MBE Advance Access published online on October 31, 2003
Molecular Biology and Evolution, doi:10.1093/molbev/msh002
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2003; all rights reserved
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1 Department of Biology, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
* To whom correspondence should be addressed. E-mail: kahouchu{at}cuhk.edu.hk.
The complete sequenced genomes of chloroplast have provided much information on the origin and evolution of this organelle. In this paper we attempted 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 were 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 green 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. Key Words:
Chloroplast, genome, plant, phylogeny
© 2003 Society for Molecular Biology and Evolution
Original Articles
Origin and Phylogeny of Chloroplasts Revealed by a Simple Correlation Analysis of Complete Genomes
2 Institute of Theoretical Physics, The Chinese Academy of Sciences, Beijing 100080, China
3 Centre in Statistical Science and Industrial Mathematics, Queensland University of Technology, GPO Box 2434, Brisbane, Queensland 4001, Australia; Department of Mathematics, Xiangtan University, Hunan 411105, China
4 Centre in Statistical Science and Industrial Mathematics, Queensland University of Technology, GPO Box 2434, Brisbane, Queensland 4001, Australia
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