Open Access This article is distributed under the terms of the Creative Commons Attribution Noncommercial License which permits any noncommercial use, distribution, <strong>and</strong> reproduction <strong>in</strong> any medium, provided the orig<strong>in</strong>al author(s) <strong>and</strong> source are credited. References 1. Bassler B et al. (2007) CP000789.1: Direct submission to GenBank 2. B<strong>in</strong>newies TT, Hall<strong>in</strong> PF, Staerfeldt HH, Ussery DW (2005) Genome update: proteome comparisons. Microbiol 151:1–4 3. Chen CY, Wu KM, Chang YC, Chang CH, Tsai HC, Liao TL, Liu YM, Chen HJ, Shen AB, Li JC, Su TL, Shao CP, Lee CT, Hor LI, Tsai SF (2003) <strong>Comparative</strong> genome analysis of Vibrio vulnificus, a mar<strong>in</strong>e pathogen. Genome Res 13:2577–2587 4. Clayton RA, Sutton G, H<strong>in</strong>kle PS, Bult C, Fields C (1995) Intraspecific variation <strong>in</strong> small-subunit rRNA sequences <strong>in</strong> GenBank: why s<strong>in</strong>gle sequences may not adequately represent prokaryotic taxa. Int J Syst Bacteriol 45:595–599 5. Colwell R, Grim CJ, Young S, Jaffe D, Gnerre S, Berl<strong>in</strong> A, Heiman D, Hepburn T, Shea T, Sykes S, Alvarado L, Kodira C, Heidelberg J, L<strong>and</strong>er E, Galagan J, Nusbaum C, Birren B (2008) NZ_AAKF00000000: Direct submission to GenBank 6. Doolittle WF (1995) Phylogenetic classification <strong>and</strong> the universal tree. Science 284:2124–2129 7. Doolittle WF, Papke RT (2006) Genomics <strong>and</strong> the bacterial species problem. Genome Biol 7:116 8. Doolittle WF, Zhaxybayeva O (2009) On the orig<strong>in</strong> of prokaryotic species. Genome Res 19:744–756 9. Edwards R, Ferriera S, Johnson J, Kravitz S, Beeson K, Sutton G, Rogers Y-H, Friedman R, Frazier M, Venter JC (2008) NZ_ACCV00000000: Direct submission to GenBank 10. Farmer JJ, J<strong>and</strong>a JM (2005) Vibrionaceae. In: Bergey’s manual of systematic bacteriology, 2nd edn, vol 2 part B. Spr<strong>in</strong>ger, New York, pp 491–546 11. Feng L, Reeves PR, Lan R, Ren Y, Gao C, Zhou Z, Ren Y, Cheng J, Wang W, Wang J, Qian W, Li D, Wang L (2008) A recalibrated molecular clock <strong>and</strong> <strong>in</strong>dependent orig<strong>in</strong>s for the cholera p<strong>and</strong>emic clones. PLoS ONE 3:e4053 12. Gevers D, Cohan FM, Lawrence JG, Sprat BG, Coeyne T, Feil EJ, Stackebr<strong>and</strong>t E, Van de Peer Y, V<strong>and</strong>amme P, Thompson FL, Sw<strong>in</strong>gs J (2005) Re-evaluat<strong>in</strong>g prokaryotic species. Nat Rev Microbiol 3:733–739 13. Hagstrom A, Ferriera S, Johnson J, Kravitz S, Beeson K, Sutton G, Rogers Y-H, Friedman R, Frazier M, Venter JC (2007) NZ_ABGR00000000: Direct submission to GenBank 14. Hall<strong>in</strong> PF, B<strong>in</strong>newies TT, Ussery DW (2008) The genome BLASTatlas—a GeneWiz extension for visualization of wholegenome homology. Mol Biosyst 4:363–371 15. Heidelberg JF, Eisen JA, Nelson WC, Clayton RA, Gw<strong>in</strong>n ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Umayam L, Gill SR, Nelson KE, Read TD, Tettel<strong>in</strong> H, Richardson D, Ermolaeva MD, Vamathevan J, Bass S, Q<strong>in</strong> H, Dragoi I, Sellers P, McDonald L, Utterback T, Fleishmann RD, Nierman WC, White O, Salzberg SL, Smith HO, Colwell RR, Mekalanos JJ, Venter JC, Fraser CM (2000) DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature 406:477–483 16. Heidelberg J, Sebastian Y. NZ_AAKJ00000000, NZ_AAUT00000000, NZ_AAKK00000000, NZ_AAUR00000000, NZ_AAWF00000000: Direct submission to GenBank 17. Hjerde E, Lorentzen MS, Holden MT, Seeger K, Paulsen S, Bason N, Churcher C, Harris D, Norbertczak H, Quail MA, S<strong>and</strong>ers S, Thurston S, Parkhill J, Willassen NP, Thomson NR (2008) The genome sequence of the fish pathogen Aliivibrio salmonicida T. Vesth et al. stra<strong>in</strong> LFI1238 shows extensive evidence of gene decay. BMC Genomics 9:616 18. Konstant<strong>in</strong>idis T, Ramette A, Tiedje JA (2006) The bacterial species def<strong>in</strong>ition <strong>in</strong> the genomic era. Phil Trans R Soc B 361:1929–1940 19. Lagesen K, Hall<strong>in</strong> P, Rødl<strong>and</strong> EA, Staerfeldt HH, Rognes T, Ussery DW (2007) RNAmmer: consistent <strong>and</strong> rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100–3108 20. Larsen TS, Krogh A (2003) EasyGene—a prokaryotic gene f<strong>in</strong>der that ranks ORFs by statistical significance. BMC Bio<strong>in</strong>formatics 4:29 21. Le Roux F, Zou<strong>in</strong>e M, Chakroun N, B<strong>in</strong>esse J, Saulnier D, Bouchier C, Zidane N, Ma L, Rusniok C, Lajus A, Buchrieser C, Médigue C, Polz MF, Mazel D (2009) Genome sequence of Vibrio splendidus: an abundant planctonic mar<strong>in</strong>e species with a large genotypic diversity. Environ Microbiol 11:1959–1970 22. L<strong>in</strong> W, Fullner KJ, Clayton R, Sexton JA, Rogers MB, Calia KE, Calderwood SB, Fraser C, Mekalanos JJ (1999) Identification of a Vibrio cholerae RTX tox<strong>in</strong> gene cluster that is tightly l<strong>in</strong>ked to the cholera tox<strong>in</strong> prophage. Proc Natl Acad Sci U S A 96:1071– 1076 23. Loytynoja A, Goldman N (2005) An algorithm for progressive multiple alignment of sequences with <strong>in</strong>sertions. Proc Natl Acad Sci U S A 102:10557–10562 24. Loytynoja A, Goldman N (2008) Phylogeny-aware gap placement prevents errors <strong>in</strong> sequence alignment <strong>and</strong> evolutionary analysis. Science 320:1632–1635 25. Mak<strong>in</strong>o K, Oshima K, Kurokawa K, Yokoyama K, Uda T, Tagomori K, Iijima Y, Najima M, Nakano M, Yamashita A, Kubota Y, Kimura S, Yasunaga T, Honda T, Sh<strong>in</strong>agawa H, Hattori M, Iida T (2003) Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism dist<strong>in</strong>ct from that of V. cholerae. Lancet 361:743–749 26. M<strong>and</strong>el MJ, Wollenberg MS, Stabb EV, Visick KL, Ruby EG (2009) A s<strong>in</strong>gle regulatory gene is sufficient to alter bacterial host range. Nature 458:215–218 27. Mazel D, Le Roux F (2008) FM954973.1: Direct submission to GenBank 28. Med<strong>in</strong>i D, Donati C, Tettel<strong>in</strong> H, Masignani V, Rappuoli R (2005) The microbial pan-genome. Curr Op<strong>in</strong> Genet Dev 15:589–594 29. Medrano-Soto A, Moreno-Hagelsieb G, V<strong>in</strong>uesa P, Christen JA, Collado-Vides J (2001) Succesful lateral transfer requires codon usage compatibility between foreign genes <strong>and</strong> recipient genomes. Mol Biol Evol 21:1884–1894 30. Mohapatra SS, Ramach<strong>and</strong>ran D, Mantri CK, Colwell RR, S<strong>in</strong>gh DV (2009) Determ<strong>in</strong>ation of relationships among non-toxigenic Vibrio cholerae O1 biotype El Tor stra<strong>in</strong>s from housekeep<strong>in</strong>g gene sequences <strong>and</strong> ribotype patterns. Res Microbiol 160: 57–62 31. Munk A, Tapia R, Green L, Rogers Y, Detter JC, Bruce D, Brett<strong>in</strong> TS, Colwell R, Grim C, Vonste<strong>in</strong> V, Bartels D. CP001485.1, NZ_ACHV00000000, NZ_ACHY00000000, NZ_ACHW00000000, NZ_ACHX00000000, NZ_ACHZ00000000, NZ_ACIA00000000, NZ_ACFQ00000000: Direct submission to GenBank 32. Murray RG, Stackebr<strong>and</strong>t E (1995) Taxonomic note: implementation of the provisional status C<strong>and</strong>idatus for <strong>in</strong>completely described procaryotes. Int J Syst Bacteriol 45:186–187 33. Nierman WC (2006) NZ_AATY00000000: Direct submission to GenBank 34. Pang B, Yan M, Cui Z, Ye X, Diao B, Ren Y, Gao S, Zhang L, Kan B (2007) Genetic diversity of toxigenic <strong>and</strong> nontoxigenic Vibrio cholerae serogroups O1 <strong>and</strong> O139 revealed by array-based comparative genomic hybridization. J Bacteriol 189:4837–4879 35. Philippe H, Douady CJ (2003) Horizontal gene transfer <strong>and</strong> phylogenetics. Curr Op<strong>in</strong> Microbiol 6:498–505
Orig<strong>in</strong>s of V. cholerae 36. P<strong>in</strong>hassi J, Pedros-Alio C, Ferriera S, Johnson J, Kravitz S, Halpern A, Rem<strong>in</strong>gton K, Beeson K, Tran B, Rogers Y-H, Friedman R, Venter JC (2006) NZ_AAND00000000: Direct submission to GenBank 37. Pupo GM, Lan R, Reeves PR (2000) Multiple <strong>in</strong>dependent orig<strong>in</strong>s of Shigella clones of Escherichia coli <strong>and</strong> convergent evolution of many of their characteristics. Proc Natl Acad Sci U S A 97:10567–10572 38. Rhee JH, Kim SY, Chung SS, Lee SE, Choy HE (2002) AE016795.2: Direct submission to GenBank 39. Riley MA, Lizotte-Waniewski M (2009) Population genomics <strong>and</strong> the bacterial species concept. Methods Mol Biol 532:367–377 40. Rowe-Magnus DA, Guérout AM, Mazel D (1999) Super<strong>in</strong>tegrons. Res Microbiol 150:641–651 41. Rosenberg E, Ferriera S, Johnson J, Kravitz S, Beeson K, Sutton G, Rogers Y-H, Friedman R, Frazier M. Venter JC (2006) NZ_ABCH00000000: Direct submission to GenBank 42. 3Ruby EG, Urbanowski M, Campbell J, Dunn A, Fa<strong>in</strong>i M, Gunsalus R, Lostroh P, Lupp C, McCann J, Millikan D, Schaefer A, Stabb E, Stevens A, Visick K, Whistler C, Greenberg EP (2005) Complete genome sequence of Vibrio fischeri: a symbiotic bacterium with pathogenic congeners. Proc Natl Acad Sci U S A 102:3004–3009 43. Sánchez J, Holmgren J (2005) Virulence factors, pathogenesis <strong>and</strong> vacc<strong>in</strong>e protection <strong>in</strong> cholera <strong>and</strong> ETEC diarrhoea. Curr Op<strong>in</strong> Immunol 17:388–398 44. Stackebr<strong>and</strong>t E, Frederiksen W, Garrity GM, Grimont PA, Kämpfer P, Maiden MC, Nesme X, Rosselló-Mora R, Sw<strong>in</strong>gs J, Trüper HG, Vauter<strong>in</strong> L, Ward AC, Whitman WB (2002) Report of the ad hoc committee for the re-evaluation of the species def<strong>in</strong>ition <strong>in</strong> bacteriology. Int J Syst Evol Microbiol 52:1043–1047 45. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599 46. Thompson FL, Iida T, Sw<strong>in</strong>gs J (2004) Biodiversity of vibrios. Microbiol Mol Biol Rev 68:403–431 47. Urbanczyk H, Ast JC, Higg<strong>in</strong>s MJ, Carson J, Dunlap PV (2007) Reclassification of Vibrio fischeri, Vibrio logei, Vibrio salmonicida <strong>and</strong> Vibrio wodanis as Aliivibrio fischeri gen. nov., comb. nov., Aliivibrio logei comb. nov., Aliivibrio salmonicida comb. nov. <strong>and</strong> Aliivibrio wodanis comb. nov. Int J Syst Evol Microbiol 57:2823–2829 48. Vezzi A, Campanaro S, D'Angelo M, Simonato F, Vitulo N, Lauro FM, Cestaro A, Malacrida G, Simionati B, Cannata N, Romualdi C, Bartlett DH, Valle G (2005) Life at depth: Photobacterium profundum genome sequence <strong>and</strong> expression analysis. Science 30:1459–1461 49. Wang L, Feng L, Reeves P, Lan R, Ren Y, Gao C, Zhou Z, Ren Y, Wang W (2008) CP001233.1. CP001235.1: Direct submission to GenBank 50. Woese CR (1987) Bacterial evolution. Microbial Rev 51:221–271
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Peter Fischer Hallin | 2009 Peter F
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Preface This Ph.D. thesis is writte
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thesis, the work is just being publ
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ved at blive publiceret i Standards
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Paper VI [Lagesen K, Hallin P] 1 ,
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3.3.3 Refining E. coli and Shigella
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xviii 2.17 Pan- and core-genome plo
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Chapter 1 Introduction Introduction
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Chapter 2 Comparative Genomics 2.1
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Comparative Genomics the publicly a
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Comparative Genomics source CDS tot
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Comparative Genomics 1 mysql -N -B
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Listing 2.8: R code to generate a 2
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1st U C A G U 2nd position C A G 3r
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1st U C A G U 2nd position C A G 3r
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Escherichia coli strain K-12, subst
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Comparative Genomics
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3M 2.5M 3.5M 2.5M 2M 0M 2M 0.5M B.
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2.4 Summary Comparative Genomics Th
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Comparative Genomics 2.5 Instant in
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‘ReSourCe is he best online submi
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up to a total of 41 different E. co
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Fig. 2 Genes (or segments) from eac
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Fig. 5 BLASTatlas of Clostridium bo
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Hallin, et al. Figure 4 | The dataf
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Genome homology: Comparing multiple
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ing platform-‐independent Java
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34. Wang H, Noordewier M, Benham CJ
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Chapter 4 Web Services and Interope
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Web Services and Interoperability i
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Web Services and Interoperability i
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Web Services and Interoperability i
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Chapter 5 Conclusion and perspectiv
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Appendix A Appendix: Workshops, tea
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Appendix B Appendix: Ph.D. study pl
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Danmarks Tekniske Universitet AFI,
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Danmarks Tekniske Universitet AFI,
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Appendix C Appendix: Courses C.1 Gl
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D.2 Sample output from queryGenomes
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Appendix: Software 13 w a r n " $ o
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Appendix: Software 109 m y ( $ m i
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Appendix: Software 25 [ ] A l t e r
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BIBLIOGRAPHY J. Rogers, P. F. Stadl
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BIBLIOGRAPHY Q. Jin, Z. Yuan, J. Xu
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BIBLIOGRAPHY Velicer, F.-J. Vorholt