Predicting the Capsid Architecture of Florendoviruses: Molecular Fossils of Ancient Caulimovirid-like Viruses

Endogenous viral elements derived from members of the family Caulimoviridae are widely distributed across plant genomes. Once integrated, they accumulate extensive mutations; most are no longer biologically active and can therefore be regarded as molecular fossils. Their loss of activity precludes the recovery of viral particles, thereby preventing direct experimental characterization of their capsid architecture. Here, we combined sequence-based phylogenetic analyses with artificial-intelligence-assisted protein structure prediction to investigate the coat proteins of florendoviruses, the most abundant endogenous caulimovirid lineage. Phylogenetic analysis placed florendovirus coat proteins in close proximity to those of the genus Petuvirus. The structural prediction of the coat protein is limited by the presence of an intrinsically disordered N-terminal region, whose structure cannot be reliably predicted. In contrast, the central capsid domain yields robust predictions, revealing similarity not only to caulimovirus coat proteins but also to retrotransposon Gag proteins. Structural comparisons indicate that the florendovirus coat domain is most closely related to those of Petuvirus. Because petuviruses assemble into isometric particles, our data support the hypothesis that the ancestral episomal forms of florendoviruses possessed a similar capsid organization. Our findings extend the study of ancient viruses whose morphology cannot be directly investigated using conventional phylogenetic and AI-assisted structure prediction methods.