The reach of the genome signature in prokaryotes - PubMed (original) (raw)

Comparative Study

The reach of the genome signature in prokaryotes

Mark W J van Passel et al. BMC Evol Biol. 2006.

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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Figures

Figure 1

Figure 1

Intrageneric comparison of the genome signature within 40 prokaryotic genera. Species with high genomic dissimilarity scores are in red circles (11: Chlorobium, 20: Helicobacter, 25; Mycoplasma and 36: Treponema) species with low genomic dissimilarity scores are in blue circles (5: Bartonella, 12: Bordetella, 31: Salmonella and 34: Yersinia). The average genomic dissimilarity between different species of the same genus is 0.046 (red line). The blue line represents the average intraspecific genomic dissimilarity from figure 2 (δ* = 0.009).

Figure 2

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).

Figure 3

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.

Figure 4

Figure 4

Intragenomic comparisons of the genome signature of 20 bacterial species (see Additional File 4). Highlighted are 10 (Burkholderia sp. 383 chromosome 1 vs. 3), 13 (Burkholderia xenovorans LB400 chromosome 1 vs. 3), 21 (Leptospira interrogans serovar Copenhageni str. Fiocruz L1–130 chromosome I vs. II) and 22 (Leptospira interrogans serovar Lai str. 56601 chromosome I vs. II). The average genomic dissimilarity between chromosomes of the same species is 0.016 (red line).

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