Characterization of syntons across bacterial genomes using non-redundant genomic contexts

Abstract Bacterial genomes are dynamic, shaped by gene gain, loss, and horizontal transfer; yet selection preserves the colocalization of functionally coupled genes into recurrent modules known as syntons. Many large-scale approaches do not explicitly account for phylogenetic relatedness between genomes which can inflate support for associations that are simply shared by close relatives. To address this, we introduce a scalable framework that clusters gene-family occurrences by genomic neighborhood and counts co-occurrences across distinct genomic contexts, reducing redundancy from vertical inheritance and uneven database sampling without explicit phylogenetic reconstruction. Applied to 32 791 RefSeq genomes comprising 123 million genes, this approach identifies 15 million syntons across 779 000 synton families, characterizing their diversity and revealing structured associations among antiphage defense systems. Leveraging this context-aware framework, we also introduce Context Residual Entropy (CRE) to quantify gene families neighborhood variability. By prioritizing independent evolutionary events over redundant genome-level counts, our approach provides a scalable, phylogenetic tree-free view of modular organization across bacterial genomes.