Comparative Genomics of CAM Species

Improved crop water-use efficiency (WUE) is critical for the long-term sustainability of agricultural production systems in the face of predicted future warmer and drier climates. Crassulacean acid metabolism (CAM) is a specialized mode of photosynthesis that enhances WUE through an inverse day/night pattern of stomatal closure/opening and improves photosynthetic efficiency by concentrating CO₂ around RUBISCO. CAM has evolved multiple times from C₃ photosynthesis and ~6.5% of higher plant species in more than 35 families have acquired CAM via parallel or convergent evolution. There are two fundamental questions to be answered to understand the molecular basis and evolutionary mechanism of CAM: 1) what are the genetic differences between CAM and non-CAM species and 2) what are the common molecular features shared among CAM plants from diverse origins? To address these questions, comparative genomics analysis was performed using multiple plant species including CAM (e.g., Agave, Kalanchoe, Mesembryanthemum), C₃ (e.g., Arabidopsis, Oryza, Populus), C₄ (e.g., Setaria, Sorghum, and Zea), and non-vascular plant species (e.g., Physcomitrella, Selaginella). Our analysis not only revealed orthologous gene groups shared between CAM and non-CAM species, but also identified genes specific to the CAM species. Also, expanded gene families were identified in CAM species compared with non-CAM species. Gene ontology and gene expression profiles were used to build hypothesis related to divergent gene functions that likely arose during CAM evolution. This research establishes a framework for CAM comparative genomics studies and provides new knowledge to inform genetic improvement in WUE and photosynthetic efficiency in crop plants under water-limiting conditions.