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PMID: 15693617 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

The origin of eukaryotes is suggested as the symbiosis of pyrococcus into gamma-proteobacteria by phylogenetic tree based on gene content.

Journal of molecular evolution ·Vol. 59 ·No. 5 ·2004-11-00 ·Pages 606-19

Horiike T, Hamada K, Miyata D, Shinozawa T

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 alpha-proteobacteria), and alpha-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 gamma-proteobacteria as the origin of eukaryotes.

MeSH Terms
Eukaryotic Cells/cytology,physiology Gammaproteobacteria/cytology,genetics,physiology Genome Mosaicism Open Reading Frames/genetics Phylogeny Pyrococcus/genetics,physiology Symbiosis/physiology
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Horiike Tokumasa
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.
Hamada Kazuo
Miyata Daisuke
Shinozawa Takao
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Article Info
Journal
Journal of molecular evolution
Abbr.
J Mol Evol
ISSN
0022-2844
DOI
10.1007/s00239-004-2652-5
Published
2004-11-00
Pages
606-19
Language
English
Region
Germany
NLM ID
0360051
Subset
IM
External Links
PubMed source DOI: 10.1007/s00239-004-2652-5 View journal details
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