The Gynandropsis gynandra genome provides insights into whole-genome duplications and the evolution of C(4) photosynthesis in Cleomaceae

Gynandropsis gynandra (Cleomaceae) is a cosmopolitan leafy vegetable and medicinal plant, which has also been used as a model to study C(4) photosynthesis due to its evolutionary proximity to C(3) Arabidopsis (Arabidopsis thaliana). Here, we present the genome sequence of G. gynandra, anchored onto 17 main pseudomolecules with a total length of 740 Mb, an N50 of 42 Mb and 30,933 well-supported gene models. The G. gynandra genome and previously released genomes of C(3) relatives in the Cleomaceae and Brassicaceae make an excellent model for studying the role of genome evolution in the transition from C(3) to C(4) photosynthesis. Our analyses revealed that G. gynandra and its C(3) relative Tarenaya hassleriana shared a whole-genome duplication event (Gg-α), then an addition of a third genome (Th-α, +1×) took place in T. hassleriana but not in G. gynandra. Analysis of syntenic copy number of C(4) photosynthesis-related gene families indicates that G. gynandra generally retained more duplicated copies of these genes than C(3)T. hassleriana, and also that the G. gynandra C(4) genes might have been under positive selection pressure. Both whole-genome and single-gene duplication were found to contribute to the expansion of the aforementioned gene families in G. gynandra. Collectively, this study enhances our understanding of the polyploidy history, gene duplication and retention, as well as their impact on the evolution of C(4) photosynthesis in Cleomaceae.