Integrated multi-omics analysis provides insights into sesame seed coat development

Sesame ( Sesamum indicum L.) is an important oilseed crop. The seed coat plays important roles in seed protection, maturation, and quality formation in sesame. However, its dynamic developmental process remains poorly understood. In this study, seed coat development was investigated using metabolomic, proteomic, and transcriptomic analyses. Morphological and histological observations showed a clear developmental progression from early structural formation (5–15 days after pollination, DAP), through structural consolidation (15–25 DAP), to maturation accompanied by extensive intracellular accumulation (25–40 DAP). Based on these developmental characteristics, seed coats collected at 10, 20, 30, and 40 DAP were selected for multi-omics analysis. Metabolomic analysis revealed dynamic metabolic changes, with lipid metabolism being prominent during the early development stage, whereas amino acid metabolism and secondary metabolite biosynthesis were associated with later developmental stages. Antioxidant-related pathways, particularly ascorbate and aldarate metabolism, were consistently enriched throughout seed coat development. Proteomic analysis showed that most differentially expressed proteins (DEPs) were downregulated, with enrichment patterns shifting from RNA processing and lipid biosynthesis at the early developmental stage to translation and redox metabolism at the middle developmental stage, and subsequently to energy metabolism and protein processing at the late developmental stage. Fatty acid biosynthesis was consistently enriched across all developmental stages. Transcriptomic analysis indicated that hormone signaling, carbon metabolism, and secondary metabolite biosynthesis were associated with seed coat development. Integrated metabolome-transcriptome and metabolome-proteome analyses showed glyoxylate and dicarboxylate metabolism as a metabolic pathway potentially associated with seed coat development. Furthermore, weighted gene co-expression network analysis (WGCNA) integrating transcriptomic and metabolomic data identified the green module (MEgreen), which contained candidate genes potentially associated with metabolic changes during seed coat development. This study provides an integrated multi-omics characterization of sesame seed coat development and reveals developmental stage-specific changes in metabolites, proteins, and transcripts. The identified candidate pathways and genes provide valuable resources for further investigating the molecular mechanisms underlying sesame seed coat development.