Comprehensive genomic and regulatory analysis of the NAC gene family reveals stress-adaptive mechanisms in Sesame (Sesamum indicum L.)

NAC (NAM, ATAF, and CUC) transcription factors are central regulators of plant development and stress adaptation. Although sesame ( Sesamum indicum L.) is recognized for its tolerance to adverse environmental conditions, a comprehensive understanding of the genomic organization and regulatory networks governing its NAC gene family remains limited. In this study, we performed a genome-wide identification and characterization of the NAC gene family in sesame. Sixty-six NAC genes (SiNACs) were identified and classified into conserved phylogenetic groups together with NACs from Arabidopsis thaliana , Brassica napus , and Oryza sativa . Collinearity analysis revealed strong evolutionary conservation with eudicot counterparts, supporting predominant single-copy retention and limited gene family expansion in sesame. Promoter analysis identified abundant stress- and hormone-responsive cis-regulatory elements, including ABRE, MBS, ARE, TGACG, and TC-rich motifs, indicating extensive transcriptional regulation under abiotic stress conditions. Membrane-bound SiNACs exhibited particularly high cis-element diversity. Furthermore, post-transcriptional analysis predicted 306 miRNAs targeting SiNACs, with miR164 and miR397 emerging as central regulatory hubs. Integration of transcriptional and miRNA-mediated regulation revealed a regulatory architecture potentially contributing to SiNAC transcriptional regulation under stress. Our results demonstrate that sesame relies on regulatory plasticity—through coordinated cis-regulatory complexity and miRNA-mediated control—rather than gene family expansion to achieve robust stress responsiveness. The integrated NAC regulatory network uncovered here provides mechanistic insight into sesame stress adaptation and offers valuable targets for improving stress tolerance through molecular breeding.