Widespread genomic islands are hotspots of genome variations and mosaicism in giant viruses.

Giant viruses in the phylum Nucleocytoviricota possess exceptionally large and mosaic genomes, yet the mechanisms underlying their remarkable plasticity remain poorly understood. Genomic islands are dynamic genomic regions that are major drivers of diversification and adaptation in bacteria. However, their contribution to giant virus evolution remains largely unexplored. Here, we characterize the genomic island landscape of giant viruses using 369 high-quality genomes spanning cultured isolates and long-read metagenome-assembled genomes. We identify 307 genomic islands across >50% of the genomes, demonstrating that these regions are pervasive across Nucleocytoviricota. These genomic islands are frequently associated with genomic hypervariability and enriched in genes involved in host interaction, particularly surface adhesion proteins, suggesting roles in host adaptation during the virus-host arms race. Comparative analyses further reveal these islands as hotspots of genome diversification, exhibiting frequent gain/loss and rearrangement even among highly similar genomes. Notably, many genomic islands are enriched in bacterial homologs, and several exhibit striking synteny with genomic regions recovered from co-occurring bacterial genomes, supporting large-scale genetic exchange between bacteria and giant viruses. Together, these findings identify genomic islands as pervasive and dynamic drivers of giant virus genome evolution, providing a framework for genome plasticity, mosaicism, and adaptive potential of giant viruses.