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

TL;DR

This study identifies 348 AP2/ERF genes in olive trees and finds key genes involved in stress responses like cold, disease, and wounds.

Contribution

A comprehensive genomic analysis of the AP2/ERF superfamily in olive trees, identifying stress-responsive candidate genes.

Findings

348 AP2/ERF genes were identified and classified into four families in the olive tree genome.

50 candidate genes showed significant expression changes under four stress treatments.

Nine genes exhibited potential protein–protein interactions related to stress responses.

Abstract

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 (Olea europaea 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 cis-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 p 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.

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