Lineage-specific expansions of polinton-like viruses in photosynthetic cryptophytes

Polinton-like viruses (PLVs) are diverse eukaryotic DNA viral elements (14-40 kbp) that often undergo significant expansion within protist genomes through repeated insertion events. Emerging evidence indicates they function as antiviral defense systems in protists, reducing the progeny yield of their infecting giant viruses (phylum Nucleocytoviricota) and influencing the population dynamics and evolution of both viruses and their hosts. Despite their increasing recovery from sequenced protists, PLVs from the abundant and ubiquitous Cryptophyte algae remained largely unexplored. To address this, we leveraged long-read sequencing to overcome challenges associated with high genomic repeat content and successfully recovered contiguous genomes from representative marine and freshwater cryptophytes. Hence, we uncovered over one thousand complete PLVs and generated one of the most comprehensive phylogenetic trees of major capsid proteins. By combining deep sequence homology annotation with biological network analyses, we discern well-defined PLV groups defined by characteristic gene-sharing patterns and the use of distinct strategies for replication and integration within host genomes. Ultimately, our findings provide a primer for understanding the evolutionary history, gene content and infection strategies of cryptophyte PLVs, with special emphasis on their expansion as endogenous viral elements (EVEs) in freshwater bloom-forming Rhodomonas lacustris.