INTRODUCTION: Ficus hirta Vahl is a common Chinese herbal medicine and edible plant resource in the Lingnan area of China. It contains coumarins, flavonoids and other chemical compounds, which have antioxidant, anti-inflammatory, antibacterial, antiviral and antitumor effects. However, F. hirta exhibits significant morphological variation in leaf shapes due to its high genetic diversity. 

RATIONALE: To investigate the relationship between the leaf shape differences and the contents of major active compounds, herein, LC-MS/MS was performed to determine the contents of psoralen and bergapten in F. hirta roots from three different leaf shapes (entirc leaf, EL; lobed leaf, LL; Palmately deeply leaf, PDL), and transcriptome sequencing was further employed to explore the potential molecular mechanisms underlying these contents variations. 

RESULTS: Results showed that PDL exhibited significantly higher psoralen content compared to EL and LL, while EL with significantly higher bergapten content than that in LL, but no significant difference was observed between EL and PDL. A total of 60.9 Gb clean reads were obtained, and 46 194 unigenes were assembled. F. hirta had the highest homology with Morus notabilis, according to the homologous sequencing alignment. 2 355, 2 067 and 2 001 differentially expressed genes (DEGs) were screened from three comparison groups PDL_vs_EL, PDL_vs_LL, and LL_vs_EL, respectively. These DEGs were primarily enriched in the pathways such as phenylpropanoid biosynthesis, starch and sucrose metabolism, and plant-pathogen interaction etc. 

CONCLUSION: There were differences in the contents of psoralen and bergapten among the three leaf shapes of F. hirta. The phenylpropanoid biosynthesis and plant-pathogen interaction pathway may play crucial roles in the biosynthesis and accumulation of psoralen and bergapten in F. hirta. This study preliminarily revealed the correlation between the leaf morphology and major active compounds of F. hirta, and extended its public transcriptome database, which will provide reference for further utilizing different leaf shape of F. hirta germplasm resources and quality breeding.