Construction of a Phylogenetic Tree of Photosynthetic Prokaryotes Based on Average Similarities of Whole Genome Sequences |
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| Authors: | Soichirou Satoh Mamoru Mimuro Ayumi Tanaka |
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| Institution: | 1. Graduate School of Life and Environmental Science, Kyoto Prefectural University, Kyoto, Japan.; 2. Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan.; 3. Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan.; 4. CREST, Japan Science and Technology Agency, Sapporo, Japan.; University of Connecticut, United States of America, |
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| Abstract: | Phylogenetic trees have been constructed for a wide range of organisms using gene sequence information, especially through the identification of orthologous genes that have been vertically inherited. The number of available complete genome sequences is rapidly increasing, and many tools for construction of genome trees based on whole genome sequences have been proposed. However, development of a reasonable method of using complete genome sequences for construction of phylogenetic trees has not been established. We have developed a method for construction of phylogenetic trees based on the average sequence similarities of whole genome sequences. We used this method to examine the phylogeny of 115 photosynthetic prokaryotes, i.e., cyanobacteria, Chlorobi, proteobacteria, Chloroflexi, Firmicutes and nonphotosynthetic organisms including Archaea. Although the bootstrap values for the branching order of phyla were low, probably due to lateral gene transfer and saturated mutation, the obtained tree was largely consistent with the previously reported phylogenetic trees, indicating that this method is a robust alternative to traditional phylogenetic methods. |
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