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Different Clustering of Genomes Across Life Using the A-T-C-G and Degenerate R-Y Alphabets: Early and Late Signaling on Genome Evolution?

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Abstract

In this study, we have calculated distances between genomes based on our previously developed compositional spectra (CS) analysis. The study was conducted using genomes of 39 species of Eukarya, Eubacteria, and Archaea. Based on CS distances, we produced two different consensus dendrograms for four- and two-letter (purine-pyrimidine) alphabets. A comparison of the obtained structure using purine-pyrimidine alphabet with the standard three-kingdom (3K) scheme reveals substantial similarity. Surprisingly, this is not the case when the same procedure is based on the four-letter alphabet. In this situation, we also found three main clusters—but different from those in the 3K scheme. In particular, one of the clusters includes Eukarya and thermophilic bacteria and a part of the considered Archaea species. We speculate that the key factor in the last classification (based on the A-T-G-C alphabet) is related to ecology: two ecological parameters, temperature and oxygen, distinctly explain the clustering revealed by compositional spectra in the four-letter alphabet. Therefore, we assume that this result reflects two interdependent processes: evolutionary divergence and superimposed ecological convergence of the genomes, albeit another process, horizontal transfer, cannot be excluded as an important contributing factor.

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Acknowledgments

We thank Stuart Newfeld and three anonymous reviewers for their helpful comments and suggestions. This work was supported by the Israeli Ministry of Absorption. A.P. was supported by a scholarship in Bioinformatics from the Eshkol Foundation of the Israeli Ministry of Science and Technology.

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Authors and Affiliations

  1. Institute of Evolution, University of Haifa, Mount Carmel, Haifa, 31905, Israel

    V. Kirzhner, A. Paz, E. Nevo & A. Korol

  2. Software Engineering Department, ORT Braude College, P.O.B. 78, Carmiel, 20101, Israel

    Z. Volkovich

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  1. V. Kirzhner
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  2. A. Paz
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  3. Z. Volkovich
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  4. E. Nevo
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Correspondence to V. Kirzhner.

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[Reviewing Editor: Dr. Stuart Newfeld]

Appendix: List of Depicted Genomic Sequences

Appendix: List of Depicted Genomic Sequences

Each record in the list is represented by species name. If only a DNA fragment rather than entire genome was taken for a species, the corresponding accession number is also presented to avoid incorrect identification.

Eukarya

Homo sapiens chromosome (chr) X (NT 011528); Homo sapiens chr Y (NT011864); Mus musculus chr 7 (AC012382); Caenorhabditis elegans chr 1; Drosophila melanogaster chr 2; Arabidopsis thaliana chr 1 (NC 003071); A thaliana mitochondrial genome (NC 001284.1); Saccharomyces cerevisiae chr ii; Leishmania major (AE001274).

Eubacteria

Bacillus subtilis; Streptococcus pyogenes; Mycoplasma genitalium; Mycoplasma pneumoniae; Mycobacterium tuberculosis; Synechocystis sp.; Helicobacter pylori; Escherichia coli; Deinococcus radiodurans; Thermotoga maritima; Aquifex aeolicus; Neisseria meningitides; Neisseria gonorrhoeae; Campylobacter jejuni; Haemophilus influenzae; Clostridium acetobutylicum; Treponema pallidum; Pseudomonas aeruginosa; Actinobacillus actinomycetemcomitans strain HK1651; Rickettsia prowazekii; Borrelia burgdorferi; Thermus thermophilus; Enterococcus faecalis.

Archaea

Halobacterium sp. NRC-1; Pyrococcus horikoshii; Pyrococcus abyssi; Archaeoglobus fulgidus; Methanococcus jannaschii; Methanobacterium thermoautotrophicum; Aeropyrum pernix; Sulfolobus solfataricus.

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Kirzhner, V., Paz, A., Volkovich, Z. et al. Different Clustering of Genomes Across Life Using the A-T-C-G and Degenerate R-Y Alphabets: Early and Late Signaling on Genome Evolution?. J Mol Evol 64, 448–456 (2007). https://doi.org/10.1007/s00239-006-0178-8

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