Photosynthesis is central to plant carbon acquisition, but the typical C3 pathway is inhibited by abiotic stresses such as water limitation. Crassulacean acid metabolism (CAM) is a form of photosynthesis that increases the plant’s water use efficiency. CAM exists across a spectrum in many lineages, including in the genus Yucca; some species, such as Y. filamentosa, are strictly C3, whereas others, such as Y. aloifolia, use mainly the CAM pathway, and others use CAM only under certain conditions (“facultative CAM” or “C3+CAM”). One such species is Y. gloriosa, a homoploid hybrid of CAM Y. aloifolia and C3 Y. filamentosa, which exhibits intraspecific variation in the degree of facultative CAM under drought.

The combination of homoploidy and unique CAM biology makes Y. gloriosa an excellent system for the study of both CAM evolution and homoploid speciation. To this end, a 24-hour timecourse RNA-seq dataset was collected for a controlled drought experiment run on both parent species and 26 naturally occurring genotypes of Y. gloriosa. These data were leveraged to understand both the expression variability arising from homoploid hybridization and that underlying intraspecific CAM variation in this species. We found that key CAM gene families were impacted by hybridization and show time-structured gene expression.