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Whole Proteome Prokaryote Phylogeny Without Sequence Alignment: A K-String Composition Approach

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Abstract

A systematic way of inferring evolutionary relatedness of microbial organisms from the oligopeptide content, i.e., frequency of amino acid K-strings in their complete proteomes, is proposed. The new method circumvents the ambiguity of choosing the genes for phylogenetic reconstruction and avoids the necessity of aligning sequences of essentially different length and gene content. The only “parameter” in the method is the length K of the oligopeptides, which serves to tune the “resolution power” of the method. The topology of the trees converges with K increasing. Applied to a total of 109 organisms, including 16 Archaea, 87 Bacteria, and 6 Eukarya, it yields an unrooted tree that agrees with the biologists’ “tree of life” based on SSU rRNA comparison in a majority of basic branchings, and especially, in all lower taxa.

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Acknowledgements

The authors thank Drs. Yang Zhong (Fudan University) and Hongya Gu (Peking University) for discussion and comments. We also thank an anonymous referee who pointed out the problem with small genomes. The use of the 64 CPU IBM Cluster at Peking University is also gratefully acknowledged. This work was supported in part by grants from the Special Funds for Major State Basic Research Project of China, the Innovation Project of CAS, and Major Innovation Research Project “248” of Beijing Municipality.

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Authors and Affiliations

  1. The Institute of Theoretical Physics, Academia Sinica, Beijing 100080, China

    Ji Qi, Bin Wang & Bai-Iin Hao

  2. The T-Life Research Center, Fudan University, Shanghai 200433, China

    Ji Qi & Bai-Iin Hao

Authors
  1. Ji Qi
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  2. Bin Wang
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  3. Bai-Iin Hao
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Corresponding author

Correspondence to Ji Qi.

Appendix

Appendix

The list of all prokaryotic genomes used in our study is given in Tables A1 and A2. The species are listed in accordance with their “Bergey Code” in order to make comparison of the trees with Bergey‘s Manual easier. The Bergey Code is a shorthand of the classification given in the 2001 edition of Bergey‘s Manual of Systematic Bacteriology (Garrity et al. 2001). For example, Lacococcus lactis is listed under Phylum BXIII (Firmicutes)—Class III (Bacilli)—Order II (Lactobacillales)—Family VI (Streptococcaceae)—Genus II (Lactococcus). We changed all Roman numerals to Arabic and wrote the lineage as B13.3.2.6.2, dropping the taxonomic units and the Latin names.

Table 2 Archaea names, abbreviations, and NCBI accession numbers, ordered by their Bergey code
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Table 3 Bacterium names, abbreviations, and NCBI accession numbers, ordered by their Bergey code
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The six eukaryotes included are Saccharomyces cerevisiae (Yeast; NC_001133–48), Caenorhabitidis elegans (worm; NC_003279–84), Arabidopsis thaliana (Arath; NC_003070.71.74.75.76), Encephalitozoon cuniculi (Enccu; NC_003242.29–38), Plasmodium falciparum (Plafa; NC_000521.910.4314–18.25–31), and Schizosaccharomyces pombe (Schpo; NC_003421. 23.24).

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Qi, J., Wang, B. & Hao, BI. Whole Proteome Prokaryote Phylogeny Without Sequence Alignment: A K-String Composition Approach . J Mol Evol 58, 1–11 (2004). https://doi.org/10.1007/s00239-003-2493-7

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