1. Polyphyly in 16S rRNA-based LVTree Versus Monophyly in Whole-genome-based CVTree
- Author
-
Guanghong Zuo, Ji Qi, and Bailin Hao
- Subjects
Biology (General) ,QH301-705.5 ,Computer applications to medicine. Medical informatics ,R858-859.7 - 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. Keywords: Archaea and bacteria taxonomy, Phylogeny, CVTree, Whole-genome sequence, 16S rRNA sequence
- Published
- 2018
- Full Text
- View/download PDF