Stones in genomic storms: transposable element-driven variation in Prunus fruit trees

Transposable elements (TEs) are major components of plant genomes and drivers of structural and functional diversification. In Prunus species, including peach, almond, apricot, cherry, and plum, TEs constitute more than half of the genome and shape evolutionary trajectories and phenotypic traits. This review synthesizes knowledge on TE composition, evolutionary dynamics and functional impacts in Prunus, highlighting advances enabled by long-read sequencing and structure-aware annotation pipelines. Both class I retrotransposons and class II DNA transposons contribute to genome expansion, gene duplication, regulatory innovation, and lineage-specific evolutionary shifts. TE insertions influence traits such as flowering time, fruit firmness, pigmentation, and the breakdown of self-incompatibility through mechanisms including promoter modulation, methylation changes, and exon disruption. We examine TE-derived small RNAs in epigenetic regulation and summarize evidence for recent TE bursts linked to hybridization, demographic bottlenecks, polyploidization, and local adaptation, collectively contributing to the diversification of Prunus genomes. Beyond their biological roles, TE insertion polymorphisms serve as powerful molecular markers for diversity assessment, phylogenetics, and breeding with both retrotransposon- and MITE-based systems showing high discriminatory power across Prunus germplasm. Integration of high-resolution TE mapping with functional genomics and epigenetic profiling promises deeper understanding of TE-mediated regulatory networks and their potential exploitation for crop improvement.