Chu Ka Hou, Qi Ji, Yu Zu-Guo, Anh Vo
Department of Biology, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China.
Mol Biol Evol. 2004 Jan;21(1):200-6. doi: 10.1093/molbev/msh002. Epub 2003 Oct 31.
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.
叶绿体的全序列基因组为该细胞器的起源和进化提供了大量信息。在本文中，我们尝试利用这些序列来测试一种基于组成向量相关性分析的全基因组系统发育分析新方法。我们分析了21个完整叶绿体基因组的所有蛋白质序列，并与选定的古细菌、真细菌和真核生物进行比较。基于距离的分析表明，叶绿体基因组与蓝细菌的关系最为密切，这与叶绿体的内共生起源一致。叶绿体基因组被分为两个主要分支，分别对应广义绿藻（绿色植物）和广义红藻（红藻）。叶绿体之间的相互关系在很大程度上与目前对叶绿体进化的理解一致。例如，分析将两种色素体藻类（Guillardia和Odontella）的叶绿体置于红藻谱系中，支持次生内共生是这些叶绿体的来源。我们构建的系统发育树中绿藻和陆地植物之间的关系也与传统系统发育分析的结果一致。因此，本研究确立了我们简单的相关性分析在阐明基因组间进化关系方面的价值。希望这种方法能为比较基因组分析提供见解。
