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Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Developing gene regulatory network models is a major challenge in systems biology. Several computational tools and pipelines have been developed to tackle ...

Duke University

Crassulacean acid metabolism (CAM) improves photosynthetic efficiency under limited water availability relative to C photosynthesis. It is widely accepted that CAM plants have evolved from C plants and it is hypothesized that CAM is under the control of the internal circadian clock. However, the role that the circadian clock plays in the evolution of CAM is not well understood. To identify the molecular basis of circadian control over CAM evolution, rhythmic gene sets were identified in a CAM model plant species () and a C model plant species () through analysis of diel time-course gene expression data using multiple periodicity detection algorithms. Based on protein sequences, ortholog groups were constructed containing genes from each of these two species. The ortholog groups were categorized into five gene sets based on conservation and diversification of rhythmic gene expression. Interestingly, minimal functional overlap was observed when comparing the rhythmic gene sets of each species. Specifcally, metabolic processes were enriched in the gene set under circadian control in  and numerous genes were found to have retained or gained rhythmic expression in . Additonally, several rhythmic orthologs, including CAM-related orthologs, displayed phase shifts between species. Results of this analysis point to several mechanisms by which the circadian clock plays a role in the evolution of CAM. These genes provide a set of testable hypotheses for future experiments.

Conservation and Diversification of Circadian Rhythmicity Between a Model Crassulacean Acid Metabolism Plant  and a Model C Photosynthesis Plant .

CO uptake and water loss in plants are regulated by microscopic pores on the surface of leaves, called stomata. This enablement of gas exchange by the opening and closing of stomata is one of the most essential processes in plant photosynthesis and transpiration, affecting water-use efficiency (WUE) and thus drought susceptibility. In plant species with crassulacean acid metabolism (CAM) photosynthesis, diel stomatal movement pattern is inverted relative to C and C photosynthesis species, resulting in much higher WUE and drought tolerance. However, little is known about the molecular basis of stomatal movement in CAM species. The goal of this study is to identify candidate genes that could play a role in stomatal movement in an obligate CAM species,  By way of a text-mining approach, proteins were identified in various plant species, spanning C, C, and CAM photosynthetic types, which are orthologous to proteins known to be involved in stomatal movement. A comparative analysis of diel time-course gene expression data was performed between  and two C species (i.e.,  and ) to identify differential gene expression between the dusk and dawn phases of the 24-h cycle. A rescheduled catalase gene known to be involved in stomatal movement was identified, suggesting a role for HO in CAM-like stomatal movement. Overall, these results provide new insights into the molecular regulation of stomatal movement in CAM plants, facilitating genetic improvement of drought resistance in agricultural crops through manipulation of stomata-related genes.

Comparative Genomics Analysis Provides New Insight Into Molecular Basis of Stomatal Movement in .

The circadian clock drives time-specific gene expression, enabling biological processes to be temporally controlled. Plants that conduct crassulacean acid metabolism (CAM) photosynthesis represent an interesting case of circadian regulation of gene expression as stomatal movement is temporally inverted relative to stomatal movement in C3 plants. The mechanisms behind how the circadian clock enabled physiological differences at the molecular level is not well understood. Recently, the rescheduling of gene expression was reported as a mechanism to explain how CAM evolved from C3. Therefore, we investigated whether core circadian clock genes in CAM plants were re-phased during evolution, or whether networks of phase-specific genes were simply re-wired to different core clock genes. We identified candidate core clock genes based on gene expression features and then applied the Local Edge Machine (LEM) algorithm to infer regulatory relationships between this new set of core candidates and known core clock genes in . We further inferred stomata-related gene targets for known and candidate core clock genes and constructed a gene regulatory network for core clock and stomata-related genes. Our results provide new insight into the mechanism of circadian control of CAM-related genes in , facilitating the engineering of CAM machinery into non-CAM plants for sustainable crop production in water-limited environments.

Robert C. Moseley

Department of Biology

Duke University

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline