CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy

Area of Science:

• Microbiology
• Bioinformatics
• Computational Biology

Background:

• Establishing a faithful phylogeny and objective taxonomy for prokaryotes is crucial for understanding microbial life.
• The increasing volume of sequenced prokaryotic genomes presents significant challenges for phylogenetic tree inference and taxonomic comparison.
• Existing methods often struggle to integrate whole-genome data with established taxonomic classifications.

Purpose of the Study:

• To present CVTree3, an enhanced alignment-free, whole-genome-based web server for prokaryotic phylogeny and taxonomy.
• To provide a scalable solution for analyzing tens of thousands of sequenced prokaryotic genomes.
• To facilitate the comparison of genomic-based phylogenetic trees with existing prokaryotic classification systems.

Main Methods:

• Utilizing an alignment-free, whole-genome-based approach for phylogenetic tree construction.
• Implementing CVTree3 on a 64-core cluster with an interactive, collapsible, and expandable tree display.
• Comparing inferred phylogenetic branching orders with prokaryotic taxonomy across all ranks (domains to species/strains).

Main Results:

• CVTree3 successfully handles large-scale prokaryotic genome data for phylogenetic analysis and taxonomic classification.
• The server allows for taxon name inquiries, lineage modification trials, and generates summaries of monophyletic/non-monophyletic taxa.
• Discrepancies between CVTree3 and 16S rRNA analyses were identified, suggesting potential taxonomic revisions.

Conclusions:

• CVTree3 offers a powerful solution for the mega-classification of prokaryotes using whole-genome data.
• The server aids in determining the taxonomic placement of newly sequenced genomes.
• Findings highlight the utility of genome-based phylogenetics for refining prokaryotic taxonomy and resolving discrepancies with traditional methods.