The Molecular Role of Phytochrome a during Red Light-Mediated Development in Tomato

Plants sense light signals to respond to changes in their environments, such as those encountered by seedlings during de-etiolation. In Solanum lycopersicum, like in Arabidopsis thaliana, there are five phytochromes responsible for light sensing in the red and far-red spectrum. The genes encoding these five phytochromes have undergone different evolutionary paths from those in A. thaliana and likely each have different specific roles in tomato development and environmental response. To identify the specific roles of each of the five tomato phytochromes in response to red light, we performed RNA-seq analysis in phy single mutant seedlings and wild-type tomato seedlings grown in the dark or exposed to red light for 60 minutes. Here we present the results from RNA-seq analysis, GO category enrichment estimation, and co-expression network analysis of PHYA. Although PHYA is best known for its responsiveness to far red light, we find that it also mediates red light signaling and plays an unexpected role in stress responses and metabolism.