An Evolutionary Perspective on the Role of Paleopolyploidy and the Specialization of the Circadian Clock in Plants

A recent examination of the Brassica rapa (B. rapa) genome revealed that following triplication and fractionation, circadian clock genes have been retained at a significantly higher rate than comparison groups of neighboring genes. This finding has led to the speculation that whole genome duplication events followed by retention of dose-sensitive circadian clock genes has provided the tools for the evolution of increasingly complex circadian clock mechanisms, consistent with the current models of clock architecture in the Green Lineage. To examine this further, we are performing a comparative analysis of the circadian clock in the well-characterized model plant Arabidopsis thaliana, the mesopolyploid B. rapa and Cleome violacea, a member of the Cleomaceae (the sister family to the Brassicaceae). Cleome is independent of the most recent Brassicaceae whole genome duplication, referred to as the alpha (At-α) event, making it a valuable tool for studying the effects of paleopolyploidy on the circadian clock.  We have developed an automated high throughput motion estimation system to measure circadian parameters by leaf movement that enables us to image large populations of plants from a variety of species. To analyze circadian period, we apply a Fourier-based analysis to the estimated motion signal. Using this new method along with RNAseq and quantitative RT-PCR we are examining the role of the circadian clock in regulating various stress responses in these three plant species in order to gain new insight into the diversification and specialization of the clock in plants.