GO4genome: A prokaryotic phylogeny based on genome organization

Journal of Molecular Evolution

Volumn 68, Issue 5, 2009, Pages 550-562

  Merkl, Rainer ^a   Wiezer, Arnim ^b  

^a UNIVERSITY OF REGENSBURG   (Germany)

^b UNIVERSITY OF GÖTTINGEN   (Germany)

Author keywords

Bacterial genomes; Computational molecular biology; Gene ontology; Prokaryotic phylogenomics; Whole genome phylogeny

Indexed keywords

ALGORITHM; ARTICLE; ESCHERICHIA COLI; GENE FUNCTION; GENE ORDER; GENE SEQUENCE; GENOME ANALYSIS; HORIZONTAL GENE TRANSFER; METHANOSARCINA; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PROKARYOTIC CELL; SHIGELLA; STREPTOCOCCUS; UNINDEXED SEQUENCE; YERSINIA;

ALGORITHMS; COMPUTATIONAL BIOLOGY; ESCHERICHIA COLI; GENE ORDER; GENE TRANSFER, HORIZONTAL; GENES, BACTERIAL; GENOME, ARCHAEAL; GENOME, BACTERIAL; METHANOSARCINA; PHYLOGENY; PROKARYOTIC CELLS; STREPTOCOCCUS; YERSINIA;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; METHANOSARCINA; PROKARYOTA; SHIGELLA; STREPTOCOCCUS; YERSINIA;

EID: 67349240746     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-009-9233-6     Document Type: Article

References (70)

1. M Achtman G Morelli P Zhu T Wirth I Diehl B Kusecek AJ Vogler DM Wagner CJ Allender WR Easterday V Chenal-Francisque P Worsham NR Thomson J Parkhill LE Lindler E Carniel P Keim 2004 Microevolution and history of the plague bacillus, Yersinia pestis Proc Natl Acad Sci USA 101 17837 17842 (Pubitemid 40051973)
2. SF Altschul W Gish W Miller EW Myers DJ Lipman 1990 Basic local alignment search tool J Mol Biol 215 403 410
3. M Anisimova J Bielawski K Dunn Z Yang 2007 Phylogenomic analysis of natural selection pressure in Streptococcus genomes BMC Evol Biol 7 154
4. RK Auerbach A Tuanyok WS Probert L Kenefic AJ Vogler DC Bruce C Munk TS Brettin M Eppinger J Ravel DM Wagner P Keim 2007 Yersinia pestis evolution on a small timescale: comparison of whole genome sequences from North America PLoS ONE 2 e770
5. E Bapteste Y Boucher J Leigh WF Doolittle 2004 Phylogenetic reconstruction and lateral gene transfer Trends Microbiol 12 406 411 (Pubitemid 39178591)
6. E Bapteste E Susko J Leigh I Ruiz-Trillo J Bucknam WF Doolittle 2008 Alternative methods for concatenation of core genes indicate a lack of resolution in deep nodes of the prokaryotic phylogeny Mol Biol Evol 25 83 91
7. E Belda A Moya FJ Silva 2005 Genome rearrangement distances and gene order phylogeny in γ-proteobacteria Mol Biol Evol 22 1456 1467 (Pubitemid 40734196)
8. PS Chain E Carniel FW Larimer J Lamerdin PO Stoutland WM Regala AM Georgescu LM Vergez ML Land VL Motin RR Brubaker J Fowler J Hinnebusch M Marceau C Medigue M Simonet V Chenal-Francisque B Souza D Dacheux JM Elliott A Derbise LJ Hauser E Garcia 2004 Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis Proc Natl Acad Sci USA 101 13826 13831 (Pubitemid 39298492)
9. PS Chain P Hu SA Malfatti L Radnedge F Larimer LM Vergez P Worsham MC Chu GL Andersen 2006 Complete genome sequence of Yersinia pestis strains Antiqua and Nepal516: evidence of gene reduction in an emerging pathogen J Bacteriol 188 4453 4463 (Pubitemid 43865765)
10. FD Ciccarelli T Doerks C von Mering CJ Creevey B Snel P Bork 2006 Toward automatic reconstruction of a highly resolved tree of life Science 311 1283 1287 (Pubitemid 43334717)
11. D Dalevi N Eriksen 2008 Expected gene-order distances and model selection in bacteria Bioinformatics 24 1332 1338
12. AC Darling B Mau FR Blattner NT Perna 2004 Mauve: multiple alignment of conserved genomic sequence with rearrangements Genome Res 14 1394 1403 (Pubitemid 39029237)
13. V Daubin M Gouy G Perrière 2002 A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history Genome Res 12 1080 1090 (Pubitemid 34785201)
14. A Del Pozo F Pazos A Valencia 2008 Defining functional distances over gene ontology BMC Bioinformatics 9 50
15. U Deppenmeier A Johann T Hartsch R Merkl RA Schmitz R Martinez-Arias A Henne A Wiezer S Bäumer C Jacobi H Brüggemann T Lienard A Christmann M Bomeke S Steckel A Bhattacharyya A Lykidis R Overbeek HP Klenk RP Gunsalus H-J Fritz G Gottschalk 2002 The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea J Mol Microbiol Biotechnol 4 453 461 (Pubitemid 34784706)
16. BE Dutilh MA Huynen WJ Bruno B Snel 2004 The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise J Mol Evol 58 527 539 (Pubitemid 38609888)
17. SF Elena TS Whittam CL Winkworth MA Riley RE Lenski 2005 Genomic divergence of Escherichia coli strains: evidence for horizontal transfer and variation in mutation rates Int Microbiol 8 271 278 (Pubitemid 43127999)
18. E Esnault M Valens O Espéli F Boccard 2007 Chromosome structuring limits genome plasticity in Escherichia coli PLoS Genet 3 e226
19. ST Fitz-Gibbon CH House 1999 Whole genome-based phylogenetic analysis of free-living microorganisms Nucleic Acids Res 27 4218 4222 (Pubitemid 29500255)
20. M Fukushima K Kakinuma R Kawaguchi 2002 Phylogenetic analysis of Salmonella, Shigella, and Escherichia coli strains on the basis of the gyrB gene sequence J Clin Microbiol 40 2779 2785 (Pubitemid 35284941)
21. S Hannenhalli C Chappey EV Koonin PA Pevzner 1995 Genome sequence comparison and scenarios for gene rearrangements: a test case Genomics 30 299 311
22. SR Henz DH Huson AF Auch K Nieselt-Struwe SC Schuster 2005 Whole-genome prokaryotic phylogeny Bioinformatics 21 2329 2335 (Pubitemid 40731587)
23. CW Hill JA Gray 1988 Effects of chromosomal inversion on cell fitness in Escherichia coli K-12 Genetics 119 771 778
24. SJ Hinchliffe KE Isherwood RA Stabler MB Prentice A Rakin RA Nichols PC Oyston J Hinds RW Titball BW Wren 2003 Application of DNA microarrays to study the evolutionary genomics of Yersinia pestis and Yersinia pseudotuberculosis Genome Res 13 2018 2029 (Pubitemid 37161759)
25. Hughes D (2000) Evaluating genome dynamics: the constraints on rearrangements within bacterial genomes. Genome Biol 1:REVIEWS0006
26. DH Huson D Bryant 2006 Application of phylogenetic networks in evolutionary studies Mol Biol Evol 23 254 267 (Pubitemid 43100040)
27. MA Huynen B Snel P Bork 2001 Inversions and the dynamics of eukaryotic gene order Trends Genet 17 304 306 (Pubitemid 32497103)
28. Y Itoh Y Kawamura H Kasai MM Shah PH Nhung M Yamada X Sun T Koyana M Hayashi K Ohkusu T Ezaki 2006 dnaJ and gyrB gene sequence relationship among species and strains of genus Streptococcus Syst Appl Microbiol 29 368 374 (Pubitemid 43974879)
29. F Jacob J Monod 1961 Genetic regulatory mechanisms in the synthesis of proteins J Mol Biol 3 318 356
30. Q Jin Z Yuan J Xu Y Wang Y Shen W Lu J Wang H Liu J Yang F Yang X Zhang J Zhang G Yang H Wu D Qu J Dong L Sun Y Xue A Zhao Y Gao J Zhu B Kan K Ding S Chen H Cheng Z Yao B He R Chen D Ma B Qiang Y Wen Y Hou J Yu 2002 Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157 Nucleic Acids Res 30 4432 4441 (Pubitemid 35277254)
31. TJ Johnson S Kariyawasam Y Wannemuehler P Mangiamele SJ Johnson C Doetkott JA Skyberg AM Lynne JR Johnson LK Nolan 2007 The genome sequence of avian pathogenic Escherichia coli strain O1:K1:H7 shares strong similarities with human extraintestinal pathogenic E. coli genomes J Bacteriol 189 3228 3236 (Pubitemid 46697413)
32. KT Konstantinidis A Ramette JM Tiedje 2006 Toward a more robust assessment of intraspecies diversity, using fewer genetic markers Appl Environ Microbiol 72 7286 7293 (Pubitemid 44748445)
33. JO Korbel B Snel MA Huynen P Bork 2002 SHOT: a web server for the construction of genome phylogenies Trends Genet 18 158 162 (Pubitemid 34164642)
34. CG Kurland B Canback OG Berg 2003 Horizontal gene transfer: a critical view Proc Natl Acad Sci USA 100 9658 9662 (Pubitemid 37086996)
35. S Kurtz A Phillippy AL Delcher M Smoot M Shumway C Antonescu SL Salzberg 2004 Versatile and open software for comparing large genomes Genome Biol 5 R12
36. WC Lathe 3rd B Snel P Bork 2000 Gene context conservation of a higher order than operons Trends Biochem Sci 25 474 479
37. JG Lawrence H Ochman 1997 Amelioration of bacterial genomes: rates of change and exchange J Mol Evol 44 383 397 (Pubitemid 27161335)
38. T Lefébure MJ Stanhope 2007 Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition Genome Biol 8 R71
39. E Lerat V Daubin NA Moran 2003 From gene trees to organismal phylogeny in prokaryotes: the case of the γ-proteobacteria PLoS Biol 1 E19
40. GN Lin Z Cai G Lin S Chakraborty D Xu 2009 ComPhy: prokaryotic composite distance phylogenies inferred from whole-genome gene sets BMC Bioinformatics 10 Suppl 1 S5
41. DR Maddison DL Swofford WP Maddison 1997 NEXUS: an extensible file format for systematic information Syst Biol 46 590 621
42. A McCann JA Cotton JO McInerney 2008 The tree of genomes: an empirical comparison of genome-phylogeny reconstruction methods BMC Evol Biol 8 312
43. R Merkl 2004 SIGI: score-based identification of genomic islands BMC Bioinformatics 5 22
44. R Merkl 2007 Modelling the evolution of the archeal tryptophan synthase BMC Evol Biol 7 59
45. KE Nelson RA Clayton SR Gill 1999 Evidence for lateral gene transfer between archaea and bacteria from genome sequence of Thermotoga maritima Nature 399 323 329 (Pubitemid 29318123)
46. H Ochman JG Lawrence EA Groisman 2000 Lateral gene transfer and the nature of bacterial innovation Nature 405 299 304 (Pubitemid 30337055)
47. MV Omelchenko KS Makarova YI Wolf IB Rogozin EV Koonin 2003 Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ Genome Biol 4 R55
48. K Oshima H Nishida 2007 Phylogenetic relationships among mycoplasmas based on the whole genomic information J Mol Evol 65 249 258 (Pubitemid 47561688)
49. GM Pupo R Lan PR Reeves 2000 Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics Proc Natl Acad Sci USA 97 10567 10572
50. A Rokas BL Williams N King SB Carroll 2003 Genome-scale approaches to resolving incongruence in molecular phylogenies Nature 425 798 804 (Pubitemid 37355944)
51. K Rolland N Lambert-Zechovsky B Picard E Denamur 1998 Shigella and enteroinvasive Escherichia coli strains are derived from distinct ancestral strains of E. coli Microbiology 144 2667 2672 (Pubitemid 28457177)
52. A Ruepp W Graml ML Santos-Martinez KK Koretke C Volker HW Mewes D Frishman S Stocker AN Lupas W Baumeister 2000 The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum Nature 407 508 513
53. N Saitou M Nei 1987 The neighbor-joining method: a new method for reconstructing phylogenetic trees Mol Biol Evol 4 406 425
54. Sankoff D (1992) Edit distance for genome comparison based on nonlocal operations. In: Apostolico A, Crochemore M, Galil Z, Manber U (eds) Third annual symposium on combinatorial pattern matching, vol 644. Springer, Heidelberg, pp 121-135
55. A Schlicker FS Domingues J Rahnenführer T Lengauer 2006 A new measure for functional similarity of gene products based on gene ontology BMC Bioinformatics 7 302
56. Y Sekiguchi Y Kamagata K Syutsubo A Ohashi H Harada K Nakamura 1998 Phylogenetic diversity of mesophilic and thermophilic granular sludges determined by 16S rRNA gene analysis Microbiology 144 2655 2665 (Pubitemid 28457176)
57. TF Smith MS Waterman 1981 Identification of common molecular subsequences J Mol Biol 147 195 197
58. B Snel P Bork MA Huynen 1999 Genome phylogeny based on gene content Nature Genet 21 108 110 (Pubitemid 29036294)
59. B Snel P Bork MA Huynen 2002 Genomes in flux: the evolution of archaeal and proteobacterial gene content Genome Res 12 17 25 (Pubitemid 34065586)
60. Y Song Z Tong J Wang L Wang Z Guo Y Han J Zhang D Pei D Zhou H Qin X Pang Y Han J Zhai M Li B Cui Z Qi L Jin R Dai F Chen S Li C Ye Z Du W Lin J Wang J Yu H Yang J Wang P Huang R Yang 2004 Complete genome sequence of Yersinia pestis strain 91001, an isolate avirulent to humans DNA Res 11 179 197 (Pubitemid 40040662)
61. E Susko J Leigh WF Doolittle E Bapteste 2006 Visualizing and assessing phylogenetic congruence of core gene sets: a case study of the γ-proteobacteria Mol Biol Evol 23 1019 1030 (Pubitemid 43726067)
62. M Suyama P Bork 2001 Evolution of prokaryotic gene order: genome rearrangements in closely related species Trends Genet 17 10 13 (Pubitemid 32332968)
63. KM Swenson M Marron JV Earnest-DeYoung BME Moret 2008 Approximating the true evolutionary distance between two genomes ACM J Exp Algorithm 12 3.5
64. Tamames J (2001) Evolution of gene order conservation in prokaryotes. Genome Biol 2:RESEARCH0020
65. G Tesler 2002 GRIMM: genome rearrangements web server Bioinformatics 18 492 493 (Pubitemid 34284955)
66. G Vergnaud Y Li O Gorgé Y Cui Y Song D Zhou I Grissa SV Dentovskaya ME Platonov A Rakin SV Balakhonov H Neubauer C Pourcel AP Anisimov R Yang 2007 Analysis of the three Yersinia pestis CRISPR loci provides new tools for phylogenetic studies and possibly for the investigation of ancient DNA Adv Exp Med Biol 603 327 338
67. M Withers L Wernisch M dos Reis 2006 Archaeology and evolution of transfer RNA genes in the Escherichia coli genome RNA 12 933 942 (Pubitemid 43788111)
68. CR Woese GE Fox 1977 Phylogenetic structure of the prokaryotic domain: the primary kingdoms Proc Natl Acad Sci USA 74 5088 5090 (Pubitemid 8241042)
69. C Xin Z Jie F Zheng N Peng Z Yang L Stefano J Tao 2005 Assignment of orthologous genes via genome rearrangement IEEE/ACM Trans Comput Biol Bioinform 2 302 315
70. J Yang H Nie L Chen X Zhang F Yang X Xu Y Zhu J Yu Q Jin 2007 Revisiting the molecular evolutionary history of Shigella spp J Mol Evol 64 71 79 (Pubitemid 46020860)