Co-Analysis of Transcriptome and Metabolome Reveals Anthocyanin Accumulation in the Female Flower Tissues of Fig Cultivar ‘Silu Hongyu’

Background/Objectives: Fig (Ficus carica L.) is considered a valuable fruit owing to its rich health-promoting ingredients, including anthocyanins. However, little information is available on the regulatory networks that reveal anthocyanin biosynthesis in figs, especially the new fig cultivar “Silu Hongyu” (HY). Methods: In this study, multi-omics analysis was performed to dissect the regulatory networks responsible for anthocyanin accumulation in the female flower tissues of HY. Results: we found that the anthocyanin content in the female flower tissues of HY is higher than that of “Chinese Ziguo” (ZG). Metabolomic profiling identified 350 differentially accumulated metabolites (DAMs), among which 108 were flavonoids. The contents of multiple metabolites responsible for anthocyanin accumulation, such as naringenin chalcones, cyanidin 3-glucoside, and pelargonidin 3,5-diglucoside, were significantly increased in the HY female flower tissues. Transcriptomic analysis revealed that 3696 differentially expressed genes (DEGs) were screened from the female flower tissues of ZG and HY, with 1730 upregulated DEGs and 1966 downregulated DEGs in HY compared to ZG. The key structural genes involved in anthocyanin biosynthesis, including FcPAL, Fc4CL, FcCHS, FcF3′H, and FcBZ1, were significantly upregulated in the female flower tissues of HY compared with ZG. KEGG analysis also demonstrated that five flavonoid biosynthesis pathways were co-enriched by DAMs and DEGs. Conclusion: These findings provide a multi-omics framework that governs anthocyanin biosynthesis in the female flower tissues of HY, which will facilitate the genetic breeding and improvement of high-anthocyanin fig cultivars.