Comparative transcriptome profiling reveals differentially expressed genes involved in flavonoid biosynthesis between biennial and triennial Sophora flavescens

•Root flavonoid contents were higher in triennial S. flavescens than biennial S. flavescens.•Taproot and lateral root expression profiles were clustered by cultivation period.•Genes involved in flavonoid biosynthesis in S. flavescens were identified.•Transcription factors are involved in flavonoid biosynthesis in S. flavescens. 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.