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Phylogeny of prokaryotes and chloroplasts revealed by a simple composition approach on all protein sequences from complete genomes without sequence alignment

Yu, Zu-Guo, Zhou, Li-Qian, Anh, Vo V., Chu, Ka-Hou, Long, Shun-Chao, & Deng, Ji-Qing (2005) Phylogeny of prokaryotes and chloroplasts revealed by a simple composition approach on all protein sequences from complete genomes without sequence alignment. Journal of Molecular Evolution, 60(4), pp. 538-545.

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Abstract

The complete genomes of living organisms have provided much information on their phylogenetic relationships. Similarly, the complete genomes of chloroplasts have helped to resolve the evolution of this organelle in photosynthetic eukaryotes. In this paper we propose an alternative method of phylogenetic analysis using compositional statistics for all protein sequences from complete genomes. This new method is conceptually simpler than and computationally as fast as the one proposed by Qi et al. (2004b) and Chu et al. (2004). The same data sets used in Qi et al. (2004b) and Chu et al. (2004) are analyzed using the new method. Our distance-based phylogenic tree of the 109 prokaryotes and eukaryotes agrees with the biologists tree of life based on 16S rRNA comparison in a predominant majority of basic branching and most lower taxa. Our phylogenetic analysis also shows that the chloroplast genomes are separated to two major clades corresponding to chlorophytes s.l. and rhodophytes s.l. The interrelationships among the chloroplasts are largely in agreement with the current understanding on chloroplast evolution.

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28 citations in Scopus
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20 citations in Web of Science®

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ID Code: 7841
Item Type: Journal Article
Additional Information: For more information or for a copy of this article contact the author at z.yu@qut.edu.au
Keywords: Phylogeny, Prokaryotes, Chloroplast, Genome, Composition vector
DOI: 10.1007/s00239-004-0255-9
ISSN: 0022-2844
Subjects: Australian and New Zealand Standard Research Classification > BIOLOGICAL SCIENCES (060000) > GENETICS (060400) > Molecular Evolution (060409)
Divisions: Past > QUT Faculties & Divisions > Faculty of Science and Technology
Copyright Owner: Copyright 2005 Springer
Copyright Statement: The original publication is available at SpringerLink http://www.springerlink.com
Deposited On: 24 May 2007
Last Modified: 01 Mar 2012 13:20

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