Short gene overlaps in bacterial genomes: evolutionary dynamics and functional associations

Authors

Sukhodolsky, A., Gelfand, M., Kaznadzey, A.

Abstract

Background Short overlaps of adjacent genes are widespread in bacterial genomes and have been proposed to contribute to coordinated gene expression through mechanisms such as translational coupling and ribosome re-initiation. However, their evolutionary dynamics and functional associations have been studied either in relatively small datasets or for individual taxonomic groups. Here, we performed a large-scale comparative analysis of bacterial gene overlaps to characterize their prevalence, structural diversity, evolutionary dynamics, and functional associations. We surveyed 3,998 representative bacterial genomes for short overlaps and analyzed a curated set of orthologous gene-pair clusters to reconstruct the evolutionary history of overlap gain and loss using ancestral-state inference. Results We confirmed that short overlaps are dominated by a small number of canonical configurations, while a substantial subset of orthologous clusters contained multiple overlap lengths or sequence motifs, indicating evolutionary flexibility. Reconstruction of ancestral states yielded repeated gains and losses of overlap within the same orthologous gene-pair lineages. Among clusters in which both states were sufficiently represented, we found no overall bias toward either overlap gain or loss. Finally, analyses of functional associations found no consistent enrichment of overlapping gene pairs among genes encoding interacting protein subunits, compared to closely spaced non-overlapping gene pairs. In contrast, metabolic linkage showed a modest positive association with overlap, although the magnitude of this association depended on the distance threshold used to define non-overlapping neighbors. Conclusions These results identify short bacterial gene overlaps as evolutionarily labile features of gene organization rather than strongly conserved genomic states and emphasize the importance of distinguishing overlap from close genomic proximity when considering their functional significance.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 13 Sep 2026.

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