PEPPAN

PEPPAN reconstructs bacterial pan- and core genomes to identify gene content, discriminate paralogs, and provide consistent gene and pseudogene annotations across diverse bacterial genomes.

Key Features:

• Comprehensive pangenome construction: Scales to thousands of genetically diverse bacterial genomes and was applied to ~40,000 genes from 3,052 representative genomes across ≥80 species of Streptococcus.
• Accurate gene and pseudogene annotation: Uses similarity-based gene predictions to label intact coding sequences as "CDS", disrupted genes as "pseudogene", and suspicious annotations as "misc_feature".
• Paralog identification and exclusion: Integrates tree- and synteny-based approaches to identify and exclude paralogous genes from pangenome reconstruction.
• Robustness to complex evolution: Accounts for homologous recombination, gene loss, gene duplications, and horizontal gene transfer in analyses.
• Comparative performance: Demonstrated higher accuracy and specificity than four state-of-the-art pangenome pipelines while achieving comparable processing speed in empirical and simulated tests.
• Downstream analysis support: Includes PEPPAN_parser for constructing phylogenetic trees based on accessory gene content or allelic differences between core genes.

Scientific Applications:

• Evolutionary and population history: Reconstructs gene presence/absence and allelic variation to inform bacterial evolutionary and population-level analyses.
• Comparative genomics: Provides genus-level overviews of genomic diversity to support comparative analyses across species and strains.
• Epidemiology and population structure: Supports investigation of genetic relationships and variation relevant to epidemiological studies.
• Phylogenetic inference from gene content and alleles: Enables construction of gene and allelic trees to assess genetic relationships among bacterial populations.

Methodology:

PEPPAN integrates tree- and synteny-based approaches with similarity-based gene predictions to identify and exclude paralogs; accuracy was validated using the SimPan simulation pipeline that simulates the evolution of bacterial pangenomes.