Different clustering of genomes across life using the A-T-C-G and degenerate R-Y alphabets: Early and late signaling on genome evolution?

V. Kirzhner, A. Paz, Z. Volkovich, E. Nevo, A. Korol

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Pages (from-to)448-456
Number of pages9
JournalJournal of Molecular Evolution
Volume64
Issue number4
DOIs
StatePublished - Apr 2007

Keywords

  • Compositional spectrum
  • Ecological convergence
  • Phylogenetic tree
  • Purine-pyrimidine alphabet
  • Sequence comparison

ASJC Scopus subject areas

  • Genetics
  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology

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