Transcriptome and metabolite profiling analyses reveal the molecular mechanism underlying the characteristic accumulation of anthocyanins and flavonols in Fritillaria unibracteata and F. delavayi.

As an important medicinal herb with high profit, Sichuan Fritillaria is on the verge of extinction because of unreasonable exploitation, but the information on flavonoids which possess diverse medicinal activities was almost unknown. Here, two representative Sichuan Fritillaria species ( F. unibracteata and F. delavayi ) were studied with UHPLC-Q-Orbitrap HRMS (ultra-high performance liquid chromatography coupled with quadrupole Orbitrap high-resolution mass spectrometry). Anthocyanins mainly accumulate in flowers especially in F. unibracteata (8.22 mg/g; mainly consisting of cyanidin 3- O -rutinoside), with trace amounts in leaves and stems, but to the lowest levels in bulbs. Flavonols accumulates considerably in all tissues of the two Fritillaria species except bulbs, to the highest level in the flower of F. delavayi (28.94 mg/g; mainly consisting of quercetin glycosides). Further transcriptomic and RT-qPCR (real-time quantitative Polymerase Chain Reaction) analysis revealed the anthocyanin-specific biosynthetic unigenes displayed the highest expression levels in the flower of F. unibracteata while most of flavonol-specific biosynthetic unigenes showed the highest transcript abundance in the flower of F. delavayi , but to the lowest expression levels in the bulbs of the two species, accounting for the tissue- and species-specific accumulation of anthocyanins and flavonols. Moreover, the functions of FcMYB90, FcTT8 and FcMYB4 was carefully studied in tobacco. These results prove that several MYB and bHLH transcription factors coordinately controlled the direction of the phenylpropanoid metabolic flux which finally resulted in the characteristic accumulation pattern of anthocyanins and flavonols in Sichuan Fritillaria . This work provides a good foundation and novel insights for the further industrial development, resource utilization and breeding of Sichuan Fritillaria . • Anthocyanins accumulate in all tissues except bulbs, to the highest level in F. unibracteata flower. • Flavonols accumulate to the highest level in F. delavayi flower, accompanied by a decrease in anthocyanin. • The difference flavonoid profiles indicate a useful chemotaxonomic feature to distinguish the origins of Fritillaria species. • The temporospatial accumulation of anthocyanins in two Fritillaria species was mainly regulated by a MYB-bHLH-WD40 complex.