Insertions of transposable elements in the S-haplotype-specific F-box gene were shown many times to confer self-compatibility in Prunus species. In apricot, we identified a miniature inverted repeat transposable element (MITE) with structural features (its 349-bp size, 82-bp terminal inverted repeats and 9-bp target site duplications) that are consistent with this MITE being a putative member of the Mutator-like transposase superfamily. This non-autonomous element was labelled as FaSt (Falling Stones). FaSt showed a preferential accumulation in short AT-rich segments within euchromatin regions of the peach genome. A bioinformatics based survey of the known Rosaceae and other genomes and a newly designed PCR-assay verified the Prunoideae-specific occurrence of FaSt elements. In addition, FaSt copies in diploid apricot and hexaploid plum showed considerable sequence variations. Several copies were found in promoter regions and introns of certain genes. This is the first study to report on a presumably active MITE in the Prunus genus that might have exhibited direct and indirect genome shaping forces. FaSts and other transposable elements are compared in their contribution to the breakdown of self-incompatibility in Prunus species.
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