A comprehensive comparative genomic analysis of the endogenous Florendovirus-1 in Prunus

Endogenous caulimovirid elements (ECVs) are widespread components of plant genomes and provide valuable information on the long-term evolution of plant viruses and their hosts. However, the mechanisms underlying their integration and subsequent genomic reorganization remain poorly understood. Here, we investigated the diversity, distribution, and structural organization of ECVs in 30 chromosome-level genome assemblies representing 15 species of the genus Prunus. A genome-wide search based on conserved reverse transcriptase (RT) domains identified 781 caulimovirid sequences, which were classified into 18 clusters belonging to the operational taxonomic units Florendovirus and Yendovirus. Florendovirus-1 (Flo-1) was the predominant lineage, accounting for 532 sequences and 68% of all RT sequences detected. To characterize this lineage in detail, we reconstructed a 7,193-bp Flo-1 consensus sequence from seven complete elements identified in a high-quality almond genome assembly. The reconstructed Flo-1 genome contained two open reading frames and the canonical caulimovirid movement protein, coat protein, aspartic protease, reverse transcriptase, and RNase H domains. A detailed nucleotide-level search identified 757 Flo-1-derived fragments in P. dulcis genome spanning 0.91 Mb, corresponding to 0.37% of the almond genome. These fragments were organized into 176 loci, of which 36% contained multiple insertions comprising complete or fragmented elements in different orientations. The inferred endogenization breakpoints of 77% of complete elements were located near the Met-tRNA binding site. Consistently, few fragments spanned this region, whereas fragment termini showed a pronounced enrichment around it, suggesting preferential viral genome linearization at or near this position. Phylogenetic analysis of RT-coding sequences within multiple-insertion loci revealed both closely related and divergent elements. These findings indicate that the present-day organization of Flo-1 loci cannot be explained by a single process and probably reflects the combined effects of concatemer integration, recurrent insertion, local duplication, recombination, fragmentation, and post-integration rearrangement. Overall, this study reveals the extensive contribution and complex evolutionary history of endogenous florendoviruses in Prunus genomes.