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Origin and phylogeny of chloroplasts revealed by a simple correlation analysis of complete genomes

Chu, Ka-Hou, Qi, Ji, Yu, Zu-Guo, & Anh, Vo V. (2004) Origin and phylogeny of chloroplasts revealed by a simple correlation analysis of complete genomes. Molecular Biology and Evolution, 21(1), pp. 200-206.

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Abstract

The complete sequenced genomes of chloroplast have provided much information on the origin and evolution of this organelle. In this paper we attempt to use these sequences to test a novel approach for phylogenetic analysis of complete genomes based on correlation analysis of compositional vectors. All protein sequences from 21 complete chloroplast genomes are analyzed in comparison with selected archaea, eubacteria, and eukaryotes. The distance-based analysis shows that the chloroplast genomes are most closely related to cyanobacteria, consistent with the endosymbiotic origin of chloroplasts. The chloroplast genomes are separated to two major clades corresponding to chlorophytes (green plants) s.l. and rhodophytes (red algae) s.l. The interrelationships among the chloroplasts are largely in agreement with the current understanding on chloroplast evolution. For instance, the analysis places the chloroplasts of two chromophytes (Guillardia and Odontella) within the rhodophyte lineage, supporting secondary endosymbiosis as the source of these chloroplasts. The relationships among the green algae and land plants in our tree also agree with results from traditional phylogenetic analyses. Thus, this study establishes the value of our simple correlation analysis in elucidating the evolutionary relationships among genomes. It is hoped that this approach will provide insights on comparative genome analysis.

Impact and interest:

45 citations in Scopus
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40 citations in Web of Science®

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ID Code: 7864
Item Type: Journal Article
Additional Information: For more information or for a copy of this article see the URL above or contact the author at z.yu@qut.edu.au
Keywords: chloroplast, genome, plant, phylogeny
DOI: 10.1093/molbev/msh002
ISSN: 0737-4038
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 2004 Society for Molecular Biology and Evolution
Deposited On: 25 May 2007
Last Modified: 05 Mar 2012 12:31

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