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The reach of the genome signature in prokaryotes.

van Passel MW, Kuramae EE, Luyf AC, Bart A, Boekhout T - BMC Evol. Biol. (2006)

Bottom Line: The genome signature has a distinct phylogenetic signal, independent of individual genetic marker genes.A reliable phylogenetic clustering cannot be based on dissimilarity values alone, as bootstrapping is not possible for this parameter.It can however be used to support or refute a given phylogeny and resulting taxonomy.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centraalbureau voor Schimmelcultures (CBS), Uppsalalaan 8, Utrecht, The Netherlands. mvpassel@email.arizona.edu

ABSTRACT

Background: With the increased availability of sequenced genomes there have been several initiatives to infer evolutionary relationships by whole genome characteristics. One of these studies suggested good congruence between genome synteny, shared gene content, 16S ribosomal DNA identity, codon usage and the genome signature in prokaryotes. Here we rigorously test the phylogenetic signal of the genome signature, which consists of the genome-specific relative frequencies of dinucleotides, on 334 sequenced prokaryotic genome sequences.

Results: Intrageneric comparisons show that in general the genomic dissimilarity scores are higher than in intraspecific comparisons, in accordance with the suggested phylogenetic signal of the genome signature. Exceptions to this trend, (Bartonella spp., Bordetella spp., Salmonella spp. and Yersinia spp.), which have low average intrageneric genomic dissimilarity scores, suggest that members of these genera might be considered the same species. On the other hand, high genomic dissimilarity values for intraspecific analyses suggest that in some cases (e.g. Prochlorococcus marinus, Pseudomonas fluorescens, Buchnera aphidicola and Rhodopseudomonas palustris) different strains from the same species may actually represent different species. Comparing 16S rDNA identity with genomic dissimilarity values corroborates the previously suggested trend in phylogenetic signal, albeit that the dissimilarity values only provide low resolution.

Conclusion: The genome signature has a distinct phylogenetic signal, independent of individual genetic marker genes. A reliable phylogenetic clustering cannot be based on dissimilarity values alone, as bootstrapping is not possible for this parameter. It can however be used to support or refute a given phylogeny and resulting taxonomy.

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Congruence between 16S rDNA sequence identity (y-axis) and δ* (x-axis) within different groups (note the different scales on the axes). See Additional File 3 for more information.
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Figure 3: Congruence between 16S rDNA sequence identity (y-axis) and δ* (x-axis) within different groups (note the different scales on the axes). See Additional File 3 for more information.

Mentions: It had been suggested previously that various genomic parameters are congruent in their phylogenetic signal [5]. We compared eight sets of genomic dissimilarity values with 16S rDNA sequence identity scores between eight different groups of species; one group containing the B. cereus cluster, and seven groups of several related species (the Chlamydia/Chlamydophila clade, the genus Mycoplasma, the genus Staphylococcus, the E. coli/Shigella/Salmonella clade, the genus Mycobacterium, the genus Ricketsia, the genus Lactobacillus and the genus Streptococcus; seven groups in total. see also Additional File 3). An inverse correlation between these two parameters is observed (Fig. 3, note the differences in scale of the 16S rDNA identity and δ*), although incongruities are visible (e.g. within the E. coli/Shigella/Salmonella clade).


The reach of the genome signature in prokaryotes.

van Passel MW, Kuramae EE, Luyf AC, Bart A, Boekhout T - BMC Evol. Biol. (2006)

Congruence between 16S rDNA sequence identity (y-axis) and δ* (x-axis) within different groups (note the different scales on the axes). See Additional File 3 for more information.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1621082&req=5

Figure 3: Congruence between 16S rDNA sequence identity (y-axis) and δ* (x-axis) within different groups (note the different scales on the axes). See Additional File 3 for more information.
Mentions: It had been suggested previously that various genomic parameters are congruent in their phylogenetic signal [5]. We compared eight sets of genomic dissimilarity values with 16S rDNA sequence identity scores between eight different groups of species; one group containing the B. cereus cluster, and seven groups of several related species (the Chlamydia/Chlamydophila clade, the genus Mycoplasma, the genus Staphylococcus, the E. coli/Shigella/Salmonella clade, the genus Mycobacterium, the genus Ricketsia, the genus Lactobacillus and the genus Streptococcus; seven groups in total. see also Additional File 3). An inverse correlation between these two parameters is observed (Fig. 3, note the differences in scale of the 16S rDNA identity and δ*), although incongruities are visible (e.g. within the E. coli/Shigella/Salmonella clade).

Bottom Line: The genome signature has a distinct phylogenetic signal, independent of individual genetic marker genes.A reliable phylogenetic clustering cannot be based on dissimilarity values alone, as bootstrapping is not possible for this parameter.It can however be used to support or refute a given phylogeny and resulting taxonomy.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centraalbureau voor Schimmelcultures (CBS), Uppsalalaan 8, Utrecht, The Netherlands. mvpassel@email.arizona.edu

ABSTRACT

Background: With the increased availability of sequenced genomes there have been several initiatives to infer evolutionary relationships by whole genome characteristics. One of these studies suggested good congruence between genome synteny, shared gene content, 16S ribosomal DNA identity, codon usage and the genome signature in prokaryotes. Here we rigorously test the phylogenetic signal of the genome signature, which consists of the genome-specific relative frequencies of dinucleotides, on 334 sequenced prokaryotic genome sequences.

Results: Intrageneric comparisons show that in general the genomic dissimilarity scores are higher than in intraspecific comparisons, in accordance with the suggested phylogenetic signal of the genome signature. Exceptions to this trend, (Bartonella spp., Bordetella spp., Salmonella spp. and Yersinia spp.), which have low average intrageneric genomic dissimilarity scores, suggest that members of these genera might be considered the same species. On the other hand, high genomic dissimilarity values for intraspecific analyses suggest that in some cases (e.g. Prochlorococcus marinus, Pseudomonas fluorescens, Buchnera aphidicola and Rhodopseudomonas palustris) different strains from the same species may actually represent different species. Comparing 16S rDNA identity with genomic dissimilarity values corroborates the previously suggested trend in phylogenetic signal, albeit that the dissimilarity values only provide low resolution.

Conclusion: The genome signature has a distinct phylogenetic signal, independent of individual genetic marker genes. A reliable phylogenetic clustering cannot be based on dissimilarity values alone, as bootstrapping is not possible for this parameter. It can however be used to support or refute a given phylogeny and resulting taxonomy.

Show MeSH
Related in: MedlinePlus