Stable and dynamic gene expression patterns over diurnal and developmental timescales in <i>Arabidopsis thaliana</i>

Developmental processes are known to be circadian-regulated in plants. For instance, the circadian clock regulates genes involved in the photoperiodic flowering pathway and the initiation of leaf senescence. Furthermore, signals that entrain the circadian clock, such as energy availability, are known to vary in strength over plant development. However, diel oscillations of the Arabidopsis transcriptome have typically been measured in seedlings. We collected RNA sequencing (RNA-seq) data from Arabidopsis leaves over developmental and diel timescales, concurrently: every 4 h d^-1, on three separate days after a synchronised vegetative-to-reproductive transition. Gene expression varied more over the developmental timescale than on the diel timescale, including genes related to a key energy sensor: the sucrose nonfermenting-1-related protein kinase complex. Moreover, regulatory targets of core clock genes displayed changes in rhythmicity and amplitude of expression over development. Cell-type-specific expression showed diel patterns that varied in amplitude, but not phase, over development. Some previously identified reverse transcription quantitative polymerase chain reaction housekeeping genes display undesirable levels of variation over both timescales. We identify which common reverse transcription quantitative polymerase chain reaction housekeeping genes are most stable across developmental and diel timescales. In summary, we establish the patterns of circadian transcriptional regulation over plant development, demonstrating how diel patterns of expression change over developmental timescales.