Genome-Scale Identification, Phylogeny, Expression Profiling, and Functional Analysis of Sugarcane DUF4228 Family Involved in Drought Stress

Domain of unknown function (DUF) proteins play important roles in plant responses to biotic and abiotic stresses. DUF4228 proteins, as members of the DUF superfamily, are widely present in plants and exert significant functions under various stress conditions. Sugarcane is an important economic and energy crop in China. However, the role of DUF4228 family members in sugarcane has not been reported. In this study, 126 ScDUF4228 genes were identified for the first time in the genome of the modern cultivar XTT22 and systematically named based on their chromosomal locations (ScDUF4228-1 to ScDUF4228-126). These genes are located on 7 chromosomes of the XTT22 genome, exhibiting an overall uneven distribution. Phylogenetic analysis revealed that the 126 ScDUF4228 proteins can be divided into 9 groups (I–IX). Gene structure analysis indicated that most ScDUF4228 family members lack introns or contain only 1–2 introns, and all members possess a complete DUF4228 domain. Ka/Ks analysis demonstrated that the family as a whole has undergone purifying selection (Ka/Ks < 1), indicating high functional conservation during evolution. Cross-species collinearity analysis showed significant species-specific expansion of the DUF4228 gene family in the Poaceae (particularly in sugarcane and its close relatives), a phenomenon not prominently observed in dicotyledons. Analysis of tissue expression patterns, developmental stages, and diurnal rhythms revealed that the spatiotemporal expression profiles of the 126 ScDUF4228 family members vary, suggesting they may function individually or synergistically during different developmental periods in sugarcane. Yeast medium assay depicted that three members of the ScDUF4228 (ScDUF4228-7, ScDUF4228-18, ScDUF4228-23) family had significant resistance potential under drought stresses. Furthermore, transcriptome analysis after drought treatment showed that ScDUF4228-23 exhibited the most significant upregulation, suggesting it may be a key gene in sugarcane’s response to drought. These results suggest that the DUF4228 gene family has undergone dramatic expansion in sugarcane and may play a crucial regulatory role in drought stress responses. This study provides the necessary molecular foundation for further exploring the functions of ScDUF4228 family members.