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Background   Ziziphora bungeana  Juz. is a folk medicine from the Xinjiang Uygur Autonomous Region. The herb or the aerial parts of it have been used to medicinally treat cardiovascular diseases. Flavonoids are the main pharmacologically active ingredients in  Z .  bungeana . Identification of the tissue-specific distribution of flavonoids in  Z .  bungeana  is crucial for effective and sustainable medicinal use of the plant. Furthermore, understanding of the biosynthesis pathways of these flavonoids in  Z .  bungeana  is of great biological significance.    Methods  The flavonoids from different tissues of  Z. bungeana  were identified using liquid chromatography-tandem mass spectrometry (LC–MS/MS). The full-length transcriptome of  Z. bungeana  was determined using a strategy based on a combination of Illumina and PacBio sequencing techniques. The functions of differentially expressed unigenes were predicted using bioinformatics methods and further investigated by real-time quantitative PCR and phylogenetic relationship analysis.    Results  Among the 12 major flavonoid components identified from  Z. bungeana  extracts, linarin was the most abundant component. Nine flavonoids were identified as characteristic components of specific tissues. Transcriptome profiling and bioinformatic analysis revealed that 18 genes were putatively involved in flavonoid biosynthesis. The gene expression and phylogenetic analysis results indicated that  ZbPALs ,  Zb4CL3 ,  ZbCHS1 , and  ZbCHI1  may be involved in the biosynthesis of the main flavonoid intermediate.  ZbFNSII ,  ZbANS , and  ZbFLS  may be involved in the biosynthesis of flavones, anthocyanins, and flavonols, respectively. A map of the biosynthesis pathways of the 12 major flavonoids in  Z. bungeana  is proposed.    Conclusions  The chemical constituent analysis revealed the compositions of 9 characteristic flavonoids in different tissues of  Z. bungeana . Linarin can be hydrolysed into acacetin to exert a pharmaceutical role. Apigenin-7- O -rutinoside is hypothesised to be the precursor of linarin in  Z. bungeana . There was greater content of linarin in the aerial parts of the plant than in the whole herb, which provides a theoretical basis for using the aerial parts of  Z. bungeana  for medicine. These results provide a valuable reference for further research on the flavonoid biosynthesis pathways of  Z. bungeana  and will be significant for the effective utilisation and ecological protection of  Z. bungeana .

chinese medicine

Integrated metabolomic and transcriptomic profiling reveals the tissue-specific flavonoid compositions and their biosynthesis pathways in Ziziphora bungeana