Flavonoids are a primary bioactive component of Sophora flavescens, which is widely used in traditional Chinese medicine. Understanding flavonoid biosynthesis is of great importance for improving the production of active compounds. In this study, both the total flavonoid content and the contents of six main flavonoid (namely, genistin, trifolirhizin, maackiain, kushenol I, kurarinone, and nor-kurarinone) were significantly higher in triennial S. flavescens than in biennial plants, and the flavonoid content of lateral roots was higher than that of taproots. We attempted to generate exhaustive molecular information on the flavonoid secondary metabolite pathway and to increase the genomic resources for S. flavescens. De novo transcriptome data provided 643,251 unigenes, and 365,572 (56.83 %) were successfully annotated in five public protein databases. The gene expression profiles of taproots and lateral roots clustered with each other and were separated by the cultivation period; the other expression profiles were clustered according to tissue pattern. The differentially expressed unigenes (DEGs) in the lateral roots, taproots and stems between biennial and triennial S. flavescens were identified and subjected to functional annotation enrichment. A total of 92 unigenes encoding well-known enzymes involved in flavonoid biosynthesis were found to show differential expression between biennial and triennial S. flavescens. Furthermore, the comparative expression results of eight unigenes were validated by real-time quantitative PCR (qRT-PCR). The most abundant transcription factors (TFs) that were differentially expressed in S. flavescens were those belonging to the bHLH-, NAC-, ERF- and MYB-related families, and these TFs were identified regardless of the tissue or cultivation period. Our study provides important resources of gene sequences and expression and insights into the molecular mechanism of flavonoid biosynthesis during S. flavescens cultivation.

黄酮类化合物是苦参的主要生物活性成分，在中药中广泛使用。了解类黄酮的生物合成对于提高活性化合物的产量非常重要。在这项研究中，三年期S中总黄酮含量和六种主要黄酮含量（即染料木素，三叶草苷，毛黑素，苦参酚I，库拉利酮和去甲库拉里酮）均显着较高。苦参总黄酮含量高于两年生植物，侧根总黄酮含量高于主根。我们试图在黄酮类二级代谢途径上产生详尽的分子信息，并增加苦参的基因组资源。从头转录组数据提供了643,251个单基因，并且在五个公共蛋白质数据库中成功注释了365,572（56.83％）。主根和侧根的基因表达谱相互聚集，并按培养时期分开；其他表达谱根据组织模式聚类。在侧根，主根的差异表达个Unigenes（DEGS）和茎二年生和三年期之间苦参被确定，并进行功能注释富集。总共发现了92个编码涉及类黄酮生物合成的著名酶的单基因，表明两年生和三年生黄萎链霉菌之间存在差异表达。。此外，通过实时定量PCR（qRT-PCR）验证了八个单基因的比较表达结果。在flavescens中差异表达的最丰富的转录因子（TF）是属于bHLH-，NAC-，ERF-和MYB相关家族的转录因子，这些TFs的识别与组织或培养时期无关。我们的研究提供了重要的基因序列和表达资源，并深入了解了苦参培养过程中类黄酮生物合成的分子机制。