Polyphyly in 16S rRNA-based LVTree Versus Monophyly in Whole-genome-based CVTree

Guanghong Zuo; Ji Qi; Bailin Hao

doi:10.1016/j.gpb.2018.06.005

Polyphyly in 16S rRNA-based LVTree Versus Monophyly in Whole-genome-based CVTree

Genomics Proteomics Bioinformatics. 2018 Oct;16(5):310-319. doi: 10.1016/j.gpb.2018.06.005. Epub 2018 Dec 11.

Authors

Guanghong Zuo¹, Ji Qi², Bailin Hao³

Affiliations

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.

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: 16S rRNA sequence; Archaea and bacteria taxonomy; CVTree; Phylogeny; Whole-genome sequence.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Genome
Genomics
Phylogeny*
RNA, Ribosomal, 16S / genetics*
Sequence Analysis, DNA

Substances

RNA, Ribosomal, 16S