Phylogenetic construction of 17 bacterial phyla by new method and carefully selected orthologs

Tokumasa Horiike, Daisuke Miyata, Kazuo Hamada, Satoshi Saruhashi, Takao Shinozawa, Sudhir Kumar, Ranajit Chakraborty, Tomoyoshi Komiyama, Yoshio Tateno

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

Here, we constructed a phylogenetic tree of 17 bacterial phyla covering eubacteria and archaea by using a new method and 102 carefully selected orthologs from their genomes. One of the serious disturbing factors in phylogeny construction is the existence of out-paralogs that cannot easily be found out and discarded. In our method, out-paralogs are detected and removed by constructing a phylogenetic tree of the genes in question and examining the clustered genes in the tree. We also developed a method for comparing two tree topologies or shapes, ComTree. Applying ComTree to the constructed tree we computed the relative number of orthologs that support a node of the tree. This number is called the Positive Ortholog Ratio (POR), which is conceptually and methodologically different from the frequently used bootstrap value. Our study concretely shows drawbacks of the bootstrap test. Our result of bacterial phylogeny analysis is consistent with previous ones showing that hyperthermophilic bacteria such as Thermotogae and Aquificae diverged earlier than the others in the eubacterial phylogeny studied. It is noted that our results are consistent whether thermophilic archaea or mesophilic archaea is employed for determining the root of the tree. The earliest divergence of hyperthermophilic eubacteria is supported by genes involved in fundamental metabolic processes such as glycolysis, nucleotide and amino acid syntheses.

Original languageEnglish (US)
Pages (from-to)59-64
Number of pages6
JournalGene
Volume429
Issue number1-2
DOIs
StatePublished - Jan 15 2009

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Archaea
Phylogeny
Bacteria
Genes
Glycolysis
Nucleotides
Genome
Amino Acids

Keywords

  • Bacterial phylogeny
  • Concatenated tree
  • Ortholog database
  • Out-paralog
  • Thermophilic eubacteria
  • Tree evaluation

ASJC Scopus subject areas

  • Genetics

Cite this

Horiike, T., Miyata, D., Hamada, K., Saruhashi, S., Shinozawa, T., Kumar, S., ... Tateno, Y. (2009). Phylogenetic construction of 17 bacterial phyla by new method and carefully selected orthologs. Gene, 429(1-2), 59-64. https://doi.org/10.1016/j.gene.2008.10.006

Phylogenetic construction of 17 bacterial phyla by new method and carefully selected orthologs. / Horiike, Tokumasa; Miyata, Daisuke; Hamada, Kazuo; Saruhashi, Satoshi; Shinozawa, Takao; Kumar, Sudhir; Chakraborty, Ranajit; Komiyama, Tomoyoshi; Tateno, Yoshio.

In: Gene, Vol. 429, No. 1-2, 15.01.2009, p. 59-64.

Research output: Contribution to journalArticle

Horiike, T, Miyata, D, Hamada, K, Saruhashi, S, Shinozawa, T, Kumar, S, Chakraborty, R, Komiyama, T & Tateno, Y 2009, 'Phylogenetic construction of 17 bacterial phyla by new method and carefully selected orthologs', Gene, vol. 429, no. 1-2, pp. 59-64. https://doi.org/10.1016/j.gene.2008.10.006
Horiike T, Miyata D, Hamada K, Saruhashi S, Shinozawa T, Kumar S et al. Phylogenetic construction of 17 bacterial phyla by new method and carefully selected orthologs. Gene. 2009 Jan 15;429(1-2):59-64. https://doi.org/10.1016/j.gene.2008.10.006
Horiike, Tokumasa ; Miyata, Daisuke ; Hamada, Kazuo ; Saruhashi, Satoshi ; Shinozawa, Takao ; Kumar, Sudhir ; Chakraborty, Ranajit ; Komiyama, Tomoyoshi ; Tateno, Yoshio. / Phylogenetic construction of 17 bacterial phyla by new method and carefully selected orthologs. In: Gene. 2009 ; Vol. 429, No. 1-2. pp. 59-64.
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