Genome-wide identification of the AP2/ERF gene family in Rosa persica and expression profiling under abiotic stresses

Abstract Background Rosa persica, the sole species in the subgenus Hulthemia of Rosaceae, thrives in the barren Gobi Desert, where its harsh environment has driven the evolution of exceptional stress-resistant traits, making it a valuable germplasm resource for studying extreme drought adaptation. With the recent completion of its telomere-to-telomere (T2T) genome assembly, an increasing number of stress-responsive gene families have been systematically characterized in R. persica. However, despite being one of the most critical transcription factor superfamilies involved in plant stress responses, the AP2/ERF superfamily has not yet been comprehensively identified or functionally analyzed in this extremophyte species, warranting in-depth investigation. Results Through comprehensive genome-wide analysis, we identified 114 AP2/ERF members in R. persica, which were classified into five subfamilies: AP2, DREB, ERF, RAV, and Soloist. The expression profiles of these AP2/ERF genes exhibited distinct tissue specificity. Notably, A005041.1, A008193.1, A013003.1, and A014479.1 were exclusively expressed in roots, while A001403.1 and A026890.1 showed stem-specific expression. Seven genes (A011282.1, A010347.1, A014504.1, A025658.1, A025595.1, A002755.1, and A024668.1) were simultaneously responsive to both drought and low temperature stress in R. persica. Among the ERF and DREB subfamilies, the abiotic stress-related genes A002909.1, A014504.1, A002755.1, A010645.1, and A009162.1 demonstrated transcriptional activation activity in yeast assays, whereas A005829.1 and A024668.1 lacked such activity. Conclusion This study provides the first systematic identification and characterization of the AP2/ERF gene family in R. persica, revealing key members involved in drought and cold stress responses. Our findings establish a theoretical foundation for elucidating the functional mechanisms of AP2/ERF genes in this extremophyte species and their roles in stress adaptation.