Genome-Wide Identification and Characterization of the DOF Gene Family and Gene Expression Pattern Analysis in Five Legume Species

Background: The DOF transcription factor family is involved in plant growth, development, and stress responses, but systematic comparative genomics studies across legume species are lacking. Methods: We identified the whole genome of the DOF gene family of five legume plants: Medicago truncatual (43), Cicer arietinum (43), Phaseolus vulgaris (44), Glycine max (79), and Lotus japonicus (32). Genome-wide identification of DOF genes was performed in five legume species, followed by phylogenetic analysis, gene structure characterization, duplication event identification, promoter element prediction, synteny analysis, and expression pattern profiling. Results: Phylogenetic comparison with Arabidopsis thaliana (47) and Oryza sativa (37) classified them into four subfamilies (Groups I–IV). The five legumes all had no more than 30% members of the subgroup. The same subfamily has similar protein structures and gene structures, and most of its members have motif1, with most plants having more than 30% of genes intronic. Gene duplication events were evenly distributed among the members of the DOF gene in all five legumes, and played an important role in its evolution. Moreover, the majority of the DOF genes showed tissue specificity in the five legumes, with most of these members being upregulated in flowers. Additionally, expression pattern analysis under abiotic stress in soybean revealed that members of different subfamilies exhibit divergent expression dynamics under salt, alkali, and cold stresses. The DOF gene family in legumes expanded primarily through segmental duplication and evolved under purifying selection. Conclusion: The subfamily-specific responses to abiotic stress and tissue-specific expression patterns provide candidate gene resources for functional studies aimed at improving stress tolerance and agronomic traits in legume crops.