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Introduction: The seeds of Cassia obtusifolia L. (Cassiae [C.] semen) have been widely used as both food and traditional Chinese medicine in China. Objectives: We aimed to analyze the metabolic mechanisms underlying C. semen germination.Materials and Methods: Different samples of C. semen at various germination stages were collected. These samples were subjected to 1 H-NMR and UHPLC/Q-Orbitrap-MS-based untargeted metabolomics analysis together with transcriptomics analysis.Results: A total of 50 differential metabolites (mainly amino acids and sugars) and 20 key genes involved in multiple pathways were identified in two comparisons of different groups (36 h vs 12 h and 84 h vs 36 h). The metabolite-gene network for seed germination was depicted. In the germination of C. semen, fructose and mannose metabolism was activated in the testa rupture period, indicating more energy was needed (36 h). In the embryonic axis elongation period (84 h), the pentose and glucuronate interconversions pathway and the phenylpropanoid biosynthesis pathway were activated, which suggested some nutrient sources (nitrogen and sugar) were in demand. Furthermore, oxygen, energy, and nutrition should be supplied throughout the whole germination process. These global views open up an integrated perspective for understanding the complex biological regulatory mechanisms during the germination process of C. semen.

Introduction The seeds of Cassia obtusifolia L. (Cassiae Semen) have been widely used as both food and traditional Chinese medicine in China. Objectives For better understanding the metabolic mechanism along with germination, different samples of Cassiae Semen at various germinating stages were collected. Methods These samples were subjected to 1H-NMR and UHPLC/Q-Orbitrap-MS based untargeted metabolomics analysis together with transcription analysis. Results A total of fifty differential metabolites (mainly amino acids and sugars) and twenty key genes involved in multiple pathways were identified in two comparisons of different groups (36 h vs 12 h and 84 h vs 36 h). The metabolic and gene network for seed germination was depicted. In the germination of C. Semen, the fructose and mannose metabolism pathway was activated, indicating energy was more needed in the testa rupture period (36 h). In the embryonic axis elongation period (84 h), the pentose and glucuronate interconversions pathway, and phenylpropanoid biosynthesis pathway were activated, which suggested some nutrient sources (nitrogen and sugar) would be demanded. Furthermore, oxygen, energy and nutrition should be supplied through the whole germination process. These global views open up an integrated perspective for understanding the complex biological regulatory mechanism during seed germination process of C. Semen.