Genome evolution of Mediterranean olives following DNA repeats diversification.

The olive tree (Olea europaea L. subsp. europaea) is one of the most representative perennial crops of the Mediterranean Basin, yet the genomic processes underlying its domestication and diversification remain poorly understood. Here, we investigated repeatome variation across 20 accessions, including 11 wild oleasters and nine cultivated varieties, using comparative clustering of high-throughput sequencing data, complemented by structural analyses of transposable elements (TEs) and tandem repeats (TRs). Repetitive DNA accounts for about 54% of the olive genomes and is composed primarily of long terminal repeat retrotransposons (LTR-REs) and TRs. Comparative analyses revealed lineage-specific differences in LTR-REs between wild and cultivated genotypes, while TRs exhibited higher abundances and greater variability in oleasters for some families (e.g., Oe-80 and Oe-178), reinforcing the view that TRs evolve rapidly and largely independently in olive. We also identified a new TR (Oe-155) and confirmed its distinct monomer sequence and chromosomal organization, suggesting that this subfamily is differentiating from TRs Oe-218 and Oe-80. To refine TE dynamics, we surveyed full-length elements in two reference assemblies (cv. Leccino and a wild sylvestris genotype). Leccino is enriched in intact LTR-REs, whereas sylvestris harbored more full-length Class II DNA transposons. Additionally, the patterns of TE-gene proximity vary significantly between them. Dating of full-length LTR-RE insertions revealed that most RE activity predates domestication, with only a small fraction of very recent insertions. These results highlight repetitive DNA as a major contributor to genome diversification in olive and provide a foundation for integrating repeatome variation with demographic history, introgression, and clonal propagation.