High-throughput transcriptomic analysis of circadian rhythm of flavonoid metabolism under different photoperiods in celery

Photoperiod is important for plants to predict the changing trend of the environment and adjust their physiological, metabolic rhythm. In this study, we investigated the transcriptional responses of celery (<italic>Apium graveolens</italic> L.), an important leaf vegetable whose physiological cycles were photoperiod-dependent, under two different light regimes for 24 h: truncated photoperiod (light/dark: 6 h/6 h, recorded as T) and full periodic illumination (light/dark: 24 h/0 h, recorded as F). Samples were collected continuously for high-throughput transcriptome sequencing and differentially expressed genes (DEGs) were annotated and analyzed. Compared with the treatment beginning, 4,466~7,398 DEGs were identified in each sample, with the largest number between T0h vs T12h. For comparison between T24h and F24h, the number of DEGs was the lowest (3,056). GO annotation showed that DEGs were mainly enriched in biological processes and cell composition. KEGG enrichment pathway analysis showed that the DEGs were mainly concentrated in the secondary metabolism-related pathways (lysine, phenylalanine, and flavonoids). Compared to truncated photoperiod, full periodic illumination for 24 h enhanced the expression of flavonoid biosynthetic genes (particularly <italic>AgCHS</italic>, <italic>AgFNS</italic>, and <italic>AgF3'H</italic>) and increased flavonoid accumulation. Our results demonstrated that the transcriptional rhythms of celery were dynamically regulated by both light-dark cycles and circadian clock mechanisms, with flavonoid pathway genes exhibiting particular sensitivity to photoperiodic changes. These findings provide important insights into the molecular mechanisms underlying plant photoperiod responses and may serve as a valuable foundation for future research on the circadian regulation of plant metabolism and development.