CRISPR–Cas diversity in Microcoleus genomes reveals a dynamic history of gene flow and mobile genetic element interactions

Background The filamentous cyanobacterial genus Microcoleus is globally distributed and plays an important role in biological soil crusts. CRISPR–Cas immunity is a prokaryotic defense mechanism that mediates interactions with mobile genetic elements, and may thereby contribute to genome evolution. Yet, its diversity and evolutionary significance in cyanobacteria remain poorly understood. Here, we integrate CRISPR–Cas locus identification, phylogenetic analyses, genome and environmental association analyses and spacer target search to examine CRISPR–Cas diversity and evolution across 14 Microcoleus species. Results We found that CRISPR–Cas systems are widespread in Microcoleus genus, but their distribution does not follow species-level phylogeny. Instead, locus heterogeneity and module-specific evolutionary histories indicate repeated gain, loss and exchange of CRISPR–Cas components, suggesting that gene flow has contributed to their diversification. CRISPR spacer composition and sharing patterns further indicate dynamic exposure to mobile genetic elements, potentially linked to environmental context. Although a large proportion of spacer targets remain unidentified, expanded protospacer searches revealed plasmid-like elements as prominent targets among the identifiable sequences. Conclusion Together, our results suggest that CRISPR–Cas systems in Microcoleus are highly dynamic and reflect interactions between gene flow, mobile genetic elements and environmental context, highlighting their potential role as variable components of cyanobacterial genome evolution.