Genometrics as an essential tool for the assembly of whole genome sequences: The example of the chromosome of Bifidobacterium longum NCC2705

BMC Microbiology

Volumn 5, Issue , 2005, Pages

  Guy, Lionel ^a   Karamata, Dimitri ^a   Moreillon, Philippe ^a   Roten, Claude Alain H ^a  

^a UNIVERSITY OF LAUSANNE   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTOSOME; BIFIDOBACTERIUM LONGUM; CHROMOSOME ANALYSIS; CONTROLLED STUDY; GASTROINTESTINAL TRACT; GENE LOCUS; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; GENOMICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PROKARYOTE; PROTEOMICS;

BIFIDOBACTERIUM; CHROMOSOMES, BACTERIAL; GENETIC TECHNIQUES; GENOME, BACTERIAL; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; SEQUENCE ALIGNMENT; SOFTWARE;

ACTINOBACTERIA; BACTERIA (MICROORGANISMS); BIFIDOBACTERIUM LONGUM; MYCOBACTERIUM TUBERCULOSIS; POSIBACTERIA; PROKARYOTA; STREPTOMYCES COELICOLOR;

EID: 28044463174     PISSN: 14712180     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-5-60     Document Type: Article

References (45)

1. Biavati B, Mattarelli P: The family Bifidobacteriaceae. In The Prokaryotes: An Evolving Electronic Resource for the Microbiological Community 3rd edition, relase 3.7 edition. Edited by: Dworkin M, Falkow S, Rosenberg E, Schleifer KH and Stackebrandt E. New York, Springer-Verlag; 2001:1-70.
2. Favier CF, Vaughan EE, De Vos WM, Akkermans ADL: Molecular monitoring of succession of bacterial communities in human neonates. Appl Environ Microbiol 2002, 68:219-226.
3. Harmsen HJ, Wildeboer-Veloo AC, Raangs GC, Wagendorp AA, Klijn N, Bindels JG, Welling GW: Analysis of intestinal flora development in breast-fed and formula-fed infants by using molecular identification and detection methods. J Pediatr Gastroenterol Nutr 2000, 30:61-67.
4. Schell MA, Karmirantzou M, Snel B, Vilanova D, Berger B, Pessi G, Zwahlen MC, Desiere F, Bork P, Delley M, Pridmore RD, Arigoni F: The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc Natl Acad Sci U S A 2002, 99:14422-14427.
5. Casjens S: The diverse and dynamic structure of bacterial genomes. Annu Rev Genet 1998, 32:339-377.
6. Tillier ERM, Collins RA: Genome rearrangement by replication-directed translocation. Nature Genet 2000, 26:195-197.
7. Eisen J, Heidelberg J, White O, Salzberg S: Evidence for symmetric chromosomal inversions around the replication origin in bacteria. Genome Biol 2000, 1:research0011.1 -11.9.
8. Brewer BJ: When polymerases collide: replication and the transcriptional organization of the E. coli chromosome. Cell 1988, 53:679-686.
9. French S: Consequences of replication fork movement through transcription units in vivo. Science 1992, 258:1362-1365.
10. Mirkin EV, Mirkin SM: Mechanisms of transcription-replication collisions in bacteria. Mol Cell Biol 2005, 25:888-895.
11. McLean MJ, Wolfe KH, Devine KM: Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes. J Mol Evol 1998, 47:691-696.
12. Guy L, Roten CAH: Genometric analyses of the organization of circular chromosomes: a universal pressure determines the direction of ribosomal RNA genes transcription relative to chromosome replication. Gene 2004, 340:45-52.
13. Frank AC, Lobry JR: Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms. Gene 1999, 238:65-77.
14. Trifonov EN: Translation framing code and frame-monitoring mechanism as suggested by the analysis of messenger-RNA and 16S ribosomal RNA nucleotide sequences. J Mol Biol 1987, 194:643-652.
15. Szybalski W, Kubinski H, Sheldrick O: Pyrimidine clusters on the transcribing strand of DNA and their possible role in the initiation of RNA synthesis. Cold Spring Harb Symp Quant Biol 1966, 31:123-127.
16. Lao PJ, Forsdyke DR: Thermophilic bacteria strictly obey Szybalski's transcription direction rule and politely purine-load RNAs with both adenine and guanine. Genome Res 2000, 10:228-236.
17. Francino MP, Ochman H: Strand asymmetries in DNA evolution. Trends Genet 1997, 13:240-245.
18. Lobry JR: Asymmetric substitution patterns in the two DNA strands of bacteria. Mol Biol Evol 1996, 13:660-665.
19. Grigoriev A: Analyzing genomes with cumulative skew diagrams. Nucleic Acids Res 1998, 26:2286-2290.
20. Tillier ERM, Collins RA: The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes. J Mol Evol 2000, 50:249-257.
21. Nakagawa I, Kurokawa K, Yamashita A, Nakata M, Tomiyasu Y, Okahashi N, Kawabata S, Yamazaki K, Shiba T, Yasunaga T, Hayashi H, Hattori M, Hamada S: Genome sequence of an M3 strain of Streptococcus pyogenes reveals a large-scale genomic rearrangement in invasive strains and new insights into phage evolution. Genome Res 2003, 13:1042-1055.
22. Stover CK, Pham XQ, Erwin AL, Mizoguchi SD, Warrener P, Hickey MJ, Brinkman FS, Hufnagle WO, Kowalik DJ, Lagrou M, Garber RL, Goltry L, Tolentino E, Westbrock-Wadman S, Yuan Y, Brody LL, Coulter SN, Folger KR, Kas A, Larbig K, Lim R, Smith K, Spencer D, Wong GK, Wu Z, Paulsen IT, Reizer J, Saier MH, Hancock RE, Lory S, Olson MV: Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature 2000, 406:959-964.
23. Comparative Genometrics Database [http://www.unil.ch/com parativegenometrics/]
24. Van Sluys MA, de Oliveira MC, Monteiro-Vitorello CB, Miyaki CY, Furlan LR, Camargo LEA, da Silva ACR, Moon DH, Takita MA, Lemos EGM, Machado MA, Ferro MIT, da Silva FR, Goldman MHS, Goldman GH, Lemos MVF, El-Dorry H, Tsai SM, Carrer H, Carraro DM, de Oliveira RC, Nunes LR, Siqueira WJ, Coutinho LL, Kimura ET, Ferro ES, Harakava R, Kuramae EE, Marino CL, Giglioti E, Abreu IL, Alves LMC, do Amaral AM, Baia GS, Blanco SR, Brito MS, Cannavan FS, Celestino AV, da Cunha AF, Fenille RC, Ferro JA, Formighieri EF, Kishi LT, Leoni SG, Oliveira AR, Rosa VEJ, Sassaki FT, Sena JAD, de Souza AA, Truffi D, Tsukumo F, Yanai GM, Zaros LG, Civerolo EL, Simpson AJG, Almeida NFJ, Setubal JC, Kitajima JP: Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa. J Bacteriol 2003, 185:1018-1026.
25. Canchaya C, Fournous G, Brussow H: The impact of prophages on bacterial chromosomes. Molecular Microbiology 2004, 53:9-18.
26. Schell MA, Karmirantzou M, Snel B, Vilanova D, Berger B, Pessi G, Zwahlen MC, Desiere F, Bork P, Delley M, Pridmore RD, Arigoni F: Correction for Schell et al., The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract, PNAS 2002 99:14422-14427. Proc Natl Acad Sci U S A 2005, 102:9430.
27. Roten CA, Gamba P, Barblan JL, Karamata D: Comparative Genometrics (CG): a database dedicated to biometric comparisons of whole genomes. Nucleic Acids Res 2002, 30:142-144.
28. Messer W: The bacterial replication initiator DnaA. DnaA and oriC, the bacterial mode to initiate DNA replication. Fems Microbiol Rev 2002, 26:355-374.
29. IS Finder [http://www-is.biotoul.fr/]
30. Greub G, Collyn F, Guy L, Roten CA: A genomic island present along the bacterial chromosome of the Parachlamydiaceae UWE25, an obligate amoebal endosymbiont, encodes a potentially functional F-like conjugative DNA transfer system. BMC Microbiol 2004, 4:48.
31. Louarn JM, Louarn J, Francois V, Patte J: Analysis and possible role of hyperrecombination in the termination region of the Escherichia coli chromosome. Journal of Bacteriology 1991, 173:5097-5104.
32. Bierne H, Michel B: When replication forks stop. Mol Microbiol 1994, 13:17-23.
33. Elisabeth R. M. Tillier Website [http://www.uhnres.utoronto.ca/tillier/]
34. Parkhill J, Wren BW, Thomson NR, Titball RW, Holden MTG, Prentice MB, Sebaihia M, James KD, Churcher C, Mungall KL, Baker S, Basham D, Bentley SD, Brooks K, Cerdeno-Tarraga AM, Chillingworth T, Cronin A, Davies RM, Davis P, Dougan G, Feltwell T, Hamlin N, Holroyd S, Jagels K, Karlyshev AV, Leather S, Moule S, Oyston PCF, Quail M, Rutherford K, Simmonds M, Skelton J, Stevens K, Whitehead S, Barrell BG: Genome sequence of Yersinia pestis, the causative agent of plague. Nature 2001, 413:523-527.
35. Deng W, Burland V, Plunkett III G, Boutin A, Mayhew GF, Liss P, Perna NT, Rose DJ, Mau B, Zhou S, Schwartz DC, Fetherston JD, Lindler LE, Brubaker RR, Plano GV, Straley SC, McDonough KA, Nilles ML, Matson JS, Blattner FR, Perry RD: Genome sequence of Yersinia pestis KIM. J Bacteriol 2002, 184:4601-4611.
36. Wren BW: The yersiniae - a model genus to study the rapid evolution of bacterial pathogens. Nat Rev Micro 2003, 1:55-64.
37. Chain PSG, Carniel E, Larimer FW, Lamerdin J, Stoutland PO, Regala WM, Georgescu AM, Vergez LM, Land ML, Motin VL, Brubaker RR, Fowler J, Hinnebusch J, Marceau M, Medigue C, Simonet M, Chenal-Francisque V, Souza B, Dacheux D, Elliott JM, Derbise A, Hauser LJ, Garcia E: Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis. Proc Natl Acad Sci U S A 2004, 101:13826-13831.
38. National Center for Biotechnology Information Website [http://www.ncbi.nlm.nih.gov/]
39. Wheeler DL, Church DM, Lash AE, Leipe DD, Madden TL, Pontius JU, Schuler GD, Schriml LM, Tatusova TA, Wagner L, Rapp BA: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2001, 29:11-16.
40. Comparative Genometrics - Bifidobacterium longum NCC2705 Webpage [http://www2.unil.ch/comparativegenometrics/bifido/index.htm]
41. Cebrat S, Dudek MR, Gierlik A, Kowalczuk M, Mackiewicz P: Effect of replication on the third base of codons. Physica A 1999, 265:78-84.
42. Kano-Sueoka T, Lobry JR, Sueoka N: Intra-strand biases in bacteriophage T4 genome. Gene 1999, 238:59-64.
43. Genometrician's company [http://www.genometrician.com/]
44. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.
45. Myllykallio H, Lopez P, Lopez-Garcia P, Heilig R, Saurin W, Zivanovic Y, Philippe H, Forterre P: Bacterial mode of replication with eukaryotic-like machinery in a hyperthermophilic archaeon. Science 2000, 288:2212-2215.