Whole Genome Sequence Comparisons in Taxonomy

Methods in Microbiology

Volumn 38, Issue , 2011, Pages 409-436

  Borriss, Rainer ^a   Rueckert, Christian ^b   Blom, Jochen ^b   Bezuidt, Oliver ^c   Reva, Oleg ^c   Klenk, Hans Peter ^d  

^a ABITEP GMBH   (Germany)

^b BIELEFELD UNIVERSITY   (Germany)

^c UNIVERSITY OF PRETORIA   (South Africa)

^d LEIBNIZ INSTITUTE DSMZ GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 83155193204     PISSN: 05809517     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-387730-7.00018-8     Document Type: Chapter

References (71)

1. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 1990, 215:403-410.
2. Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-33402.
3. Auch A.F., von Jan M., Klenk H.-P., Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand. Genomic Sci. 2010, 2:142-148.
4. Auch A.F., Klenk H.-P., Göker M. Standard operation procedure for calculating genome-to-genome distances based on high scoring segment pairs. Stand. Genomic Sci. 2010, 2:142-148.
5. Badger J.H., Olsen G.J. CRITICA: Coding Region Identification Tool Invoking Comparative Analysis. Mol. Biol. Evol. 1999, 16:512-524.
6. Betley M.J., Mekalanos J.J. Staphylococcal enterotoxin A is encoded by phage. Science 1985, 229:185-187.
7. Blom J., Albaum S.P., Doppmeier D., Pühler A., Vorhölter F.J., Zakrzewski M., Goesmann A. EDGAR: asoftware framework for the comparative analysis of prokaryotic genomes. BMC Bioinformatics 2009, 10:154.
8. T and Bacillus amyloliquefaciens subsp. plantarum subsp. nov. based on their discriminating complete genome sequences. Int. J. Syst. Evol. Microbiol. 2010, 2010. [September 3; epub ahead of print].
9. Brune I., Becker A., Paarmann D., Albersmeier A., Kalinowski J., Pühler A., Tauch A. Under the influence of the active deodorant ingredient 4-hydroxy-3-methoxybenzyl alcohol, the skin bacterium Corynebacterium jeikeium moderately responds with differential gene expression. J. Biotechnol. 2006, 127:21-33.
10. Butler J.E., He Q., Nevin K.P., He Z., Zhou J., Lovley D.R. Genomic and microarray analysis of aromatics degradation in Geobacter metallireducens and comparison to a Geobacter isolate from a contaminated field site. BMC Genom. 2007, 8:180.
11. Carver T.J., Rutherford K.M., Berriman M., Rajandream M.A., Barrell B.G., Parkhill J. ACT: the Artemis comparison tool. Bioinformatics 2005, e21:3422-3423.
12. Chen X.H., Koumoutsi A., Scholz R., Eisenreich A., Schneider K., Heinemeyer I., Morgenstern B., Voss B., Hess W.R., Reva O., Junge H., Voigt B., Jungblut P.R., Vater J., Süssmuth R., Liesegang H., Strittmatter A., Gottschalk G., Borriss R. Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42. Nat. Biotechnol. 2007, 25:1007-1014.
13. Chevreux B., Wetter T., Suhai S. Genome sequence assembly using trace signals and additional sequence information. Comput. Sci. Biol., Proc. German Conference on Bioinformatics GCB'99 GCB 1999, 45-56.
14. Choi I.-G., Kim S.-H. Global extent of horizontal gene transfer. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:4489-4494.
15. Delcher A.L., Harmon D., Kasif S., White O., Salzberg S.L. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 1999, 27:4636-4641.
16. Deloger M., El Karoui M., Petit M.-A. A genomic distance based on MUM indicates discontinuity between most bacterial species and genera. J. Bacteriol. 2009, 191:91-99.
17. Dobrindt U., Hochhut B., Hentschel U., Hacker J. Genomic islands in pathogenic and environmental microorganisms. Nat. Rev. Microbiol. 2004, 2:414-424.
18. Dondrup M., Goesmann A., Bartels D., Kalinowski J., Krause L., Linke B., Rupp O., Sczyrba A., Pühler A., Meyer F. EMMA: a platform for consistent storage and efficient analysis of microarray data. J. Biotechnol. 2003, 106:135-146.
19. Dondrup M., Hüser A.T., Mertens D., Goesmann A. An evaluation frame work for statistical tests on microarray data. J. Biotechnol. 2009, 140:18-26.
20. Earl A.M., Losick R., Kolter R. Bacillus subtilis genome diversity. J. Bacteriol. 2007, 189:1163-1170.
21. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32:1972.
22. Felsenstein J. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 1978, 27:401-410.
23. Felsenstein J. PHYLIP (Phylogeny Inference Package), Version 3.57 c 1995, University of Washington, Seattle.
24. Ganesan H., Rakitianskaia A.S., Davenport C.F., Tummler B., Reva O.N. The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage. BMC Bioinformatics 2008, 9:333.
25. Garcia-Vallve S., Guzman E., Montero M.A., Romeu A. HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes. Nucleic Acids Res. 2003, 31:187-189.
26. Gatson J.W., Benz B.F., Chandrasekaran C., Satomi M., Venkateswaran K., Hart M.E. Bacillus tequilensis sp. nov., isolated from 2000-year-old Mexican shaft-tomb, is closely related to Bacillus subtilis. Int. J. Syst. Evol. Microbiol. 2006, 56:1475-1484.
27. Giuntini E., Mengoni A., De Filippo C., Cavalieri D., Aubin-Horth N., Landry C.R., Becker A., Bazzicalupo M. Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains. BMC Genom. 2005, 6:158.
28. Gontcharov A.A., Marin B., Melkonian M. Are combined analyses better than single gene phylogenies? A case study using SSU rDNA and rbcL sequence comparisons in the Zygnematophyceae (Streptophyta). Mol. Biol. Evol. 2004, 21:612-624.
29. Gordon D., Abajian C., Green P. Consed: a graphical tool for sequence finishing. Genome Res. 1998, 8:195-202.
30. Gordon D., Desmarais C., Green P. Automated finishing with Autofinish. Genome Res. 2001, 11:614-625.
31. Goris J., Konstantinidis K.T., Klappenbach J.A., Coenye T., Vandamme P., Tiedje J.M. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol. 2007, 57:81-91.
32. Hartman A.B., Essiet I.I., Isenbarger D.W., Lindler L.E. Epidemiology of tetracycline resistance determinants in Shigella spp. and enteroinvasive Escherichia coli: characterization and dissemination of tet(A)-1. J. Clin. Microbiol. 2003, 41:1023-1032.
33. Henz S.R., Huson D.H., Auch A.F., Nieselt-Struwe K., Schuster S.C. Whole-genome prokaryotic phylogeny. Bioinformatics 2005, 21:2329-2335.
34. Hsiao W., Wan I., Jones S.J., Brinkman F.S.L. IslandPath: aiding detection of genomic islands in prokaryotes. Bioinformatics 2003, 19:418-420.
35. Hyatt D., Chen G.L., Locascio P.F., Land M.L., Larimer F.W., Hauser L.J. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010, 11:119.
36. Kent W.J. BLAT - the BLAST-like alignment tool. Genome Res. 2002, 12:656-664.
37. Konstantinidis K.T., Ramette A., Tiedje J.M. The bacterial species definition in the genomic era. Philos. Trans. R. Soc. Lond. B Biol. Sci. 2006, 361:1929-1940.
38. Kozarewa I., Ning Z., Quail M.A., Sanders M.J., Berriman M., Turner D.J. Amplification-free illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat. Methods 2009, 6:291-295.
39. Krause L., McHardy A.C., Nattkemper T.W., Pühler A., Stoye J., Meyer F. GISMO - gene identification using a support vector machine for ORF classification. Nucleic Acids Res. 2007, 35:540-549.
40. Kurtz S., Phillippy A., Delcher A.L., Smoot M., Shumway M., Antonescu C., Salzberg S.L. Versatile and open software for comparing large genomes. Genome Biol. 2004, 5:R12.
41. Langille M.G.I., Brinkman F.S.L. IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinformatics 2009, 25:664-665.
42. Leplae R., Hebrant A., Wodak S.J., Toussaint A. ACLAME: a CLAssification of Mobile genetic Elements. Nucleic Acids Res. 2004, 32:D45-D49.
43. Leplae R., Lima-Mendez G., Toussaint A. A first global analysis of plasmid encoded proteins in the ACLAME database. FEMS Microbiol. Rev. 2006, 30:980-994.
44. Lerat E., Daubin V., Moran N.A. From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria. PLoS Biol. 2003, 1:E19.
45. Lima-Mendez G., Helden J.V., Toussaint A., Leplae R. Reticulate representation of evolutionary and functional relationships between phage genomes. Mol. Biol. Evol. 2008, 25:762-777.
46. Lima-Mendez G., Helden J.V., Toussaint A., Leplae R. Prophinder: a computational tool for prophage prediction in prokaryotic genomes. Bioinformatics 2008, 24:863-865.
47. Linke B., McHardy A.C., Neuweger H., Krause L., Meyer F. REGANOR: a gene prediction server for prokaryotic genomes and a database of high quality gene predictions for prokaryotes. Appl. Bioinformatics 2006, 5:193-198.
48. Logan N.A., Berge O., Bishop A.H., Busse H.-J., de Vos P., Fritze D., Henydrickx M., Kämpfer P., Rabinovitch L., Salkinoja-Salonen M.S., Seldin L., Ventosa A. Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria. Int. J. Syst. Evol. Microbiol. 2009, 59:2114-2121.
49. Margulies M., Egholm M., Altman W.E., Attiya S., Bader J.S., Bemben L.A., Berka J., Braverman M.S., Chen Y.-J., Chen Z., Dewell S.B., Du L., Fierro J.M., Gomes X.V., Goodwin B.C., He W., Helgesen S., He Ho.C., Irzyk G.P., Jando S.C., Alenquer M.L.I., Jarvie T.P., Jirage K.B., Kim J.-B., Knight J.R., Lanza J.R., Leamon J.H., Lefkowitz S.M., Lei M., Li J., Lohman K.L., Lu H., Makhijani V.B., McDade K.E., McKenna M.P., Myers E.W., Nickerson E., Nobile J.R., Plant R., Puc B.P., Ronan M.T., Roth G.T., Sarkis G.J., Simons J.F., Simpson J.W., Srinivasan M., Tartaro K.R., Tomasz A., Vogt K.A., Volkmer G.A., Wang S.H., Wang Y., Weiner M.P., Yu P., Begley R.F., Rothberg J.M. Genome sequencing in open microfabricated high density picoliter reactors. Nature 2006, 437:376-380.
50. Medini D., Donati C., Tettelin H., Masignani V., Rappuoli R. The microbial pan-genome. Curr. Opin. Genet. Dev. 2005, 15:589-594.
51. Meyer F., Goesmann A., McHardy A.C., Bartels D., Bekel T., Clausen J., Kalinowski J., Linke B., Rupp O., Giegerich R., Pühler A. GenDB-an open source genome annotation system for prokaryote genomes. Nucleic Acids Res. 2003, 31:2187-2195.
52. Oelschlaeger T.A., Dobrindt U., Hacker J. Pathogenicity islands of uropathogenic E. coli and the evolution of virulence. Int. J. Antimicrob. Agents 2002, 19:517-521.
53. Peterson J.D., Umayam L.A., Dickinson T., Hickey E.K., White O. The comprehensive microbial resource. Nucleic Acids Res. 2001, 29:123-125.
54. Pezzella C., Ricci A., DiGiannatale E., Luzzi I., Carattoli A. Tetracycline and streptomycin resistance genes, transposons, and plasmids in Salmonella enterica isolates from animals in Italy. Antimicrob. Agents Chemother. 2004, 48:903-908.
55. Reva O.N., Tummler B. Global features of sequences of bacterial chromosomes, plasmids and phages revealed by analysis of oligonucleotide usage patterns. BMC Bioinformatics 2004, 5:90.
56. Reva O.N., Tummler B. Differentiation of regions with atypical oligonucleotide composition in bacterial genomes. BMC Bioinformatics 2005, 6:251.
57. Ronaghi M., Karamohamed S., Pettersson B., Uhlén M., Nyrén P. Real-time DNA sequencing using detection of pyrophosphate release. Anal. Biochem. 1996, 242:84-89.
58. Rooney A.P., Price N.P., Ehrhardt C., Swezey J.L., Bannan J.D. Phylogeny and molecular taxonomy of the Bacillus subtilis species complex and description of Bacillus subtilis subsp. inaquosorum subsp. nov. Int. J. Syst. Evol. Microbiol. 2009, 59:2420-2436.
59. T reveals differences to plant-associated B. amyloliquefaciens FZB42. J. Biotechnol. 2011, 2011. [January 22; epub ahead of print].
60. Sanger F., Coulson A.R. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J. Mol. Biol. 1975, 94:441-448.
61. Schwartz S., Kent W.J., Smit A., Zhang Z., Baertsch R., Hardison R.C., Haussler D., Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003, 13:103-107.
62. Simpson J.T., Wong K., Jackman S.D., Schein J.E., Jones S.J., Birol I. ABySS: A parallel assembler for short read sequence data. Genome Res. 2009, 19:1117-1123.
63. Stackebrandt E., Frederiksen W., George M., Garrity G.M., Grimont P.A.D., Kaempfer P., Maiden M.C.J., Nesme X., Rossello-Mora R., Jean Swings J., Trueper H.G., Vauterin L., Ward A.C., Whitman W.B. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int. J. Syst. Evol. Microbiol. 2002, 52:1043-1047.
64. Talavera G., Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 2007, 56:564-577.
65. Tettelin H., Masignani V., Cieslewicz M.J., Donati C., Medini D., Ward N.L., Angiuoli S.V., Crabtree J., Jones A.L., Durkin A.S., Deboy R.T., Davidsen T.M., Mora M., Scarselli M., Margarit Y., Ros I., Peterson J.D., Hauser C.R., Sundaram J.D., Nelson W.C., Madupu R., Brinkac L.M., Dodson R.J., Rosovitz M.J., Sullivan S.A., Daugherty S.C., Haft D.H., Selengut J., Gwinn M.L., Zhou L., Zafar N., Khouri H., Radune D., Dimitrov G., Watkins K., O'Connor K.J.B., Smith S., Utterback T.R., White O., Rubens C.E., Grandi G., Madoff L.C., Kasper D.L., Telford J.L., Wessels M.R., Rappuoli R., Fraser C.M. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc. Natl. Acad. Sci. U.S.A. 2005, 102:13950-13955.
66. Tindall B.J., Rossello-Mora R., Busse H.-J., Ludwig W., Kämpfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int. J. Syst. Evol. Microbiol. 2010, 60:249-266.
67. Uchiumi T., Ohwada T., Itakura M., Mitsui H., Nukui N., Dawadi P., Kaneko T., Tabata S., Yokoyama T., Tejima K., Saeki K., Omori H., Hayashi M., Maekawa T., Sriprang R., Murooka Y., Tajima S., Simomura K., Nomura M., Suzuki A., Shimoda Y., Sioya K., Abe M., Minamisawa K. Expression islands clustered on the symbiosis island of the Mesorhizobium loti genome. J. Bacteriol. 2004, 186:2439-2448.
68. Uchiyama I., Higuchi T., Kawai M. MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity. Nucleic Acids Res. 2010, 38(Suppl. 1):D361-D365.
69. Waack S., Keller O., Asper R., Brodag T., Damm C., Fricke W.F., Surovcik K., Meinicke P., Merkl R. Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. BMC Bioinformatics 2006, 16:142.
70. Wayne L.G., Brenner D.J., Colwell R.R., Grimont P.A.D., Kandler O., Krichevsky M.I., Moore L.H., Moore W.E.C., Murray R.G.E., Stackebrandt E., Starr M.P., Trüper H.G. Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics. Int. J. Syst. Bacteriol. 1987, 37:463-464.
71. Zerbino D.R., Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008, 18:821-829.