Water caltrop (Trapa spp.) is a kind of typical orphan crop, which has been consciously collected and domesticated as early as the Neolithic period. During the Tang and Song Dynasties, after further artificial selection, more than 20 varieties, e.g. "Wuling," "Nanhuling," were cultivated.

With the development of genomic technologies, pangenome research has become an essential approach for comprehensively understanding the mechanisms underlying agronomic trait.

In October 2023, a research paper titled "Pangenome of water caltrop reveals structural variations and asymmetric subgenome divergence after allopolyploidization," was published in Horticulture Research by Dr. Yingxiong Qiu's research team from the Wuhan Botanical Garden, Chinese Academy of Sciences.

The annual herbaceous and aquatic genus Trapa L. (Lythraceae), has traditionally been divided into two species, i.e. T. natans L. with diploid (2n = 2x = 48, AA) and tetraploid (2n = 4x = 96, AABB) cytotypes, and diploid T. incisa Sieb. and Zucc. (2n = 2x = 48, BB). Cultivated water caltrop was derived from the diploid T. natans with larger fruit size.

In this study, the authors generated two chromosome-level genome assemblies of diploid T. natans and T. incisa. In conjunction with four previously published (sub)genomes of Trapa, a gene-based pangenome was constructed.

The results show that core, dispensable, and private gene clusters accounted for 48.05%, 28.92% and 23.03% of all gene clusters, respectively. To precisely identify the potential presence-absence variations (PAVs) that may contribute to reproductive isolation and phenotypic divergence between T. incisa and diploid T. natans, the authors also constructed a graph-based pangenome based on 211,598 non-redundant PAVs among the six (sub)genomes.