Background Genistein and genistin are the main active constituents of Flemingia macrophylla (Willd.) Prain and the amount of active constituents in the roots varies depending on the cultivation time. The harvesting period has a great influence on its quality, and there are fewer studies on the optimal harvesting time of F. macrophylla, which is urgently needed to explore the optimal harvesting period to improve its use value. Purpose F. macrophylla (Willd.) Prain is an important medicinal plant distributed in China. This study aimed to enhance the accumulation of active ingredients genistin and genistein in F. macrophylla, and explore the mechanism of biological synthesis of these active compounds at molecular levels. Methods Transcriptome sequencing and high-performance liquid chromatography (HPLC) technology were applied to F. macrophylla tissue culture seedlings for 30 days after culturing (DAC), 45 DAC, 60 DAC, and 75 DAC. Then, gene expression, representative active substances, and important phenotypic indexes were analyzed. Results The highest fresh weight and root thickness were attained at 45 DAC, the highest plant height at 60 DAC, and the maximum rooting rate at 75 DAC. The genistin content reached the highest level at 45 DAC, and the content of genistein reached the highest level at 30 DAC. The total content of genistin and genistein achieved the maximum levels at 45 DAC. A total of 7,735 differently expressed genes (DEGs) in the three comparable groups, including T45d vs T30d, T60d vs T30d, and T60d vs T45d, were identified. Through the Kyoto Encyclopedia Genes and Genomes (KEGG) enrichment analysis of DEGs, isoflavonoid biosynthesis and phenylpropanoid biosynthesis pathways were significantly enriched in two groups, including T45d vs T30d and T60d vs T30d. A total of 41 DEGs involved in the production of isoflavones were discovered in the three groups. Conclusion The optimism culture time for the accumulation of genistein and genistin in F. macrophylla seedlings ranged from 30 to 45 days. Forty-one DEGs in the genistein and genistin synthesis pathways were found through transcriptomics analysis. This study sheds light on the biosynthesis of genistin and genistein in F. macrophylla.
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