Arabidopsis thaliana Col-0 and phyQ under dark and red light

In Arabidopsis thaliana, light is one of the major environmental cues that triggers changes in splicing patterns. Two pathways have been proposed to mediate this response: one that depends on the action of sensory photoreceptors and another where a retrograde signal from the chloroplast travels to the cell nucleus and modulates splicing. The extent to which each pathway regulates splicing remains unknown.Phytochromes are red and far red light sensing photoreceptors that interact with several splicing factors. The Arabidopsis genome encodes for five phytochromes (PHYA-PHYE). Here, we used high-throughput RNA sequencing (RNA-seq) to evaluate the effect of a red light pulse on expression and alternative splicing in light grown wild type (WT) (Col-0) plants and quintuple phytochrome mutants (phyQ).