Comprehensive transposon-insertion profiling unravels the asexual breeding history of sweet orange cultivars.

Sweet orange has one of the largest cultivar groups in Citrus, characterized by diverse horticultural traits developed through the selection of bud sports (somatic mutants). However, the role of transposable-element activity in its diversification is largely unknown. Here, we comprehensively surveyed transposon activity in sweet orange genomes and identified six transposon families whose activity is increased up to 8974.2-fold in modern cultivars. These insertions serve as mutational markers, enabling the tagging of major sweet orange cultivar groups and distinguishing over 99% of sweet orange accessions. Moreover, they are significantly enriched in genes that affect plant development and hormone signaling. The widespread insertions of these hyperactive transposons enabled us to trace the lineage history of nearly all sweet orange cultivars, dating them to a common ancestor ∼500 years ago, and to infer three major dispersal events. The activation of these transposons has resulted in significantly higher transposon activity in sweet orange compared to its parental species, revealing their unrecognized and crucial role in sweet orange breeding.