Polyphyly in 16S rRNA-based LVTree Versus Monophyly in Whole-genome-based CVTree.
10.1016/j.gpb.2018.06.005
- Author:
Guanghong ZUO
1
;
Ji QI
2
;
Bailin HAO
3
Author Information
1. T-Life Research Center, Department of Physics, Fudan University, Shanghai 200433, China. Electronic address: ghzuo@fudan.edu.cn.
2. State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China.
3. T-Life Research Center, Department of Physics, Fudan University, Shanghai 200433, China.
- Publication Type:Journal Article
- Keywords:
16S rRNA sequence;
Archaea and bacteria taxonomy;
CVTree;
Phylogeny;
Whole-genome sequence
- MeSH:
Genome;
Genomics;
Phylogeny;
RNA, Ribosomal, 16S;
genetics;
Sequence Analysis, DNA
- From:
Genomics, Proteomics & Bioinformatics
2018;16(5):310-319
- CountryChina
- Language:English
-
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.
