VBCG

VBCG identifies and uses a curated set of 20 validated bacterial core genes to generate high-fidelity phylogenomic reconstructions of bacterial species and strains.

Key Features:

• High Phylogenetic Fidelity: Evaluates 148 previously used bacterial core genes across 30,522 complete genomes from 11,262 species by comparing each gene's phylogeny to the 16S rRNA gene tree to assess fidelity.
• Comprehensive Gene Set: Selects 20 genes with the highest phylogenetic fidelity from the initial pool, minimizing missing data across species.
• Enhanced Resolution: Delivers superior resolution at species and strain levels, demonstrated on Escherichia coli strains and outperforming the 16S rRNA gene tree alone.
• Improved Analysis Speed: Reduces computational burden by focusing on a smaller, reliable gene set, accelerating phylogenomic analyses.

Scientific Applications:

• Bacterial Evolution Studies: Facilitates detailed reconstruction and analysis of bacterial evolutionary relationships using high-fidelity core-gene phylogenies.
• Strain Typing and Tracking: Enables typing and tracking of bacterial strains, including human pathogens, for epidemiological and public health investigations.
• Research on Bacterial Diversity: Supports comparative analyses of bacterial species diversity and microbial ecology using the curated core-gene set.

Methodology:

The approach evaluated 148 candidate core genes across 30,522 complete genomes (11,262 species) and selected 20 genes based on presence, single-copy ratio, and phylogenetic fidelity measured by comparing individual gene trees to the 16S rRNA gene tree, with the workflow implemented as a Python pipeline.