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

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 o...

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Bibliographic Details
Published in:Gene 2009-01, Vol.429 (1), p.59-64
Main Authors: Horiike, Tokumasa, Miyata, Daisuke, Hamada, Kazuo, Saruhashi, Satoshi, Shinozawa, Takao, Kumar, Sudhir, Chakraborty, Ranajit, Komiyama, Tomoyoshi, Tateno, Yoshio
Format: Article
Language:English
Subjects:
Aquificae
Archaea
Bacteria - classification
Bacteria - genetics
Bacterial phylogeny
Concatenated tree
Eubacteria
Ortholog database
Out-paralog
Phylogeny
Sequence Analysis - methods
Sequence Homology, Nucleic Acid
Thermophilic eubacteria
Tree evaluation
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Summary: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.
ISSN:0378-1119
1879-0038
DOI:10.1016/j.gene.2008.10.006