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MICROBIOLOGY COMMENT |
Academic Medical Center, Department of Medical Microbiology, PO Box 22700, 1100 DE Amsterdam, The Netherlands
Correspondence
A. van der Ende
(a.vanderende{at}amc.uva.nl)
Recently, Binnewies and colleagues described the proteome comparisons of eight Mycoplasma genome sequences in Microbiology Comment (Binnewies et al., 2005
). The presence of a species from a different genus, Ureaplasma urealyticum, between the different Mycoplasma species is merely indicative of the problems taxonomy may experience in the genomic era.
The diversity of the different Mycoplasma species has been attributed to the rapid (degenerative) evolution of the species (Rogers et al., 1985). The diversity within the genus is illustrated by the large differences in genome size (ranging from 0·58 to 1·36 Mbp) and percentage G+C (from 24 to 40 mol%) between the eight sequenced Mycoplasma species.
With the current availability of whole-genome sequences, some efforts have been made to initiate genome-based taxonomy (Coenye et al., 2005; Konstantinidis & Tiedje, 2005). Previously, Coenye & Vandamme (2003) described various phylogenetic information sources, and compared the sequences of 16S RNA genes and several housekeeping genes with the fraction of shared orthologous genes between related genomes, the conservation of gene order, the dinucleotide relative abundance values and the codon usage. They concluded, using the lactic acid bacteria as a test case, that the different kinds of phylogenetic information agree and that whole-genome sequence comparisons may be of value in taxonomy, e.g. to enhance the phylogenetic signal derived by more traditional methods. Would this approach also show that the different Mycoplasma species are closely related?
The parameters used by Coenye & Vandamme show that for Mycoplasma, the sequence identity values for 16S RNA genes are generally low (between 71·5 and 98·1 %) and that dinucleotide relative abundance differences between their genomes, also known as the genome signature dissimilarity, are very high (Table 1), much higher than between representatives of the Enterobacteriaceae (Table 2). For three Mycoplasma species, this had already been found (Sandberg et al., 2003), but this trend continues with the eight known Mycoplasma genome sequences. Recently, Gophna et al. (2005) devised several weighted whole-genome trees in which it is clearly visible that the Mycoplasma genus branches at a great depth, indicating a high level of diversity within this genus. Together, these data confirm the limits of current taxonomy for the genus Mycoplasma. Results with Buchnera and Wolbachia indicate that this may be true for all genera which are thought to undergo rapid genome evolution, such as endosymbionts (data not shown).
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the concepts of species as (functional) categories and species as evolutionary groups are in conflict. The division of the Tenericutes (wall-less bacteria), to which Mycoplasma belongs, forms a fine example of this conflict, as the category ‘cell-wall-less' seems to consist of evolutionary descendants of some Gram-positive organism. The genus Mycoplasma itself clearly comprises members that would be classified as a different genus if evolutionary distances comparable to those that discriminate enterobacterial genera were used.
In the pre-genomic era it was proposed that nomenclature should agree with and reflect genomic information (Wayne et al., 1987). With the imminent release of over 1000 whole-genome sequences, including 10 more Mycoplasma species (www.genomesonline.org, June 2005), it is due time to reconsider the relative importance of the properties that provide the basis for Mycoplasma taxonomy and bacterial taxonomy in general.
REFERENCES
Binnewies, T. T., Hallin, P. F., Staerfeldt, H. H. & Ussery, D. W. (2005). Genome update: proteome comparisons. Microbiology 151, 1–4.
Coenye, T. & Vandamme, P. (2003). Extracting phylogenetic information from whole-genome sequencing projects: the lactic acid bacteria as a test case. Microbiology 149, 3507–3517.
Coenye, T., Gevers, D., Van de Peer, Y., Vandamme, P. & Swings, J. (2005). Towards a prokaryotic genomic taxonomy. FEMS Microbiol Rev 29, 147–167.[CrossRef][Medline]
Gophna, U., Doolittle, W. F. & Charlebois, R. L. (2005). Weighted genome trees: refinements and applications. J Bacteriol 187, 1305–1316.
Hey, J. (2001). The mind of the species problem. Trends Ecol Evol 16, 326–329.[CrossRef][Medline]
Konstantinidis, K. T. & Tiedje, J. M. (2005). Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci U S A 102, 2567–2572.
Rogers, M. J., Simmons, J., Walker, R. T. & 8 other authors (1985). Construction of the mycoplasma evolutionary tree from 5S rRNA sequence data. Proc Natl Acad Sci U S A 82, 1160–1164.
Sandberg, R., Branden, C. I., Ernberg, I. & Coster, J. (2003). Quantifying the species-specificity in genomic signatures, synonymous codon choice, amino acid usage and G+C content. Gene 311, 35–42.[CrossRef][Medline]
Wayne, L. G., Brenner, D. J., Colwell, R. R. & 9 other authors (1987). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463–464.
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, shaded) among nine different Mollicutes