Population Genomics of Bacteria

Bacterial Population Genetics in Infectious Disease

Volumn , Issue , 2010, Pages 121-151

  Guttman, David S ^a   Stavrinides, John ^b  

^a UNIVERSITY OF TORONTO   (Canada)

^b University of Arizona   (United States)

Author keywords

Bacterial population genomics genetics transferable flexible genome; Microarray based population genomics single nucleotide polymorphisms (SNPs) detection; Next gen genomics technology genomic sequencing and data analyzing

Indexed keywords

EID: 80053565432     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9780470600122.ch7     Document Type: Chapter

References (128)

1. Achtman , M. ( 2004 ) Population structure of pathogenic bacteria revisited . International Journal of Medical Microbiology 294 ( 2 - 3 ), 67-73 .
2. Achtman , M. ( 2008 ) Evolution, population structure, and phylogeography of genetically monomorphic bacterial pathogens . Annual Review of Microbiology 62 , 53-70 .
3. Allen , E. E. , Tyson , G. W. et al. ( 2007 ) Genome dynamics in a natural archaeal population . Proceedings of the National Academy of Sciences of the United States of America 104 ( 6 ), 1883-1888 .
4. Arnold , D. L. , Pitman , A. et al. ( 2003 ) Pathogenicity and other genomic islands in plant pathogenic bacteria . Molecular Plant Pathology 4 ( 5 ), 407-420 .
5. Aziz , R. K. , Bartels , D. et al. ( 2008 ) The RAST server: Rapid Annotations using Subsystems Technology . BMC Genomics 9 , 75 .
6. Bagnoli , F. , Moschioni , M. et al. ( 2008 ) A second pilus type in Streptococcus pneumoniae is prevalent in emerging serotypes and mediates adhesion to host cells . Journal of Bacteriology 190 ( 15 ), 5480-5492 .
7. Bandelt , H. J. and Dress , A. W. ( 1992 ) Split decomposition: A new and useful approach to phylogenetic analysis of distance data . Molecular Phylogenetics and Evolution 1 ( 3 ), 242-252 .
8. Baumberg , S. , Young , J. P. W. et al., eds. ( 1995 ) Population genetics of bacteria . Symposium of the Society for General Microbiology, Cambridge University Press , Cambridge, UK .
9. Black , W. C. , Baer , C. F. et al. ( 2001 ) Population genomics: Genome - wide sampling of insect populations . Annual Review of Entomology 46 , 441-469 .
10. Brendel , V. , Kurtz , S. et al. ( 2007 ) Visualization of syntenic relationships with SynBrowse . Methods in Molecular Biology 396 , 153-163 .
11. Buckingham , S. D. ( 2008 ) Scientifi c software: Seeing the SNPs between us . Nature Methods 5 ( 10 ), 903-908 .
12. Caugant , D. A. , Mocca , L. F. et al. ( 1987 ) Structure of Neisseria meningitidis populations in relation to serogroup, serotype, and outer membrane protein pattern . Journal of Bacteriology 169 ( 6 ), 2781-2792 .
13. Chain , P. S. , Carniel , E. et al. ( 2004 ) Insights into the evolution of Yersinia pestis through whole - genome comparison with Yersinia pseudotuberculosis . Proceedings of the National Academy of Sciences of the United States of America 101 ( 38 ), 13826-13831 .
14. Chau , T. T. , Campbell , J. I. et al. ( 2007 ) Antimicrobial drug resistance of Salmonella enterica serovar Typhi in Asia and molecular mechanism of reduced susceptibility to the fl uoroquinolones . Antimicrobial Agents and Chemotherapy 51 ( 12 ), 4315-4323 .
15. Cover , T. L. ( 1996 ) The vacuolating cytotoxin of Helicobacter pylori . Molecular Microbiology 20 ( 2 ), 241-246 .
16. Darling , A. C. E. , Mau , B. et al. ( 2004 ) Mauve: Multiple alignment of conserved genomic sequence with rearrangements . G enome Research 14 ( 7 ), 1394-1403 .
17. DeLong , E. F. ( 2002 ) Microbial population genomics and ecology . Current Opinion in Microbiology 5 ( 5 ), 520-524 .
18. DeLong , E. F. ( 2004 ) Microbial population genomics and ecology: The road ahead . Environmental Microbiology 6 ( 9 ), 875-878 .
19. Dobrindt , U. and Hacker , J. ( 2001 ) Whole genome plasticity in pathogenic bacteria . Current Opinion in Microbiology 4 ( 5 ), 550-557 .
20. Drake , J. W. , Charlesworth , B. , et al. ( 1998 ) Rates of spontaneous mutation . Genetics 148 ( 4 ), 1667-1686 . Endo , T. , Ikeo , K. et al. ( 1996 ) Large - scale search for genes on which positive selection may operate . Molecular Biology and Evolution 13 ( 5 ), 685-690 .
21. Engels , R. , Yu , T. et al. ( 2006 ) Combo: A whole genome comparative browser . Bioinformatics 22 ( 14 ), 1782-1783 .
22. Enright , M. C. and Spratt , B. G. ( 1998 ) A multilocus sequence typing scheme for Streptococcus pneumoniae: Identifi cation of clones associated with serious invasive disease . Microbiology 144 ( Pt 11 ), 3049-3060 .
23. Fleischmann , R. D. , Adams , M. D. et al. ( 1995 ) Whole - genome random sequencing and assembly of Haemophilus infl uenzae Rd . Science 269 ( 5223 ), 496-512 .
24. Fox , G. E. , Pechman , K. R. et al. ( 1977 ) Comparative catologing of 16S ribosomal ribonucleic acid - molecular approach to procaryotic systematics . International Journal of Systematic Bacteriology 27 ( 1 ), 44-57 .
25. Griffith , F. ( 1928 ) The signifi cance of pneumococcal types . Journal of Hygiene 27 , 113-159 .
26. Gulcher , J. and Stefansson , K. ( 1998 ) Population genomics: Laying the groundwork for genetic disease modeling and targeting . Clinical Chemistry and Laboratory Medicine 36 ( 8 ), 523-527 .
27. Guttman , D. S. ( 1997 ) Recombination and clonality in natural population of Escherichia coli . Trends in Ecology and Evolution 12 ( 1 ), 16-22 .
28. Guttman , D. S. and Dykhuizen , D. E. ( 1994 ) Clonal divergence in Escherichia coli as a result of recombination, not mutation . Science 266 , 1380-1383 .
29. Hacker , J. and Carniel , E. ( 2001 ) Ecological fi tness, genomic islands and bacterial pathogenicity - A Darwinian view of the evolution of microbes . EMBO Reports 2 ( 5 ), 376-381 .
30. Hacker , J. and Kaper , J. B. ( 2000 ) Pathogenicity islands and the evolution of microbes . Annual Review of Microbiology 54 , 641-679 .
31. Hagblom , P. , Segal , E. et al. ( 1985 ) Intragenic recombination leads to pilus antigenic variation in Neisseria gonorrhoeae . Nature 315 ( 6015 ), 156-158 .
32. Hava , D. and Camilli A. ( 2002 ) Large - scale identifi cation of serotype 4 Streptococcus pneumoniae virulence factors . Molecular Microbiology 45 ( 5 ), 1389-1405 .
33. Hava , D. L. , Hemsley , C. J. et al. ( 2003 ) Transcriptional regulation in the Streptococcus pneumoniae RlrA pathogenicity islet by RlrA . Journal of Bacteriology 185 ( 2 ), 413-421 .
34. Henriques - Normark , B. , Blomberg , C. et al. ( 2008 ) The rise and fall of bacterial clones: Streptococcus pneumoniae . Nature Reviews. Microbiology 6 ( 11 ), 827-837 .
35. Hernandez , D. , Francois , P. et al. ( 2008 ) De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer . Genome Research 18 (5), 802-809 .
36. Hill , W. G. and Robertson , A. I. ( 1966 ) Effect of linkage on limits to artifi cial selection . Genetical Research 8 ( 3 ), 269-294 .
37. Hinchliffe , S. J. , Isherwood , K. E. et al. ( 2003 ) Application of DNA microarrays to study the evolutionary genomics of Yersinia pestis and Yersinia pseudotuberculosis . Genome Research 13 ( 9 ), 2018-2029 .
38. Holt , K. E. , Parkhill , J. et al. ( 2008 ) High - throughput sequencing provides insights into genome variation and evolution in Salmonella typhi . Nature Genetics 40 ( 8 ), 987-993 .
39. Huang , W. and Marth , G. ( 2008 ) EagleView: A genome assembly viewer for next - generation sequencing technologies . Genome Research 18 ( 9 ), 1538-1543 .
40. Huson , D. H. ( 1998 ) SplitsTree: Analyzing and visualizing evolutionary data . Bioinformatics 14 ( 1 ), 68-73
41. Jiang , H. and Wong , W. H. ( 2008 ) SeqMap: Mapping massive amount of oligonucleotides to the genome . Bioinformatics 24 ( 20 ), 2395-2396 .
42. Kahvejian , A. , Quackenbush , J. et al. ( 2008 ) What would you do if you could sequence everything? Nature Biotechnology 26 ( 10 ), 1125-1133 .
43. Kent , W. J. , Sugnet , C. W. et al. ( 2002 ) The human genome browser at UCSC . Genome Research 12 ( 6 ), 996-1006 .
44. Koonin , E. V. and Wolf , Y. I. ( 2008 ) Genomics of bacteria and archaea: The emerging dynamic view of the prokaryotic world . Nucleic Acids Research 36 ( 21 ), 6688-6719 .
45. Lander , E. S. , Linton , L. M. et al. ( 2001 ) Initial sequencing and analysis of the human genome . Nature 409 ( 6822 ), 860-921 .
46. Leavis , H. , Top , J. et al. ( 2004 ) A novel putative enterococcal pathogenicity island linked to the esp virulence gene of Enterococcus faecium and associated with epidemicity . Journal of Bacteriology 186 ( 3 ), 672-682 .
47. Leavis , H. L. , Bonten , M. J. M. et al. ( 2006 ) Identifi cation of high - risk enterococcal clonal complexes: Global dispersion and antibiotic resistance . Current Opinion in Microbiology 9 ( 5 ), 454-460 .
48. Lenski , R. E. , Rose , M. R. et al. ( 1991 ) Long - term experimental evolution in Escherichia coli . I. Adaptation and divergence during 2,000 generations . American Naturalist 138 , 1315-1341 .
49. Lewontin , R. C. and Hubby , J. L. ( 1966 ) A molecular approach to the study of genic heterozygosity in natural populations. II. Amount of variation and degree of heterozygosity in natural populations of Drosophila pseudoobscura . Genetics 54 ( 2 ), 595-609 .
50. Li , H. ( 2008 ) Maq: Mapping and Assembly with Qualities. Software for Short-read Mapping Assemblies.
51. Li , R. , Li , Y. et al. ( 2008 ) SOAP: Short oligonucleotide alignment program . Bioinformatics 24 ( 5 ), 713-414 .
52. Ma , W. and Guttman , D. S. ( 2008 ) Evolution of prokaryotic and eukaryotic virulence effectors . Current Opinion in Plant Biology 11 ( 4 ), 412-419 .
53. Maiden , M. C. J. ( 2008 ) Population genomics: Diversity and virulence in the Neisseria . Current Opinion in Microbiology 11 ( 5 ), 467-471 .
54. Maiden , M. C. J. , Bygraves , J. A. et al. ( 1998 ) Multilocus sequence typing: A portable approach to the identifi cation of clones within populations of pathogenic microorganisms . Proceedings of the National Academy of Sciences of the United States of America 95 ( 6 ), 3140-3145 .
55. Marth , G. T. , Korf , I. et al. ( 1999 ) A general approach to single - nucleotide polymorphism discovery . Nature Genetics 23 ( 4 ), 452-456 .
56. Maynard Smith , J. ( 1991 ) The population genetics of bacteria . Proceedings of the Royal Society of London. Series B, Biological Sciences 245 , 37-41 .
57. Maynard Smith , J. ( 1999 ) The detection and measurement of recombination from sequence data . Genetics 153 ( 2 ), 1021-1027 .
58. Maynard Smith , J. , Dowson , C. G. et al. ( 1991 ) Localized sex in bacteria . Nature 349 , 29-31 .
59. Maynard Smith , J. , Feil , E. J. et al. ( 2000 ) Population structure and evolutionary dynamics of pathogenic bacteria . Bioessays 22 ( 12 ), 1115-1122 .
60. Maynard Smith , J. , Smith , N. H. et al. ( 1993 ) How clonal are bacteria? Proceedings of the National Academy of Sciences of the United States of America 90 , 4384-4388 .
61. McDougal , L. K. , Steward , C. D. et al. ( 2003 ) Pulsed - fi eld gel electrophoresis typing of oxacillin - resistant Staphylococcus aureus isolates from the United States: Establishing a national database . Journal of Clinical Microbiology 41 ( 11 ), 5113-5120 .
62. Medini , D. , Donati , C. et al. ( 2005 ) The microbial pan - genome . Current Opinion in Genetics & Development 15 ( 6 ), 589-594 .
63. Medini , D. , Serruto , D. et al. ( 2008 ) Microbiology in the post - genomic era . Nature Reviews. Microbiology 6 ( 6 ), 419-430 .
64. Milkman , R. ( 1973 ) Electrophoretic variation in Escherichia coli from natural sources . Science 182 , 1024-1026 .
65. Miller , J. R. , Delcher , A. L. et al. ( 2008 ) Aggressive assembly of pyrosequencing reads with mates . Bioinformatics 24 ( 24 ), 2818-2824 .
66. Mueller , U. G. and Wolfenbarger , L. L. ( 1999 ) AFLP genotyping and fi ngerprinting . Trends in Ecology & Evolution 14 ( 10 ), 389-394 .
67. Musser , J. M. , Bemis , D. A. et al. ( 1987 ) Clonal diversity and host distribution in Bordetella bronchiseptica . Journal of Bacteriology 169 ( 6 ), 2793-2803 .
68. Musser , J. M. , Kroll , J. S. et al. ( 1988 ) Clonal population structure of encapsulated Haemophilus infl uenza . Infection and Immunity 56 , 1837-1845 .
69. Musser , J. M. , Kroll , J. S. et al. ( 1990 ) Global genetic - structure and molecular epidemiology of encapsulated Haemophilus infl uenzae . Reviews of Infectious Diseases 12 ( 1 ), 75-111 .
70. Ochman , H. and Davalos , L. M. ( 2006 ) The nature and dynamics of bacterial genomes . Science 311 ( 5768 ), 1730-1733 .
71. Ochman , H. and Santos , S. R. ( 2005 ) Exploring microbial microevolution with microarrays . Infection, Genetics and Evolution 5 ( 2 ), 103-108 .
72. Pan , X. K. , Stein , L. et al. ( 2005 ) SynBrowse: A synteny browser for comparative sequence analysis . Bioinformatics 21 ( 17 ), 3461-3468 .
73. Parry , C. M. , Hien , T. T. et al. ( 2002 ) Typhoid fever . New England Journal of Medicine 347 ( 22 ), 1770-1782 .
74. Perron , G. G. , Zasloff , M. et al. ( 2006 ) Experimental evolution of resistance to an antimicrobial peptide . Proceedings of the Royal Society. Series B, Biological Sciences 273 ( 1583 ), 251-256 .
75. Pitman , A. R. , Jackson , R. W. et al. ( 2005 ) Exposure to host resistance mechanisms drives evolution of bacterial virulence in plants . Current Biology 15 ( 24 ), 2230-2235 .
76. Pouillot , F. , Fayolle , C. et al. ( 2008 ) Characterization of chromosomal regions conserved in Yersinia pseudotuberculosis and lost by Yersinia pestis . Infection and Immunity 76 ( 10 ), 4592-4599 .
77. Prevost , G. , Jaulhac , B. et al. ( 1992 ) DNA fi ngerprinting by pulsed - fi eld gel - electrophoresis is more effective than ribotyping in distinguishing among methicillin - resistant Staphylococcus aureus isolates . Journal of Clinical Microbiology 30 ( 4 ), 967-973 .
78. Romualdi , A. , Felder , M. et al. ( 2007 ) GenColors: Annotation and comparative genomics of prokaryotes made easy . Methods in Molecular Biology 395 , 75-96 .
79. Romualdi , A. , Siddiqui , R. et al. ( 2005 ) GenColors: Accelerated comparative analysis and annotation of prokaryotic genomes at various stages of completeness . Bioinformatics 21 ( 18 ), 3669-3671 .
80. Rossello - Mora , R. and Amann , R. ( 2001 ) The species concept for prokaryotes . FEMS Microbiology Reviews 25 ( 1 ), 39-67 .
81. Rothberg , J. M. and Leamon , J. H. ( 2008 ) The development and impact of 454 sequencing . Nature Biotechnology 26 ( 10 ), 1117-1124 .
82. Roumagnac , P. , Weill , F. X. et al. ( 2006 ) Evolutionary history of Salmonella typhi . Science 314 ( 5803 ), 1301-1304 .
83. Rozenfeld , A. F. , Arnaud - Haond , S. et al. ( 2007 ) Spectrum of genetic diversity and networks of clonal organisms . Journal of the Royal Society Interface 4 ( 17 ), 1093-1102 .
84. Salaun , L. , Audibert , C. et al. ( 1998 ) Panmictic structure of Helicobacter pylori demonstrated by the comparative study of six genetic markers . FEMS Microbiology Letters 161 ( 2 ), 231-239 .
85. Salzberg , S. L. , Sommer , D. D. et al. ( 2008 ) Gene - boosted assembly of a novel bacterial genome from very short reads . PLoS Computational Biology 4 ( 9 ), e1000186 .
86. Sarkar , S. F. , Gordon , J. S. et al. ( 2006 ) Comparative genomics of host - specifi c virulence in Pseudomonas syringae . Genetics 174 ( 4 ), 1041-1056 .
87. Schatz , M. C. , Trapnell , C. et al. ( 2007 ) High - throughput sequence alignment using Graphics Processing Units . BMC Bioinformatics 8 , 1-10 .
88. Seifert , H. S. , Ajioka , R. S. et al. ( 1988 ) DNA transformation leads to pilin antigenic variation in Neisseria gonorrhoeae . Nature 336 ( 6197 ), 392-395 .
89. Selander , R. K. , Beltran , P. et al. ( 1990 ) Evolutionary genetic relationships of clones of Salmonella serovars that cause human typhoid and other enteric fevers . Infection and Immunity 58 ( 7 ), 2262-2275 .
90. Selander , R. K. , Caugant , D. A. et al. ( 1986 ) Methods of multilocus enzyme electrophoresis for bacterial population genetics and systematics . Applied and Environmental Microbiology 51 , 873-884 .
91. Selander , R. K. and Levin , B. R. ( 1980) Genetic diversity and structure in Escherichia coli populations . Science 210 , 545-547 .
92. Selander , R. K. , McKinney , R. M. et al. ( 1985 ) Genetic Structure of populations of Legionella pneumophila . Journal of Bacteriology 163 ( 3 ), 1021-1037 .
93. Shankar , N. , Baghdayan , A. S. et al. ( 2002 ) Modulation of virulence within a pathogenicity island in vancomycin - resistant Enterococcus faecalis . Nature 417 ( 6890 ), 746-750 .
94. Shankar , V. , Baghdayan , A. S. et al. ( 1999 ) Infection - derived Enterococcus faecalis strains are enriched in esp , a gene encoding a novel surface protein . Infection and Immunity 67 ( 1 ), 193-200 .
95. Sheppard , S. K. , McCarthy , N. D. et al. ( 2008 ) Convergence of Campylobacter species: Implications for bacterial evolution . Science 320 ( 5873 ), 237-239 .
96. Smith , A. , Xuan , Z. et al. ( 2008 ) Using quality scores and longer reads improves accuracy of Solexa read mapping . BMC Bioinformatics 9 ( 1 ), 128 .
97. Sokurenko , E. V. , Chesnokova , V. et al. ( 1998 ) Pathogenic adaptation of Escherichia coli by natural variation of the FimH adhesin . Proceedings of the National Academy of Sciences of the United States of America 95 ( 15 ), 8922-8926 .
98. Sokurenko , E. V. , Hasty , D. L. et al. ( 1999 ) Pathoadaptive mutations: Gene loss and variation in bacterial pathogens . Trends in Microbiology 7 ( 5 ), 191-195 .
99. Souza , V. , Turner , P. E. et al. ( 1997 ) Long - term experimental evolution in Escherichia coli . 5. Effects of recombination with immigrant genotypes on the rate of bacterial evolution . Journal of Evolutionary Biology 10 ( 5 ), 743-769 .
100. Spratt , B. G. and Maiden , M. C. J. ( 1999) Bacterial population genetics, evolution and epidemiology . Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 354 ( 1384 ), 701-710 .
101. Spratt , B. G. , Smith , N. H. et al. ( 1995 ) The population genetics of the pathogenic Neisseria . In Population Genetics of Bacteria (eds. S. Baumberg , J. P. W. Young , E. M. H. Wellington , and S. R. Saunders ), p. 52 . Cambridge University Press , Cambridge, U.K .
102. Srivatsan , A. , Han , Y. et al. ( 2008 ) High - precision, whole - genome sequencing of laboratory strains facilitates genetic studies . PLoS Genetics 4 ( 8 ), e1000139 .
103. Stein , L. D. ( 2008 ) Towards a cyberinfrastructure for the biological sciences: Progress, visions and challenges . Nature Reviews. Genetics 9 ( 9 ), 678-688 .
104. Stein , L. D. , Mungall , C. et al. ( 2002 ) The Generic Genome Browser: A building block for a model orga nism system database . Genome Research 12 ( 10 ), 1599-1610 .
105. Suerbaum , S. and Josenhans , C. ( 2007 ) Helicobacter pylori evolution and phenotypic diversifi cation in a changing host . Nature Reviews. Microbiology 5 ( 6 ), 441-452 .
106. Suerbaum , S. , Smith , J. M. et al. ( 1998 ) Free recombination within Helicobacter pylori . Proceedings of the National Academy of Sciences of the United States of America 95 ( 21 ), 12619-12624 .
107. Sung , J. M. L. , Lloyd , D. H. et al. ( 2008 ) Staphylococcus aureus host specifi city: Comparative genomics of human versus animal isolates by multi - strain microarray . Microbiology 154 , 1949-1959 .
108. Tettelin , H. , Masignani , V. et al. ( 2005 ) Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial " pan - genome. " Proceedings of the National Academy of Sciences of the United States of America 102 ( 39 ), 13950-13955 .
109. Tettelin , H. , Riley , D. et al. ( 2008 ) Comparative genomics: The bacterial pan - genome . Current Opinion in Microbiology 11 ( 5 ), 472-477 .
110. Tibayrenc , M. ( 1999 ) Toward an integrated genetic epidemiology of parasitic protozoa and other pathogens . Annual Review of Genetics 33 , 449-477 .
111. Treangen , T. J. , Ambur , O. H. et al. ( 2008 ) The impact of the neisserial DNA uptake sequences on genome evolution and stability . Genome Biology 9 ( 3 ), R60 .
112. Uchiyama , I. ( 2008 ) Multiple genome alignment for identifying the core structure among moderately related microbial genomes . BMC Genomics 9 , 515 .
113. Ueda , K. , Seki , T. et al. ( 1999 ) Two distinct mechanisms cause heterogeneity of 16S rRNA . Journal of Bacteriology 181 ( 1 ), 78-82 .
114. Velicer , G. J. , Raddatz , G. et al. ( 2006 ) Comprehensive mutation identifi cation in an evolved bacterial cooperator and its cheating ancestor . Proceedings of the National Academy of Sciences of the United States of America 103 ( 21 ), 8107-8112 .
115. Venter , J. C. , Adams , M. D. et al. ( 2001 ) The sequence of the human genome . Science 291 ( 5507 ), 1304-1351 .
116. Warren , R. L. , Sutton , G. G. et al. ( 2007 ) Assembling millions of short DNA sequences using SSAKE . Bioinformatics 23 ( 4 ), 500-501 .
117. Weissman , S. J. , Chattopadhyay , S. et al. ( 2006 ) Clonal analysis reveals high rate of structural mutations in fi mbrial adhesins of extraintestinal pathogenic Escherichia coli . Molecular Microbiology 59 ( 3 ), 975-988 .
118. Welch , R. A. , Burland , V. et al. ( 2002 ) Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli . Proceedings of the National Academy of Sciences of the United States of America 99 ( 26 ), 17020-17024 .
119. Whitaker , R. J. and Banfi eld , J. F. ( 2006 ) Population genomics in natural microbial communities . Trends in Ecology & Evolution 21 ( 9 ), 508-516 .
120. Wilkinson , M. , Schoof , H. et al. ( 2005 ) BioMOBY successfully integrates distributed heterogeneous bioinformatics web services. The PlaNet exemplar case . Plant Physiology 138 ( 1 ), 5-17 .
121. Wilkinson , M. D. and Links , M. ( 2002 ) BioMOBY: An open source biological web services proposal . Briefi ngs in Bioinformatics 3 ( 4 ), 331-341 .
122. Wirth , T. , Falush , D. et al. ( 2006 ) Sex and virulence in Escherichia coli: An evolutionary perspective . Molecular Microbiology 60 ( 5 ), 1136-1151 .
123. Woese , C. R. , Fox , G. E. et al. ( 1975 ) Conservation of primary structure in 16S ribosomal - RNA . Nature 254 ( 5495 ), 83-86 .
124. Zerbino , D. and Birney , E. ( 2007 ) Velvet: Sequence assembler for very short reads .
125. Zerbino , D. and Birney , E. ( 2008 ) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs . Genome Research 18 ( 5 ), 821-829 .
126. Zhu , P. , van der Ende , A. et al. ( 2001 ) Fit genotypes and escape variants of subgroup III Neisseria meningitidis during three pandemics of epidemic meningitis . Pro ceedings of the National Academy of Sciences of the United States of America 98 ( 9 ), 5234-5239 .
127. Ziebuhr , W. , Ohlsen , K. et al. ( 1999 ) Evolution of bacterial pathogenesis . Cellular and Molecular Life Sciences 56 , 719-728 .
128. Zwick , M. E. , McAfee , F. et al. ( 2005 ) Microarray - based resequencing of multiple Bacillus anthracis isolates . Genome Biology 6 , R10 .