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

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 phenomen...

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Bibliographic Details
Published in:Genomics, proteomics & bioinformatics proteomics & bioinformatics, 2018-10, Vol.16 (5), p.310-319
Main Authors: Zuo, Guanghong, Qi, Ji, Hao, Bailin
Format: Article
Language:English
Subjects:
16S rRNA sequence
Archaea and bacteria taxonomy
CVTree
Original Research
Phylogeny
Whole-genome sequence
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Summary: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.
ISSN:1672-0229
2210-3244
DOI:10.1016/j.gpb.2018.06.005