Abstract
BACKGROUND: The APETALA2/ETHYLENE-RESPONSIVE FACTOR (AP2/ERF) transcription factor family plays a crucial role in plant development and stress responses. Characterized by the conserved AP2 DNA-binding domain, this family includes key subfamilies such as ERF, AP2, and RAV. Understanding the composition and evolutionary dynamics of the AP2/ERF family in coffee is essential for advancing the development of stress-resilient cultivars. Leveraging recent genomic resources for Coffea canephora (robusta coffee), Coffea arabica, and Coffea eugenioides, this study aims to provide a comprehensive genome-wide characterization and evolutionary analysis of the AP2/ERF family within these economically important species. RESULTS: A total of 453 AP2/ERF genes were identified across the three Coffea species, constituting approximately 0.48% of their protein-coding genes. Chromosomal mapping and synteny analysis revealed a high degree of conservation among C. canephora, C. arabica, and C. eugenioides, reflecting their close evolutionary relationships. Gene duplication events were found to significantly contribute to the expansion of the AP2/ERF family, accounting for 16% of the total gene count. Subgroup IX, associated with disease resistance, exhibited substantial variation between the two parental species and their descendant subgenomes in C. arabica, indicating possible lineage-specific gene loss or expansion. Similarly, Subgroup III, linked to temperature tolerance, showed distinct expansion patterns among the coffee species, hinting at adaptive responses to varied environments. CONCLUSIONS: These comparative analyses of the AP2/ERF transcription factor family in Coffea species provide valuable insights into the adaptive evolution of this gene family under diverse environmental stresses. The observed subgroup-specific variations provide a basis for further functional studies and underscore potential candidates for breeding programs aimed at enhancing stress resilience and sustainability in coffee production. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-025-11850-0.