Phylogenetic Position of Aquificales Based on the Whole Genome Sequences of Six Aquificales Species

Kenro Oshima,Yoko Chiba,Masaharu Ishii,Hiroyuki Arai,Yasuo Igarashi

doi:10.1155/2012/859264

Kenro Oshima, Yoko Chiba + Show 3 more

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https://doi.org/10.1155/2012/859264

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Abstract

Species belonging to the order Aquificales are believed to be an early branching lineage within the Bacteria. However, the branching order of this group in single-gene phylogenetic trees is highly variable; for example, it has also been proposed that the Aquificales should be grouped with ε-proteobacteria. To investigate the phylogenetic position of Aquificales at the whole-genome level, here we reconstructed the phylogenetic trees of 18 bacteria including six Aquificales species based on the concatenated data of proteins shared by these bacteria. In the phylogenetic tree based on the whole-genome information, Aquificales was more closely related to Thermotogales than to Proteobacteria, suggesting that the Aquificales is a relatively early branching lineage within the Bacteria. Moreover, we classified the phylogenetic tree of each conserved orthologous protein by its topology. As a result, in the most major type of the phylogenetic trees, Aquificales was closely related to the Thermotogales. However, Aquificales was closely related to ε-proteobacteria in 21.0% of all phylogenetic trees, suggesting that many proteins phylogenetically related to the ε-proteobacteria may be encoded in the genomes of the members of the Aquificales. This unique feature may be responsible for the high variability in the branching order of Aquificales in single-gene phylogenetic trees.

Highlights

Species belonging to the order Aquificales are non-sporeforming, Gram-negative rods that are strictly thermophilic with optimal growth usually occurring above 65◦C [1,2,3]
We constructed maximum likelihood (ML) trees based on the 16S rRNA sequences of 18 bacteria (Figure 1(a))
In the phylogenetic tree based on the whole-genome information, the Archaea group was evolutionarily closely related to the Thermotogales, and Aquificales was a neighbor to Thermotogales with 76% bootstrap value (Figure 2). These analyses suggest that Aquificales is more closely related to Thermotogales than to Proteobacteria, which is consistent with the phylogenetic relationship showed by Boussau et al [28]

Summary

Introduction

Species belonging to the order Aquificales are non-sporeforming, Gram-negative rods that are strictly thermophilic with optimal growth usually occurring above 65◦C [1,2,3]. To construct the phylogenetic tree of six Aquificales species, two Thermotogales species, two γ-proteobacteria, and two ε-proteobacteria, we used 12 genome sequences from Aquifex aeolicus, Hydrogenobacter thermophilus TK6, Hydrogenobaculum sp. To construct the phylogenetic tree of Thermales-Deinococcales species, Thermotogales species, γ-proteobacteria, and ε-proteobacteria, we used 8 genome sequences from Campylobacter jejuni subsp.

Results

Conclusion