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Phylogeny of Prokaryotes and Chloroplasts Revealed by a Simple Composition Approach on All Protein Sequences from Complete Genomes Without Sequence Alignment

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Abstract

The complete genomes of living organisms have provided much information on their phylogenetic relationships. Similarly, the complete genomes of chloroplasts have helped to resolve the evolution of this organelle in photosynthetic eukaryotes. In this paper we propose an alternative method of phylogenetic analysis using compositional statistics for all protein sequences from complete genomes. This new method is conceptually simpler than and computationally as fast as the one proposed by Qi et al. (2004b) and Chu et al. (2004). The same data sets used in Qi et al. (2004b) and Chu et al. (2004) are analyzed using the new method. Our distance-based phylogenic tree of the 109 prokaryotes and eukaryotes agrees with the biologists “tree of life” based on 16S rRNA comparison in a predominant majority of basic branching and most lower taxa. Our phylogenetic analysis also shows that the chloroplast genomes are separated to two major clades corresponding to chlorophytes s.l. and rhodophytes s.l. The interrelationships among the chloroplasts are largely in agreement with the current understanding on chloroplast evolution.

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Acknowledgments

One of the authors, Zu-Guo Yu, would like to express his thanks to Dr. Ji Qi, ITP, Chinese Academy of Science, for useful discussion and sharing of his data and source code. Financial support was provided by the Youth Foundation of the Chinese National Natural Science Foundation (Grant 10101022) and Postdoctoral Research Support Grant 9900658 from Queensland University of Technology (Z.-G. Yu), and by the AoE Fund of The Chinese University of Hong Kong (K.H. Chu).

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Authors and Affiliations

  1. School of Mathematics and Computing Science, Xiangtan University, Hunan, 411105, China

    Z.G. Yu, L.Q. Zhou, S.C. Long & J.Q. Deng

  2. Program in Statistics and Operations Research, Queensland University of Technology, Brisbane, Queensland, 4001, Australia

    Z.G. Yu & V.V. Anh

  3. Department of Biology, Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China

    K.H. Chu

  4. School of Mathematical Sciences, Queensland University of Technology, GPO Box 2434, Brisbane, Queensland, 4001, Australia

    Z.G. Yu

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  1. Z.G. Yu
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  2. L.Q. Zhou
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  3. V.V. Anh
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  4. K.H. Chu
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Correspondence to Z.G. Yu.

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Yu, Z., Zhou, L., Anh, V. et al. Phylogeny of Prokaryotes and Chloroplasts Revealed by a Simple Composition Approach on All Protein Sequences from Complete Genomes Without Sequence Alignment. J Mol Evol 60, 538–545 (2005). https://doi.org/10.1007/s00239-004-0255-9

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