Genometrics as an essential tool for the assembly of whole genome sequences: the example of the chromosome of Bifidobacterium longum NCC2705
© Guy et al; licensee BioMed Central Ltd. 2005
Received: 29 April 2005
Accepted: 13 October 2005
Published: 13 October 2005
Analysis of the first reported complete genome sequence of Bifidobacterium longum NCC2705, an actinobacterium colonizing the gastrointestinal tract, uncovered its proteomic relatedness to Streptomyces coelicolor and Mycobacterium tuberculosis. However, a rapid scrutiny by genometric methods revealed a genome organization totally different from all so far sequenced high-GC Gram-positive chromosomes.
Generally, the cumulative GC- and ORF orientation skew curves of prokaryotic genomes consist of two linear segments of opposite slope: the minimum and the maximum of the curves correspond to the origin and the terminus of chromosome replication, respectively. However, analyses of the B. longum NCC2705 chromosome yielded six, instead of two, linear segments, while its dnaA locus, usually associated with the origin of replication, was not located at the minimum of the curves. Furthermore, the coorientation of gene transcription with replication was very low.
Comparison with closely related actinobacteria strongly suggested that the chromosome of B. longum was misassembled, and the identification of two pairs of relatively long homologous DNA sequences offers the possibility for an alternative genome assembly proposed here below. By genometric criteria, this configuration displays all of the characters common to bacteria, in particular to related high-GC Gram-positives. In addition, it is compatible with the partially sequenced genome of DJO10A B. longum strain. Recently, a corrected sequence of B. longum NCC2705, with a configuration similar to the one proposed here below, has been deposited in GenBank, confirming our predictions.
Genometric analyses, in conjunction with standard bioinformatic tools and knowledge of bacterial chromosome architecture, represent fast and straightforward methods for the evaluation of chromosome assembly.
Bifidobacterium longum is an obligate anaerobe, belonging to the Actinomycetales, a branch of the high-GC Gram-positive bacteria which includes, among others, corynebacteria, mycobacteria and streptomycetes. B. longum is a natural colonizer of the gastrointestinal tract (GIT) and the vagina . It is one of the very first bacteria which colonize the sterile GIT of newborns, predominating in breast-fed infants until weaning . Thereafter, its numerical importance decreases, while Bacteroides and other taxa replace it . B. longum, a harmless bacterium, considered to play an important role in maintaining a healthy GIT by preventing diarrhea, improving lactose intolerance, and participating to immunomodulation , is now widely used in health-promoting foods.
Recently, the whole genome of B. longum strain NCC2705 has been sequenced . Comparison with other high-GC Gram-positives revealed high levels of protein homology with Streptomyces coelicolor A3(2) (34% of best hits), Mycobacterium tuberculosis (9.3% of best hits) and, to a lesser extent, with other actinobacteria as well as with some unrelated genera such as Clostridium and Streptococcus. Surprisingly, it contains a very high number of genetic entities related to mobile elements such as transposons and plasmids. There are 14 integrases/recombinases, 16 intact insertion sequences (ISs), many remnants of ISs, one integrated plasmid, many possible remnants of integrated plasmids and prophages. The origin and the terminus of chromosome replication of B. longum NCC2705 could not be accurately localized along the initial whole genome sequence. Today, DJO10A, another strain of B. longum, is almost fully sequenced, but not assembled.
The presence of many ISs and IS remnants in B. longum NCC2705 leaves open the possibility of major chromosomal rearrangements . These internal recombination events were already advanced to explain the poor conservation of gene order during the evolution of prokaryotic genomes .
It appears that major chromosomal rearrangements almost always consist in inversions of a segment of the chromosome centered on the origin of replication [6, 7]. Other inversions are probably counter-selected , since, unlike inversions around the origin of replication, they change the orientation of transcription relative to DNA replication or they change the length of chromosome arms. Such events have adverse effects on both replication speed and transcription [9, 10]. Alternatively, it has been proposed that rearrangements preferentially centered on the origin of replication are favored by the bidirectional DNA replication: starting simultaneously from the origin of chromosome replication, the two replication forks are at the same distance from it and are likely to be in close contact . Thus, DNA breaks produced by topoisomerases would generate structures suitable for recombinations between the two chromosomal arms, leading to origin-centered rearrangements .
The coorientation between gene transcription and DNA replication is apparently a fundamental feature of bacterial chromosome architecture. More specifically, ORFs and tRNA genes follow a similar tendency and all so far identified ribosomal RNA operons are cooriented with DNA replication [11, 12]. The asymmetric bias in the nucleotide composition at the genome level is another relevant feature (for a review see ). The leading strand, defined by chromosome replication, is generally enriched in guanines (Gs) and depleted in cytosines (Cs). To explain this observation several proposals have been advanced: (i) a preferential usage of certain codons to avoid frameshifting during translation , (ii) the enrichment of coding sequences in purines so as to avoid mRNAs secondary structures [15, 16], (iii) mutational biases targeting single-stranded DNA present during transcription  or (iv) during DNA replication . Mechanisms that would lead to the observed biases in models (i) to (iii) rest on the widespread coorientation of gene transcription and chromosome replication (see above). These asymmetric biases have allowed to unambiguously determine the origin of replication in almost all bacteria [12, 18–20] as well as the terminus of replication in a large majority of the species .
Genomic rearrangements are often highlighted by comparison of whole chromosomal sequences belonging to the same species or genus. For example, dot-plot analyses revealed two recombination events in Streptococcus pyogenes SSI-1, with respect to other S. pyogenes strains, leading to an inversion around the origin of replication . Since they do not change the orientation of transcription relative to DNA replication, these symmetric rearrangement were not revealed by nucleotide bias (skew) analysis.
However, several examples of asymmetric rearrangements are known, pointed out by nucleotide skew analyses. Several isolates of the original clone of Pseudomonas aeruginosa PAO1, a high-GC gamma-proteobacterium and an opportunistic pathogen, have an inversion of a third of their chromosome. The inversion occurs by homologous recombination between two rRNA loci: rrnA and rrnB. As a consequence, the circular chromosome is divided into two inequal arms of one and two thirds, instead of the usual two halves . This asymmetry is obvious on a cumulative GC- or TA skew curve (see the P. aeruginosa PAO1 page on Comparative Genometrics website ). The citrus pathogen Xylella fastidiosa 9a5c is another example of asymmetric rearrangements, that is highlighted when compared with another X. fastidiosa strain, Temecula1 [24, 25]. In this case, the rearrangements occur between three pairs of prophage-related elements , also dividing the chromosome of strain 9a5c in two arms of inequal lenghts (one third and two thirds), as in P. aeruginosa PAO1 (see pages for X. fastidiosa strains on Comparative Genometrics ). In Yersinia pestis strains, the high number of insertion sequence (IS) copies leads to frequent recombination events, inverting segments of the chromosome and changing their orientation of transcription with respect to replication. These inversions are easily spotted on a GC skew plot (see pages for Y. pestis strains on Comparative Genometrics ). In all three above cases, the rearrangements occur naturally, and do not constitute an incorrect genome assembly.
In this contribution we assess the assembly of the initially deposited genome sequence of B. longum NCC2705 by genometric methods, rapid and efficient tools suitable for testing the assembly of prokaryotic chromosomes . Our analysis, strongly suggesting that the chromosome of B. longum NCC2705 was initially misassembled, was confirmed by Schell et al.  during the review of this contribution.
Results and discussion
Analysis of the initial Bifidobacterium longum NCC2705 genome sequence
Investigation with genometric tools of the initially released nucleotide sequence of B. longum NCC2705 (Configuration I [GenBank:NC_004307.1]) revealed several atypical features.
The presence of dnaA at a place other than the minimum of the cumulative ORF orientation curve has never been reported in high-GC Gram-positive bacteria. For a large majority of bacterial species, it was shown that dnaA, a gene whose product binds to the origin of replication and participates in the initiation of replication, is located close to the origin [12, 28]. More generally, in archaea, gene orc1/cdc6, which encodes the archaeal counterpart of DnaA, is very often also located close to the origin of chromosome replication. Finally, in sequenced genomes, half of archaea and most of bacterial genes encoding origin binding proteins are close to the minimum of the cumulative GC skew and ORF orientation curves .
Coorientation indexes of different genome subsets in some high G+C Gram-positive bacteria
B. longum NCC2705 initial sequence
B. longum NCC2705 configuration II
M. tuberculosis CDC1551
S. coelicolor A3(2)
In summary, genometric analyses revealed major anomalies in the organization of the B. longum NCC2705 genome: (i) several changes in the sign of the slope of the cumulative nucleotide skew curves, and location of the dnaA gene far from the minimum of the curve, (ii) low gene coorientation indexes and (iii) absence of correlation between B. longum NCC2705 and related species in between-species whole-genome alignments.
Relationship of B. longum strains NCC2705 and DJO10A
Genetic elements on the initial sequence of Bifidobacterium longum NCC2705
5' end location
3' end location
Analysis of the configuration II of the B. longum NCC2705 chromosome
Genometric analyses of the B. longum NCC2705 chromosome in configuration II reveal a genome architecture typical of high-GC Gram-positive organisms. Indeed, the cumulative GC-skew curve performed on the first codon positions and the cumulative ORF orientation skew curves are very similar to those characteristic of high-GC Gram-positive chromosomes (Figure 1C). First, both skew curves exhibit essentially one minimum and one maximum corresponding, respectively, to the origin and the terminus of chromosome replication; dnaA being at the minimum of the curve while the integrated plasmid is close to the probable terminus of replication, at the maximum of the skew curves. The two minor peaks correspond to the extremities of the integrated plasmid. This genetic element is antioriented, so that the majority of its genes are transcribed in the opposite direction with respect to chromosome replication, leading to a short reversal both in the cumulative ORF orientation skew and the cumulative first codon GC skew curves. This fact was already reported for other integrated elements (for example in Parachlamydiaceae UWE25 ) and is possibly a consequence of the instability of the integration. Integration of foreign DNA stretches close to the terminus is common, for example in prophages . A higher frequency of recombination at the terminus of replication was proposed as the source of this instability [31, 32]. It appears that of the six changes in the sign of the skew slopes of strain NCC2705 in configuration I, one does actually correspond to the origin of chromosome replication and a recombination site, three to other recombination sites, one to the likely terminus of replication, and the last one to the distal extremity of an integrated plasmid. Second, in configuration II, the CIs of protein encoding- and tRNA genes are 0.66 and 0.61, respectively, while all rRNA operons are cooriented, a situation characteristic of prokaryotes (Table 1). Third, between-species whole-genome alignments of B. longum in configuration II and S. coelicolor A3(2) or M. tuberculosis CDC1551 display a fair conservation of gene order (Figure 2C, 2D). Correlation coefficients of type II regressions for direct and indirect homologous DNA segment subsets are much closer to 1 or -1, respectively, than those obtained with the sequence of B. longum NCC2705 in configuration I (Figure 2C, 2D). Finally, each of the scaffolds 1, 8 and 9 of B. longum DJO10A has hits in one single region of the B. longum NCC2705 chromosome in configuration II (Figure 1C).
A genome sequence corresponding approximatively to configuration II of B. longum NCC2705 [GenBank:NC_004307.2] has been recently deposited in the GenBank database by Schell et al. . Whereas we hypothesized that the two pairs of IS, ISBlo2a, ISBlo2b, ISBlo5c and ISBlo5d were the only four chromosomal rearrangement loci, these authors found experimental evidences that, moreover, the initial sequence of NCC2705 had been misassembled at the level of the three ribosomal RNA operons. The sequence in configuration II proposed in this contribution has three DNA segments (totalizing 226 kb, i.e. 10% of the genome) which are differently assembled than the corrected sequence. These assembly discrepancies have only very limited consequences on the results of our analyses.
Thus, configuration II, similar to the recently deposited sequence of the B. longum NCC2705 genome [Genbank:NC_004307.2], is endowed with all chromosomal features common to high-GC Gram-positive bacteria: (i) cumulative GC-and ORF orientation skew curves are typical and the dnaA gene is located at the minimum of the curves, (ii) between-species whole-genome alignments provide the expected X-shape and the coefficients of correlation are relatively close to 1 or -1 and (iii) relevant contigs of B. longum DJO10A are each homologous to a single continuous region of the proposed NCC2705 chromosome.
Genometric analyses – nucleotide skews, coorientation indexes, BLAST comparisons and between-species whole-genome alignments – revealed a most peculiar chromosomal architecture of the initially reported sequence of the B. longum NCC2705 genome. This observation may have two explanations.
First, it is highly probable that in the final stages of the sequencing process, the genome of B. longum NCC2705 was misassembled, a possibility presently favored by Schell and coworkers, in particular since independently performed long-range PCR experiments confirm the presence of configuration II, but could not detect configuration I (F. Arigoni, personal communication). This is in full agreement with genometric analyses of more than 150 genome sequences ( and supplementary material of Tillier and Collins [20, 33]) which reveal a near universal architecture of prokaryotic chromosomes, also found in configuration II of B. longum NCC2705.
Second, the genome of NCC2705 may possibly undergo major chromosomal rearrangements, yielding either of the two alternative configurations I and II. The interconversion between them, achieved by two crossovers between two pairs of homologous insertion sequences (IS), would have drastic consequences. In particular, in configuration II, the cooriented transcription of the majority of the genes, including all rRNA operons, with chromosome replication would allow higher growth rates in suitable conditions. Absence of significant coorientation in configuration I due to the inversion of large segments b and d, representing about 50% of the chromosome, would probably considerably increase the generation time because of collisions between the DNA- and the RNA polymerase . However, as discussed here above, the adverse effects of inversions, other than those around the origin of replication, would render the existence of configuration I highly unlikely. Actually, the latter has apparently not been detected in long range PCR experiments (F. Arigoni, personal communication). However, inversions of relatively long segments – leading to the antiorientation of the majority of the genes in the segment – have been reported, for example, in Yersinia pestis [34–37], and thus may not be completely excluded in B. longum NCC2705.
For the first time, our analyses illustrate the potential of fast and straightforward genometric methods to test genome assembly. They almost immediately revealed gross anomalies of the B. longum NCC2705 initially published sequence, pointing to an incorrect assembling. In conclusion, although their results have to be supported by experimental verification, these simple and powerful tools are essential for the assembly of a chromosome sequence, and for its final validation.
Full genome sequences and annotation files of B. longum NCC2705,S. coelicolor A3(2), M. tuberculosis CDC1551 and contigs of an unfinished sequence of B. longum DJO10A were retrieved from NCBI database [38, 39]. For B. longum NCC2705, the initial [GenBank:NC_004307.1] and the second [GenBank:NC_004307.2] versions of the chromosome (released on August, 27th, 2002 and on January, 21st, 2005 respectively) were downloaded. Sequence of configuration II as proposed in this contribution, and both initial and corrected versions of the B. longum NCC2705 genome are available in fasta format . As proposed by Cebrat et al. , we term the genome sequences available on databases and those of the complementary strands the Watson- and Crick strands, respectively.
Genomes were investigated by cumulative genomic GC skew, first codon position GC skew, and ORF orientation skew [19, 20, 42]. We used the algorithms described in [27, 30] and implemented in the Genometrician's Scooter .
As defined by Lobry , a GC skew is the difference between the number of Gs and Cs normalized to the G+C content. In our contribution we used the non-normalized nucleotide skew, calculated in 1-kb windows along the genome. In the genomic GC skew, the whole genome sequence is used. For GC skew on the first codon position, only nucleotides at the first position of codons are considered for the skew calculation.
Cumulative nucleotide skews
Slightly different from the definition of Grigoriev , the cumulative nucleotide skew of any given window is the nucleotide skew of the latter (see above) added to the sum of skews of all preceding windows.
Cumulative ORF orientation skews
As in , in the ORF orientation skew analysis, the value attributed to each ORF corresponds to its length, considered as positive if the ORF is located on the Watson strand, and negative if encoded on the Crick strand. The cumulative ORF orientation analysis is calculated as a cumulative nucleotide skew by replacing windows and GC skews by genes and ORF orientation skews: the value corresponding to a given ORF is added to the sum of the values of all upstream-located ORFs. A cumulative ORF orientation skew is represented as a function of the position of the center of each gene. We used the number of nucleotide per gene, and not the number of ORFs to normalize the signal to the length of the gene, otherwise, in the cumulative ORF orientation skew plot, small genes would have a greater importance than long ones.
Coorientation Indexes (CI)
For all genomes, coorientation indexes (CI), i.e. the percentage of all or of certain categories of genes – protein encoding genes, rRNAs, tRNAs – transcribed in the direction of DNA replication, were calculated according to . For that purpose, the origin and the terminus of chromosome replication are determined by cumulative GC skew. For B. longum NCC2705, where the cumulative GC skew did not reveal the origin and/or the terminus of replication, the first codon position cumulative GC skew and ORF orientation skews were used. In most so far sequenced bacterial genomes, the origin of replication is located at the minimum of the cumulative skew curves. S. coelicolor A3(2), that has an extremely high G+C content, is an exception since its origin of replication is located at the maximum of the genomic GC skew curve. Generally, the origin of replication was shown to be close to the dnaA gene. The terminus of replication is assumed to be at the maximum of the skew curves, except in S. coelicolor A3(2), where it is assumed to be at the minimum, corresponding to both ends of the linear chromosome. However, for the first reported sequence of B. longum NCC2705, where the skew analyses did not provide the origin or the terminus of replication, we assumed that they are respectively located close to dnaA and at the putative terminus of replication in the integrated plasmid, about 180° from the dnaA gene on the circular chromosome.
Basic Local Alignment Search Tool (BLAST) 2.2.4  analysis was performed with the software kindly provided by the NCBI  using as a cutoff an expected E-value of 10-2 for alignments of the full genome sequence of B. longum NCC2705 vs. the available contigs of B. longum DJO10A. An E-value of 10-2 indicates that a hit with the same or a better alignment score occurs with a probability of 10-2 when searching the same database with a random sequence. BLAST results with an alignment length below 1000 nucleotides were discarded. BLAST analysis was performed with an expected E-value of 10 for alignments of S. coelicolor A3(2) and M. tuberculosis CDC1551 vs. B. longum NCC2705 in its actual as well as putative alternative chromosomal configuration. For the latter analyses only, hits with an alignment score below 100 were discarded. A hit is defined as direct or indirect if the DNA segments are in the same, or respectively opposite, orientation in both genomes.
Between-species alignments of whole genomes
Also called dot-plot analyses [6, 21], genome-to-genome comparisons were achieved according to . The relative positions of homologous segments in pairwise comparisons of bacterial genomes were determined by BLAST (see above).
Correlation coefficients of type II regression (major axis regression) were determined for both direct and indirect hit subsets. If a genome had undergone only exactly symmetric rearrangements around the origin of replication, the correlation coefficients of the direct- and indirect BLAST hit sets would be 1 and -1, respectively. Correlation coefficients close to zero show no correlation between relative chromosomal positions of homologous segments.
Bifidobacterium longum NCC2705, [GenBank:NC_004307.1] and [GenBank:NC_004307.2]; S. coelicolor A3(2), [GenBank:NC_003888]; M. tuberculosis CDC1551, [GenBank:NC_002755]; B. longum DJO10A, [GenBank:NZ_AABM00000000].
List of abbreviations
We would like to thank Alexandre Panchaud who drew our attention at the particular genome configuration presented by the first reported sequence of B. longum NCC2705. We warmly thank Fabrizio Arigoni and Bernard Berger for sharing unpublished results in discussions initiated by our poster presentation at Genomes 2004: International Conference on the Analysis of Microbial and Other Genomes (Guy L., Karamata D., Moreillon P. and Roten CAH, The genome of Bifidobacterium longum NCC2705: an example of major chromosomal rearrangements revealed by genometric analyses. April 14–17, 2004, The Wellcome Trust Conference Centre, Cambridge, UK). We are particularly grateful to them for informing us in late 2004, after submission of the first version of our paper (July 2004), that they and their colleagues consider that their initial published sequence of B. longum NCC2705 was misassembled.
- Biavati B, Mattarelli P: The family Bifidobacteriaceae. The Prokaryotes: An Evolving Electronic Resource for the Microbiological Community. Edited by: Dworkin M, Falkow S, Rosenberg E, Schleifer KH and Stackebrandt E. 2001, New York, Springer-Verlag, 1-70. 3rd edition, relase 3.7Google Scholar
- 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. 10.1128/AEM.68.1.219-226.2002.PubMed CentralView ArticlePubMedGoogle Scholar
- 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. 10.1097/00005176-200001000-00019.View ArticlePubMedGoogle Scholar
- 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. 10.1073/pnas.212527599.PubMed CentralView ArticlePubMedGoogle Scholar
- Casjens S: The diverse and dynamic structure of bacterial genomes. Annu Rev Genet. 1998, 32: 339-377. 10.1146/annurev.genet.32.1.339.View ArticlePubMedGoogle Scholar
- Tillier ERM, Collins RA: Genome rearrangement by replication-directed translocation. Nature Genet. 2000, 26: 195-197. 10.1038/79918.View ArticlePubMedGoogle Scholar
- 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. 10.1186/gb-2000-1-6-research0011.View ArticleGoogle Scholar
- Brewer BJ: When polymerases collide: replication and the transcriptional organization of the E. coli chromosome. Cell. 1988, 53: 679-686. 10.1016/0092-8674(88)90086-4.View ArticlePubMedGoogle Scholar
- French S: Consequences of replication fork movement through transcription units in vivo. Science. 1992, 258: 1362-1365.View ArticlePubMedGoogle Scholar
- Mirkin EV, Mirkin SM: Mechanisms of transcription-replication collisions in bacteria. Mol Cell Biol. 2005, 25: 888-895. 10.1128/MCB.25.3.888-895.2005.PubMed CentralView ArticlePubMedGoogle Scholar
- 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.View ArticlePubMedGoogle Scholar
- 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. 10.1016/j.gene.2004.06.056.View ArticlePubMedGoogle Scholar
- Frank AC, Lobry JR: Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms. Gene. 1999, 238: 65-77. 10.1016/S0378-1119(99)00297-8.View ArticlePubMedGoogle Scholar
- 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. 10.1016/0022-2836(87)90241-5.View ArticlePubMedGoogle Scholar
- 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.View ArticlePubMedGoogle Scholar
- 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. 10.1101/gr.10.2.228.PubMed CentralView ArticlePubMedGoogle Scholar
- Francino MP, Ochman H: Strand asymmetries in DNA evolution. Trends Genet. 1997, 13: 240-245. 10.1016/S0168-9525(97)01118-9.View ArticlePubMedGoogle Scholar
- Lobry JR: Asymmetric substitution patterns in the two DNA strands of bacteria. Mol Biol Evol. 1996, 13: 660-665.View ArticlePubMedGoogle Scholar
- Grigoriev A: Analyzing genomes with cumulative skew diagrams. Nucleic Acids Res. 1998, 26: 2286-2290. 10.1093/nar/26.10.2286.PubMed CentralView ArticlePubMedGoogle Scholar
- 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.PubMedGoogle Scholar
- 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. 10.1101/gr.1096703.PubMed CentralView ArticlePubMedGoogle Scholar
- 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. 10.1038/35023079.View ArticlePubMedGoogle Scholar
- Comparative Genometrics Database.http://www.unil.ch/comparativegenometrics/
- 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. 10.1128/JB.185.3.1018-1026.2003.PubMed CentralView ArticlePubMedGoogle Scholar
- Canchaya C, Fournous G, Brussow H: The impact of prophages on bacterial chromosomes. Molecular Microbiology. 2004, 53: 9-18. 10.1111/j.1365-2958.2004.04113.x.View ArticlePubMedGoogle Scholar
- 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-Google Scholar
- 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. 10.1093/nar/30.1.142.PubMed CentralView ArticlePubMedGoogle Scholar
- Messer W: The bacterial replication initiator DnaA. DnaA and oriC, the bacterial mode to initiate DNA replication. Fems Microbiol Rev. 2002, 26: 355-374. 10.1016/S0168-6445(02)00127-4.PubMedGoogle Scholar
- IS Finder.http://www-is.biotoul.fr/
- 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: 48-10.1186/1471-2180-4-48.PubMed CentralView ArticlePubMedGoogle Scholar
- 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.PubMed CentralPubMedGoogle Scholar
- Bierne H, Michel B: When replication forks stop. Mol Microbiol. 1994, 13: 17-23.View ArticlePubMedGoogle Scholar
- Elisabeth R. M. Tillier Website.http://www.uhnres.utoronto.ca/tillier/
- 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. 10.1038/35097083.View ArticlePubMedGoogle Scholar
- 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. 10.1128/JB.184.16.4601-4611.2002.PubMed CentralView ArticlePubMedGoogle Scholar
- Wren BW: The yersiniae - a model genus to study the rapid evolution of bacterial pathogens. Nat Rev Micro. 2003, 1: 55-64. 10.1038/nrmicro730.View ArticleGoogle Scholar
- 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. 10.1073/pnas.0404012101.PubMed CentralView ArticlePubMedGoogle Scholar
- National Center for Biotechnology Information Website.http://www.ncbi.nlm.nih.gov/
- 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. 10.1093/nar/29.1.11.PubMed CentralView ArticlePubMedGoogle Scholar
- Comparative Genometrics - Bifidobacterium longum NCC2705 Webpage.http://www2.unil.ch/comparativegenometrics/bifido/index.htm
- 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. 10.1016/S0378-4371(98)00657-8.View ArticleGoogle Scholar
- Kano-Sueoka T, Lobry JR, Sueoka N: Intra-strand biases in bacteriophage T4 genome. Gene. 1999, 238: 59-64. 10.1016/S0378-1119(99)00296-6.View ArticlePubMedGoogle Scholar
- Genometrician's company.http://www.genometrician.com/
- 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. 10.1093/nar/25.17.3389.PubMed CentralView ArticlePubMedGoogle Scholar
- 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. 10.1126/science.288.5474.2212.View ArticlePubMedGoogle Scholar
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