Genomic resequencing unravels species differentiation and polyploid origins in the aquatic plant genus Trapa

SUMMARY Trapa L. is a non‐cereal aquatic crop with significant economic and ecological value. However, debates over its classification have caused uncertainties in species differentiation and the mechanisms of polyploid speciation. This study employed whole‐genome resequencing together with the fruit morphology of 229 Trapa accessions (153 Asian and 76 North American samples) to elucidate species differentiation and polyploidization events in Trapa . For the species with AA genome and large fruits, clear genetic differentiation was found between two clades with different geographic origins, that is, from the Yangtze River and Amur River basins. The invasive AA species in North America ( T. natans ) was identified as originating from the Amur River based on genetic and morphological similarities, while all the cultivated accessions were AA species originating from the Yangtze River with severe genetic impoverishment. The separation of the two BB species with small seeds, that is, T. incisa and T. maximowiczii , was strongly supported by both morphological and genetic evidence. For the tetraploids, Asian and North American tetraploids were revealed to have distinct evolutionary origins. Asian allotetraploids (AABB) originated through hybridization between AA diploids from the Yangtze River Basin and BB diploids T. maximowiczii , supported by nuclear and chloroplast evidence. In contrast, the invasive North American tetraploids ( T. bispinosa var. iinumai ) exhibited an AACC‐like genome, suggesting an independent polyploidization involving an unknown “CC” diploid. These findings provide critical insights into Trapa 's complex evolutionary history, polyploidizations, and invasive origins, offering a genomic foundation for the conservation and sustainable utilization of the underutilized aquatic crop amid global environmental challenges.