Genome-wide identification and characterization of a plant-specific Dof transcription factor gene family in olive (Olea europaea) and its comparison with Arabidopsis

DNA binding with one finger (Dof) proteins are encoded by a ubiquitous plant-specific transcription factor gene family that plays a critical role in various biological processes including fruit ripening and organogenesis. The wild olive (Olea europaea var. sylvestris v1.0) genome was used to identify Dof gene family members using a set of bioinformatics tools. Gene structure, chromosome locations, phylogeny, protein motifs, miRNA targets and tissue-specific expression patterns were analyzed. Here, we identified 51 potential Dof genes unevenly distributed on all chromosomes and a few scaffolds. Dof proteins in olive clustered into eight subgroups (D1, B2, C3, C2.2, C1, C2.1, B1, and A) based on the established Arabidopsis classification. The prevalence of segmental duplication was observed as compared to tandem duplication, and this was the main factor underlying the expansion of the Dof gene family in olive. Tissue-specific expression profiling of OeuDof genes revealed that the majority of OeuDof genes were highly expressed in flowers, stem and meristem tissues. In seed and meristem tissues, cis-regulatory element (CRE) analysis revealed the presence of elements that are specifically responsive to light, circadian, auxin, and ABA. In addition, a comparative analysis between Dof genes in olive and Arabidopsis revealed eight groups or sub-families, although the C3 group of Arabidopsis was not represented in olive. This extensive genome evaluation of the Dof gene family in olive presents a reference for cloning and functional analysis of the members of this gene family.