Comprehensive Analysis of the AP2/ERF Superfamily Identifies Key Genes Related to Various Stress Responses in Olive Tree (Olea europaea L.)

The AP2/ERF superfamily is a key class of transcription factors involved in plant responses to various stresses. As an ancient species, the olive tree (<i>Olea europaea</i> L.) exhibits considerable stress tolerance and wide adaptability. In this study, we identified 348 AP2/ERF genes in the cultivated olive variety 'Arbequina' at the whole-genome level. According to protein sequence alignments and phylogenetic analyses via the Maximum Likelihood method, these genes were classified into four major families: AP2, ERF/DREB, RAV, and Soloist. The ERF/DREB family was further divided into DREB and ERF subfamilies, each encompassing six groups (A1-A6 and B1-B6), with the ERF subfamily being the largest. Members of each group exhibited relatively consistent gene structures and domain/motif compositions of their encoded proteins; however, the distribution of <i>cis</i>-elements and expression patterns varied. Each AP2/ERF gene contained 12 light-responsive, three MeJA-responsive, three ABA-responsive, two anaerobic induction, and one MYB binding site on average. With the threshold of <i>p</i> value < 0.5, control TPM > 0, and |log₂(fold change)| > 0, 50 candidate genes were simultaneously up-regulated (30) or down-regulated (20) under four stress treatments (acid-aluminum, cold, disease, and wound), among which nine showed potential protein-protein interactions. This study provides a comprehensive genomic characterization of the AP2/ERF family in olive and identifies key candidate stress-responsive genes, establishing a foundation for future functional studies on the molecular mechanisms of stress adaptation in the olive tree.