Prokaryote phylogeny based on ribosomal proteins and aminoacyl tRNA synthetases by using the compositional distance approach |
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Authors: | Wei?Haibin Qi?Ji Email author" target="_blank">Hao?BailinEmail author |
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Institution: | 1. College of Life Sciences,Zhejiang University,Hangzhou 310027,China;Hangzhou Branch,Beijing Genomics Institute,Chinese Academy of Sciences,Hangzhou 310008,China 2. T-Life Research Center,Fudan University,Shanghai 200433,China;Institute of Theoretical Physics,Academia Sinica,Beijing 100080,China 3. T-Life Research Center,Fudan University,Shanghai 200433,China;Hangzhou Branch,Beijing Genomics Institute,Chinese Academy of Sciences,Hangzhou 310008,China |
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Abstract: | In order to show that the newly developed K-string composition distance method, based on counting oligopeptide frequencies,
for inferring phylogenetic relations of prokaryotes works equally well without requiring the whole proteome data, we used
all ribosomal proteins and the set of aminoacyl tRNA synthetases for each species. The latter group has been known to yield
inconsistent trees if used individually. Our trees are obtained without making any sequence alignment. Altogether 16 Archaea,
105 Bacteria and 2 Eucarya are represented on the tree. Most of the lower branchings agree well with the latest, 2003, Outline of the second edition of the Bergey’s Manual of Systematic Bacteriology and the trees also suggest some relationships among higher taxa. |
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Keywords: | prokaryote Archaea phylogeny phylogenetic tree composition distance |
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