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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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Intraspecific comparisons of genome signature of 33 bacterial species. Species with high genomic dissimilarity scores are in red circles. The average genomic dissimilarity between genomes of the same species is 0.009 (blue line). The red line depicts the average intrageneric genomic dissimilarity from Figure 1 (δ* = 0.046).
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Figure 2: Intraspecific comparisons of genome signature of 33 bacterial species. Species with high genomic dissimilarity scores are in red circles. The average genomic dissimilarity between genomes of the same species is 0.009 (blue line). The red line depicts the average intrageneric genomic dissimilarity from Figure 1 (δ* = 0.046).

Mentions: Although no archaeal genome sequences of the same species are currently available, for 33 bacterial species there are two or more genome sequences available (Additional File 2), allowing the detection of variation of δ* of genome sequences from the same species. The average intraspecific genomic dissimilarity values are depicted in Figure 2, with an average intraspecific δ* of 0.009. Four clear outliers are detected with substantially higher δ* values (red circles in Figure 2), originating from intraspecific comparisons between the genomes from Rhodopseudomonas palustris, Prochlorococcus marinus, Buchnera aphidicola and Pseudomonas fluorescens (intraspecific δ* values of 0.0295, 0.0639, 0.0396 and 0.0822, respectively).


The reach of the genome signature in prokaryotes.

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

Intraspecific comparisons of genome signature of 33 bacterial species. Species with high genomic dissimilarity scores are in red circles. The average genomic dissimilarity between genomes of the same species is 0.009 (blue line). The red line depicts the average intrageneric genomic dissimilarity from Figure 1 (δ* = 0.046).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Intraspecific comparisons of genome signature of 33 bacterial species. Species with high genomic dissimilarity scores are in red circles. The average genomic dissimilarity between genomes of the same species is 0.009 (blue line). The red line depicts the average intrageneric genomic dissimilarity from Figure 1 (δ* = 0.046).
Mentions: Although no archaeal genome sequences of the same species are currently available, for 33 bacterial species there are two or more genome sequences available (Additional File 2), allowing the detection of variation of δ* of genome sequences from the same species. The average intraspecific genomic dissimilarity values are depicted in Figure 2, with an average intraspecific δ* of 0.009. Four clear outliers are detected with substantially higher δ* values (red circles in Figure 2), originating from intraspecific comparisons between the genomes from Rhodopseudomonas palustris, Prochlorococcus marinus, Buchnera aphidicola and Pseudomonas fluorescens (intraspecific δ* values of 0.0295, 0.0639, 0.0396 and 0.0822, respectively).

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