The pangenome variability index: a quantitative measure for assessing gene content diversity in microbial genomes

Abstract

Accurately characterizing the structure and variability of microbial pangenomes is essential for understanding genome evolution, adaptation, and functional diversity. Traditional descriptive measures such as genomic fluidity and the openness coefficient (α) have provided valuable insights into gene content diversity and pangenome expansion dynamics. Still, they often lose resolution in transitional genome states where conserved and accessory genes coexist. Here, we introduce the pangenome variability index (PVI), a frequency-aware sampling-independent measure that captures gene presence-absence variability across microbial genomes. Unlike the openness coefficient (α) or genomic fluidity, PVI exhibits a unimodal response across the core genome continuum and peaks in intermediate regimes, reflecting maximal compositional heterogeneity. We validate PVI across simulated pangenomes ranging from fully open to fully closed states and show that it captures dimensions of gene content structure orthogonal to conventional measures. Unlike classical measures that saturate in transitional regimes, PVI retains discriminative power and offers a robust, interpretable summary of genomic variability. We recommend integrating PVI into pangenome analysis pipelines as a complementary measure to guide comparative analyses, especially in studies targeting transitional genome architectures and genome evolution in dynamic environments. Future directions include extending PVI to strain-resolved metagenomics, functional annotation layers, and longitudinal analyses of microbial communities.