Differential response of AP2/ERF genes under hormone and light in Coptis chinensis

Background The AP2/ERF transcription factor family is crucial for regulating plant growth, development, and responses to environmental stimuli. However, the genomic characterization and functional dynamics of this family in the medicinal plant Coptis chinensis remain largely unexplored. Results A total of 125 CchAP2/ERF genes were identified in the C. chinensis genome and classified into four subfamilies: AP2 (25), ERF (94), RAV (4), and Soloist (2). Chromosomal localization and synteny analyses indicated that the expansion of the CchAP2/ERF family was primarily driven by whole-genome and segmental duplications. Significant divergence in the cis-acting elements of duplicated gene pairs suggested functional neofunctionalization or subfunctionalization. Gene structure analysis revealed lower intron polymorphism in the ERF and RAV subfamilies compared to the AP2 and Soloist subfamilies, implying a potential capacity for rapid transcriptional activation. Expression profiling demonstrated distinct spatial and temporal patterns, with specific genes exhibiting tissue-specific (e.g., CchERF02 in roots, CchERF03 in leaves) and age-dependent (e.g., CchERF50 and CchERF53 ) regulation. Furthermore, qRT-PCR analyses under hormone and light treatments identified CchERF45 as a central regulatory hub, exhibiting remarkable induction by abscisic acid (peaking at 5 µmol), methyl jasmonate, red light, a 12 h/12 h photoperiod, and moderate light intensity (2K Lux). Conversely, CchERF14 was significantly suppressed by both ABA and MeJA, implicating it as a potential negative regulator in hormone signaling crosstalk. Conclusion This study comprehensively elucidates the evolutionary divergence and expression dynamics of the CchAP2/ERF family in C. chinensis . The identification of key transcription factors, particularly CchERF45 and CchERF14 , provides crucial genetic targets for understanding hormone and light signaling networks, offering valuable genetic resources for the molecular breeding and targeted cultivation of C. chinensis .