A genomic distance based on MUM indicates discontinuity between most bacterial species and genera

Journal of Bacteriology

Volumn 91, Issue 1, 2009, Pages 91-99

  Deloger, Marc ^a,b   El Karoui, Meriem ^a   Petit, Marie Agnès ^a  

^a CEMAGREF   (France)

^b UNIVERSITÉ LYON 1   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; CONTROLLED STUDY; DNA CONTENT; DNA SEQUENCE; GENOME ANALYSIS; MICROBIAL COMMUNITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; BACTERIUM; CLASSIFICATION; ESCHERICHIA COLI; GENETIC VARIABILITY; GENETICS; NEISSERIA GONORRHOEAE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SHIGELLA; SPECIES DIFFERENCE;

BACTERIA (MICROORGANISMS);

BACTERIAL DNA;

BACTERIA; BASE SEQUENCE; DNA, BACTERIAL; ESCHERICHIA COLI; GENETIC VARIATION; GENOME, BACTERIAL; NEISSERIA GONORRHOEAE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, NUCLEIC ACID; SHIGELLA; SPECIES SPECIFICITY;

EID: 58149527706     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.01202-08     Document Type: Article

References (33)

1. Auch, A. F., S. R. Henz, B. R. Holland, and M. Goker. 2006. Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences. BMC Bioinform. 7:350.
2. Canchaya, C., M. J. Claesson, G. F. Fitzgerald, D. van Sinderen, and P. W. O'Toole. 2006. Diversity of the genus Lactobacillus revealed by comparative genomics of five species. Microbiology 152:3185-3196.
3. Chain, P. S., E. Carniel, F. W. Larimer, J. Lamerdin, P. O. Stoutland, W. M. Regala, A. M. Georgescu, L. M. Vergez, M. L. Land, V. L. Motin, R. R. Brubaker, J. Fowler, J. Hinnebusch, M. Marceau, C. Medigue, M. Simonet, V. Chenal-Francisque, B. Souza, D. Dacheux, J. M. Elliott, A. Derbise, L. J. Hauser, and E. Garcia. 2004. Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis. Proc. Natl. Acad. Sci. USA 101:13826-31.
4. Chen, X., M. Li, B. Ma, and J. Tromp. 2002. DNACompress: fast and effective DNA sequence compression. Bioinformatics 18:1696-1698.
5. Chiapello, H., I. Bourgait, F. Sourivong, G. Heuclin, A. Gendrault-Jacquemard, M. A. Petit, and M. El Karoui. 2005. Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops. BMC Bioinform. 6:171.
6. Darling, A. C., B. Mau, F. R. Blattner, and N. T. Perna. 2004. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14:1394-1403.
7. Daubin, V., and H. Ochman. 2004. Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli. Genome Res. 14:1036-1042.
8. Edgar, R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797.
9. Gascuel, O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol. Biol. Evol. 14:685-695.
10. Goris, J., K. T. Konstantinidis, J. A. Klappenbach, T. Coenye, P. Vandamme, and J. M. Tiedje. 2007. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol. 57:81-91.
11. Grimont, P. A. 1988. Use of DNA reassociation in bacterial classification. Can. J. Microbiol. 34:541-546.
12. Guyon, F., and A. Guénoche. 2008. Comparing bacterial genomes from linear orders of patterns. Discrete Appl. Math. 156:1251-1262.
13. Halpern, A., D. Huson, and K. Reinert. 2002. Segment match refinement and applications, p. 126-139. In Proceedings of the 2nd Workshop on Algorithms Bioinformatics (WABI-02).
14. Hanage, W. P., C. Fraser, and B. G. Spratt. 2005. Fuzzy species among recombinogenic bacteria. BMC Biol. 3:6.
15. Hayashi, T., K. Makino, M. Ohnishi, K. Kurokawa, K. Ishii, K. Yokoyama, C. G. Han, E. Ohtsubo, K. Nakayama, T. Murata, M. Tanaka, T. Tobe, T. Iida, H. Takami, T. Honda, C. Sasakawa, N. Ogasawara, T. Yasunaga, S. Kuhara, T. Shiba, M. Hattori, and H. Shinagawa. 2001. Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res. 8:11-22.
16. Henz, S. R., D. H. Huson, A. F. Auch, K. Nieselt-Struwe, and S. C. Schuster. 2005. Whole-genome prokaryotic phylogeny. Bioinformatics 21:2329-2335.
17. Hohl, M., S. Kurtz, and E. Ohlebusch. 2002. Efficient multiple genome alignment. Bioinformatics 18(Suppl. 1):S312-S320.
18. Huson, D. H., and D. Bryant. 2006. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23:254-267.
19. Koeppel, A., E. B. Perry, J. Sikorski, D. Krizanc, A. Warner, D. M. Ward, A. P. Rooney, E. Brambilla, N. Connor, R. M. Ratcliff, E. Nevo, and F. M. Cohan. 2008. Identifying the fundamental units of bacterial diversity: a paradigm shift to incorporate ecology into bacterial systematics. Proc. Natl. Acad. Sci. USA 105:2504-2509.
20. Konstantinidis, K. T., A. Ramette, and J. M. Tiedje. 2006. The bacterial species definition in the genomic era. Phil. Trans. R. Soc. Lond. B 361:1929-1940.
21. Konstantinidis, K. T., A. Ramette, and J. M. Tiedje. 2006. Toward a more robust assessment of intraspecies diversity, using fewer genetic markers. Appl. Environ. Microbiol. 72:7286-7293.
22. Konstantinidis, K. T., and J. M. Tiedje. 2005. Genomic insights that advance the species definition for prokaryotes. Proc. Natl. Acad. Sci. USA 102:2567-2572.
23. Kurtz, S., A. Phillippy, A. L. Delcher, M. Smoot, M. Shumway, C. Antonescu, and S. L. Salzberg. 2004. Versatile and open software for comparing large genomes. Genome Biol. 5:R12.
24. Makino, K., K. Oshima, K. Kurokawa, K. Yokoyama, T. Uda, K. Tagomori, Y. Iijima, M. Najima, M. Nakano, A. Yamashita, Y. Kubota, S. Kimura, T. Yasunaga, T. Honda, H. Shinagawa, M. Hattori, and T. Iida. 2003. Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V. cholerae. Lancet 361:743-749.
25. Noe, L., and G. Kucherov. 2005. YASS: enhancing the sensitivity of DNA similarity search. Nucleic Acids Res. 33:W540-W543.
26. Rivals, E., M. Dauchet, J. P. Delahaye, and O. Delgrange. 1996. Compression and genetic sequence analysis. Biochimie 78:315-322.
27. Rossello-Mora, R., and R. Amann. 2001. The species concept for prokaryotes. FEMS Microbiol. Rev. 25:39-67.
28. Snel, B., P. Bork, and M. A. Huynen. 1999. Genome phylogeny based on gene content. Nat. Genet. 21:108-110.
29. Tettelin, H., V. Masignani, M. J. Cieslewicz, C. Donati, D. Medini, N. L. Ward, S. V. Angiuoli, J. Crabtree, A. L. Jones, A. S. Durkin, R. T. Deboy, T. M. Davidsen, M. Mora, M. Scarselli, I. Margarit y Ros, J. D. Peterson, C. R. Hauser, J. P. Sundaram, W. C. Nelson, R. Madupu, L. M. Brinkac, R. J. Dodson, M. J. Rosovitz, S. A. Sullivan, S. C. Daugherty, D. H. Haft, J. Selengut, M. L. Gwinn, L. Zhou, N. Zafar, H. Khouri, D. Radune, G. Dimitrov, K. Watkins, K. J. O'Connor, S. Smith, T. R. Utterback, O. White, C. E. Rubens, G. Grandi, L. C. Madoff, D. L. Kasper, J. L. Telford, M. R. Wessels, R. Rappuoli, and C. M. Fraser. 2005. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome." Proc. Natl. Acad. Sci. USA 102:13950-5.
30. Treangen, T. J., and X. Messeguer. 2006. M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species. BMC Bioinform. 7:433.
31. Varre, J. S., J. P. Delahaye, and E. Rivals. 1999. Transformation distances: a family of dissimilarity measures based on movements of segments. Bioinformatics 15:194-202.
32. Vinga, S., and J. Almeida. 2003. Alignment-free sequence comparison - a review. Bioinformatics 19:513-523.
33. Wu, T. J., Y. H. Huang, and L. A. Li. 2005. Optimal word sizes for dissimilarity measures and estimation of the degree of dissimilarity between DNA sequences. Bioinformatics 21:4125-4132.