Transcriptome and genome analysis of carbon fixation pathway in land plants: implications for origin and mechanism of CAM in orchids raw sequence reads

CAM plants have a CO2 fixation pathway that maximizes water use efficiency (WUE) when compared to C3 metabolism plants. CAM plants are able to fixate CO2 both in the dark and light, providing an excellent opportunity to produce crops with enhanced photosynthetic performance and low WUE that could be useful as bioenergy crops via genetic engineering. We have annotated and analyzed the genome and transcriptomes of 13 orchids covering CAM and C3 metabolism plants, with emphasis on comparing the 13 gene families involved in carbon fixation pathway. We show that dosage of core photosynthesis-related genes play no substantial roles in evolution of CAM in orchids. However, in orchids CAM pathway may be primarily regulated by changes at the transcription levels of some key genes. We first propose that in both conditions; dark and light, CO2 is primarily fixed/released through two metabolic pathways via regulating known genes, such as PPC1, PPDK and PPCK, respectively. This study is the first comprehensive comparison of carbon fixation pathway genes across different photosynthetic plants, and reveals the importance of controlling gene expression levels to explain the origin and evolution of CAM.