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The Origin of Eukaryotes Is Suggested as the Symbiosis of Pyrococcus into γ-Proteobacteria by Phylogenetic Tree Based on Gene Content

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Abstract

Attempts were made to define the relationship among the three domains (eukaryotes, archaea, and eubacteria) using phylogenetic tree analyses of 16S rRNA sequences as well as of other protein sequences. Since the results are inconsistent, it is implied that the eukaryotic genome has a chimeric structure. In our previous studies, the origin of eukaryotes to be the symbiosis of archaea into eubacteria using the whole open reading frames (ORF) of many genomes was suggested. In these studies, the species participating in the symbiosis were not clarified, and the effect of gene duplication after speciation (in-paralog) was not addressed. To avoid the influence of the in-paralog, we developed a new method to calculate orthologous ORFs. Furthermore, we separated eukaryotic in-paralogs into three groups by sequence similarity to archaea, eubacteria (other than α-proteobacteria), and α-proteobacteria and treated them as individual organisms. The relationship between the three ORF groups and the functional classification was clarified by this analysis. The introduction of this new method into the phylogenetic tree analysis of 66 organisms (4 eukaryotes, 13 archaea, and 49 eubacteria) based on gene content suggests the symbiosis of pyrococcus into γ-proteobacteria as the origin of eukaryotes.

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Acknowledgments

We wish to thank Yoshio Tateno, National Institute of Genetics, for valuable suggestions. We also thank Satoshi Saruhashi and Takehiko Tanaka for their assistance in the analyses. This research was supported in part by Grant-in-Aid for Scientific Research (A) No. 13309002 to T.S. from the Ministry of Education, Science, Sports, Culture and Technology of Japan.

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Authors and Affiliations

  1. Center of Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka, 411-8540, Japan

    Tokumasa Horiike

  2. Advanced Research Institute for Science and Engineering, Waseda University, Honjyo, Saitama, 367-0035, Japan

    Kazuo Hamada

  3. Department of Environment Systems, Faculty of Geo-Environmental Science, Rissho University, Kumagaya, Saitama, 360-0194, Japan

    Daisuke Miyata

  4. Graduate School of Science and Engineering, Waseda University, Waseda Research Park, IOC Honjo-Waseda, Honjo, Saitama, 367-0035, Japan

    Takao Shinozawa

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  1. Tokumasa Horiike
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  2. Kazuo Hamada
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  3. Daisuke Miyata
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  4. Takao Shinozawa
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Correspondence to Takao Shinozawa.

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Horiike, T., Hamada, K., Miyata, D. et al. The Origin of Eukaryotes Is Suggested as the Symbiosis of Pyrococcus into γ-Proteobacteria by Phylogenetic Tree Based on Gene Content. J Mol Evol 59, 606–619 (2004). https://doi.org/10.1007/s00239-004-2652-5

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