Variation in Gene Expression and Regulation of CAM in Yucca (Asparagaceae)

Crassulacean acid metabolism (CAM) is a modification of the photosynthetic pathway that allows plants to successfully grow in water-limited environments. Using an emerging model system in the genus Yucca (Asparagaceae), with a single origin of CAM ~2-5 million years ago, we employ a comparative genomics approach to better understand transcriptional regulation of the CAM pathway. We experimentally drought stressed C₃ Y. filamentosa, CAM Y. aloifolia, and an intermediate C₃-CAM hybrid of the two, Y. gloriosa. We generated time series RNAseq data collected every four hours over a 24-hour period in well-watered and drought stressed samples. We performed polynomial regression analysis to distinguish genes exhibiting time-structured expression patterns from genes that did not have variation in expression across time. Genes that had time-structured expression were further clustered and compared across species. Canonical CAM pathway genes, genes involved in carbohydrate metabolism and degradation, and circadian clock regulators were identified within specific gene expression clusters. We found that the CAM and C₃-CAM species share expression patterns for key CAM genes, while CAM genes in the C₃ species exhibited much lower transcript abundances but had similar time-structured expression. Further analysis of carbohydrate metabolism genes revealed reciprocal and alternative expression patterns between CAM and C₃ species, possibly due to differences in their carbohydrate needs. Finally, analysis of co-expressed gene networks highlights the central role of circadian clock transcription factors in the CAM and C₃-CAM hybrid species, especially in clusters containing CAM genes, but no such role for clock genes was evident in the C₃ species.