Pyrrosiae Folium (PF) is a commonly used Chinese herb medicine originating from three Pyrrosia species for the treatment of urinary infection and urolithiasis. According to Chinese medicine practice, different specie origins led to some variations in the therapeutic effects of PF. To ensure the safety and efficacy of PF in clinical practice, it is necessary to establish a reliable and integrative method to distinguish PF occurring from the three species. In the present paper, a HPLC–DAD method was developed and applied to simultaneously analyze five major compounds in PF. Afterwards, multivariate statistical analyses including principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were applied for specie discrimination and integrative quality evaluation based on quantitative data. The chemical determination and pattern recognition results of 35 batches of PF samples indicated that PF samples from three species showed different chemical profiles and could be discriminated clearly. In conclusion, the present method is rapid and reliable for the quality assessment and species discrimination of PF.

Background: F. hirta vahl is a famous Chinese medicinal plant. The root is the main organ accumulating bioactive compounds, and its development is directly related to the yield and quality of the harvested F. hirta. However, the molecular mechanisms underlying the bioactive compound biosynthesis occurring during the root development of F. hirta are unknown. Method: Transcriptome and widely targeted metabolome analyses were performed to investigate gene expression and metabolite variation during the development of F. hirta taproots. Results: A total of 3792 differentially expressed genes (DEGs) were identified between the one- and three-year-old F. hirta taproots; they are related to circadian rhythm–plant, phenylpropanoid biosynthesis, starch and sucrose metabolism, and plant–pathogen interaction pathways. In total, 119 differentially accumulated metabolites (DAMs) were identified between the one- and three-year-old F. hirta taproots, including flavonols, phenolic acids, and coumarins compounds. Integrative transcriptome and metabolome analyses revealed a significant correlation between 172 DEGs and 21 DAMs; they were predominantly enriched for processes associated with phenylpropanoid biosynthesis, flavonoid biosynthesis, plant hormone signal transduction, and stilbenoid, diarylheptanoid, and ginerol biosynthesis. In addition, 26 DEGs were identified to be significantly correlated with the DAMs that accumulated in the phenylpropanoid biosynthesis pathway, and these DEGs may be the key genes for the biosynthesis of F. hirta active compounds. Conclusions: The phenylpropanoid biosynthesis pathway plays a dual role in both development and bioactive compound synthesis in F. hirta taproots. These findings provide a molecular regulatory network in the relationships between F. hirta taproot development and the accumulation of secondary metabolites. The identification of candidate genes and pathways provides a genetic resource for quality control and future molecular breeding in F. hirta.