of a new variant strain
    • Seth-Smith HM, Harris SR, Persson K et al. Co-evolution of genomes and plasmids within Chlamydia trachomatis and the emergence in Sweden of a new variant strain. BMC Genomics 10, 239 (2009).
    • (2009) BMC Genomics , vol.10 , pp. 239
    • Seth-Smith, H.M.1    Harris, S.R.2    Persson, K.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.