Phytochrome evolution in green and nongreen plants

Photoreceptors are critical molecules that function at the interface between organism and environment. Plants use specific light signals to determine their place in time and space, allowing them to synchronize their growth, metabolism, and development to the environments in which they occur. Thus, innovation in light sensing mechanisms is expected to coincide with adaptation and diversification. Three studies involving the well-characterized phytochrome photoreceptor system in plants indicate that much work is yet needed to test this expectation. In early diverging flowering plants, episodic positive selection influenced the evolution of phytochrome A, but little of the functional data needed to link molecular adaptation with a change in gene function are available. In the model plant Arabidopsis thaliana, known functional differences between a recently duplicated gene pair remain difficult to characterize at the sequence level. In parasitic plants, patterns of development that in autotrophs are under the control of light signals are highly modified, suggesting that phytochromes and other photoreceptors function differently in nonphotosynthetic plants. Analyses of phytochrome A coding sequences indicate that they are evolving under relaxed constraints in nonphotosynthetic Orobanchaceae, consistent with the expectation of functional change. Further work is needed to determine which of the processes mediated by phyA may have been altered, a line of investigation that may improve our understanding of divergence points in downstream signaling pathways.