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

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 d

SUBMITTER: Zuo G 

PROVIDER: S-EPMC6364046 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature