Molecular Networks Underlying the Phytochrome A Mediated Red Light Response in Tomato

Plants interpret 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 have different specific roles in tomato development and environmental response. To identify the specific role of canonical far-red light responsive PHYA in response to red light, we performed RNA-seq and proteomic analyses on phya mutant and wild-type seedlings grown in the dark or exposed to red light for 60 minutes. Here we support previous findings that gene and protein expression data do not clearly correlate, though the differentially expressed genes and proteins do share enriched functional categories. Both data sets also show that PHYA plays a role in the development of dark grown seedlings, not just those exposed to light. We also present gene co-expression networks derived from the RNA-seq data and GO category enrichment analysis of these networks. These results confirm known roles of phytochromes in the red light response as well as form unexpected links to roles in metabolism, respiration, and post-translational protein regulation.