Raw sequencing data of Physalis floridana P106

The fruits of Physalis (Solanaceae) feature a unique fruit structure, the lantern-like fruiting calyx known as the inflated calyx syndrome (ICS) or Chinese lantern, and are rich in steroid-related compounds. However, the genetic variations underlying the origin of these characteristic traits and diversity in Physalis remain largely unknown. Here, through evolutionary genomics and experimental approaches, we found that the loss of the SEP-like MADS-box gene MBP21 subclade is another key mutation that, together with the well-known mutation of floral MPF2 expression, contributed to the origin of the ICS in the Physaleae, hence suggesting that the origin of a morphological novelty may have resulted from an evolutionary scenario in which one mutation compensated for another deleterious mutation. Moreover, significant expansion of squalene epoxidase genes is associated with natural variation of steroid-related compounds in Physalis fruits. This study provides new insights into the origin of the Chinese lantern and the natural variation in steroid-related compounds. The results reveal the importance of gene gain (duplication) and / or subsequent loss as genetic bases for the evolution of distinct fruit traits, and the data serve as a valuable resource for evolutionary genetics and the breeding of solanaceous crops.