Polyphyly in 16S rRNA-based LVTree Versus Monophyly in Whole-genome-based CVTree |
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Authors: | Guanghong Zuo Ji Qi Bailin Hao |
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Institution: | 1. T-Life Research Center, Department of Physics, Fudan University, Shanghai 200433, China;2. State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China |
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Abstract: | We report an important but long-overlooked manifestation of low-resolution power of 16S rRNA sequence analysis at the species level, namely, in 16S rRNA-based phylogenetic trees polyphyletic placements of closely-related species are abundant compared to those in genome-based phylogeny. This phenomenon makes the demarcation of genera within many families ambiguous in the 16S rRNA-based taxonomy. In this study, we reconstructed phylogenetic relationship for more than ten thousand prokaryote genomes using the CVTree method, which is based on whole-genome information. And many such genera, which are polyphyletic in 16S rRNA-based trees, are well resolved as monophyletic clusters by CVTree. We believe that with genome sequencing of prokaryotes becoming a commonplace, genome-based phylogeny is doomed to play a definitive role in the construction of a natural and objective taxonomy. |
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Keywords: | Archaea and bacteria taxonomy Phylogeny CVTree Whole-genome sequence 16S rRNA sequence |
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