The hexaploid sweetpotato is one of the most important root crops worldwide. However, its genetic origins remain controversial. In this study, we identified two likely progenitors of sweetpotato by analyzing the horizontally transferred IbT-DNA and a haplotype-based phylogenetic analysis. The diploid form of I. aequatoriensis contributed the B1 subgenome, the IbT-DNA2 and the lineage 2 type of the chloroplast genome to sweetpotato. The tetraploid progenitor of sweetpotato is I. batatas 4x, donating the B2 subgenome, IbT-DNA1 and the lineage 1 type of chloroplast genome. Sweetpotato is derived from reciprocal crosses between the diploid and the tetraploid progenitor, and a subsequent whole genome duplication. We also detected biased gene exchanges between subgenomes. The B1 to B2 subgenome conversions were almost 3-fold higher than the B2 to B1 subgenome conversions. This study sheds lights on the evolution of sweetpotato and paves the way for the improvement of the crop.
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