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A Practical Guide to Phylogenetics for Nonexperts
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LVTree Viewer: An Interactive Display for the All-Species Living Tree Incorporating Automatic Comparison with

Guanghong Zuo1, Xiaoyang Zhi2, Zhao Xu3

  • 1T-Life Research Center, Department of Physics, Fudan University, Shanghai 200433, China.

Genomics, Proteomics & Bioinformatics
|March 29, 2016
PubMed
Summary

We developed an interactive viewer for the All-Species Living Tree (LVTree) to compare 16S rRNA phylogeny with prokaryotic taxonomy. This tool facilitates identifying and resolving discrepancies between evolutionary relationships and classification systems.

Keywords:
16S rRNA phylogenyArchaea and BacteriaCollapsing and expanding a treeLineage modificationsMonophyly

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Systematics

Background:

  • Prokaryotic systematics heavily relies on 16S rRNA sequence analysis for classification.
  • Discrepancies between phylogenetic data and current taxonomic structures can hinder accurate biological understanding.
  • The All-Species Living Tree (LVTree) project provides a comprehensive framework for microbial taxonomy.

Purpose of the Study:

  • To introduce an interactive viewer for the All-Species Living Tree (LVTree).
  • To facilitate the comparison of 16S rRNA sequence phylogeny with prokaryotic taxonomy.
  • To enable users to explore and potentially resolve taxonomic inconsistencies.

Main Methods:

  • Development of an interactive tree viewer integrating ARB-SILVA data.
  • Implementation of functionalities for collapsing and expanding tree branches at various taxonomic ranks.
  • Automated reporting of taxon statistics at all ranks following tree manipulations.
  • Enabling users to simulate lineage modifications and observe their impact on tree topology.

Main Results:

  • The viewer allows dynamic exploration of tree topology and taxonomic congruence.
  • A small number of lineage modifications (24) can resolve most phyla in LVTree into monophyletic groups.
  • The system effectively highlights discrepancies between 16S rRNA phylogeny and established prokaryotic taxonomy.

Conclusions:

  • The interactive LVTree viewer is a valuable tool for analyzing microbial phylogeny and taxonomy.
  • It aids in identifying and rectifying inconsistencies within prokaryotic classification systems.
  • The tool supports the refinement of taxonomic structures based on molecular data.