The genomic origins of cyanobacterial morphological diversity.

Cyanobacteria are the only prokaryotes to have evolved oxygenic photosynthesis, transforming the geochemistry and biology of the planet. They exhibit remarkable morphological diversity and represent one of the earliest known multicellular organisms, including filamentous growth and cellular differentiation. However, the genomic mechanisms underlying their repeated transitions between unicellularity and multicellularity remain unresolved. Here, we implement phylogenomic and Bayesian molecular clock analyses, estimate ancestral protein-coding gene contents, and examine gene gains and losses associated with major morphological transitions across their phylogeny. Our analyses reveal a dynamic evolutionary history characterized by independent gains and losses of multicellularity-associated traits. Convergent evolution plays a crucial role in the repeated emergence of similar gene functions, particularly within pathways related to signal transduction, cell division, and transcriptional control. Filamentous lineages consistently preserve genes that support cellular coordination and structural integration, while reversions to unicellularity often involve losing genes linked to motility, regulatory complexity, and cytoskeletal organization. Notably, many lost genes trace back to deep ancestral innovations, suggesting that reductions in complexity often reverse previous genomic acquisitions. Together, these findings highlight the modular and reversible nature of cyanobacterial morphological evolution and illustrate how functional convergence affects genome architecture during significant phenotypic transitions.