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MBE Advance Access originally published online on October 31, 2003
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Mol. Biol. Evol. 21(1):200-206. 2004
DOI: 10.1093/molbev/msh002
© 2004 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038

Origin and Phylogeny of Chloroplasts Revealed by a Simple Correlation Analysis of Complete Genomes

Ka Hou Chu*, Ji Qi{dagger}, Zu-Guo Yu{ddagger},§ and Vo Anh{ddagger}

* Department of Biology, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
{dagger} Institute of Theoretical Physics, The Chinese Academy of Sciences, Beijing, China
{ddagger} Programs in Statistics and Operations Research, Queensland University of Technology, Brisbane, Australia
§ Department of Mathematics, Xiangtan University, Hunan, China

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 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.

Key Words: chloroplast • genome • plant • phylogeny


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