A chromosome-level genome assembly for Ficus carica provides genetic insights into flowerless fig fruit development, psoralen biosynthesis, and drought tolerance.

Ficus carica L., an ancient crop of considerable economic value, exhibits distinctive biological traits, including flowerless fruit (syconium) development, psoralen biosynthesis, and drought tolerance. In this study, we present a chromosome-level genome assembly (323.03 Mb, N50 = 23.82 Mb) of F. carica, revealing an evolutionary divergence from the closely related genus Broussonetia approximately 50 million years ago. Comparative genomic analyses revealed a contraction in the s-domain receptor-like kinase gene family, which is associated with unisexual fruit formation, and identified conserved MADS-box transcription factor genes (FcAGL6, FcAP2, and FcSEP1/2) that regulate syconium development through spatiotemporal expression patterns. Metabolomic profiling demonstrated tissue-specific accumulation of bioactive compounds, with roots serving as the primary reservoir for psoralen. We also identified key genes-FcANS and FcCHS10, involved in anthocyanin biosynthesis, and FcMS, involved in psoralen biosynthesis-and validated their functions using a newly established transient transformation system. Transcriptomic analysis under drought stress identified the NAC transcription factor FcJA2 as a central regulator of stress tolerance that enhances reactive oxygen species scavenging and osmotic regulation by activating FcPP2C5 and FcP5CS. Overexpression of FcJA2 significantly improved drought resistance. Further analyses demonstrated that FcJA2-mediated drought-response modules are conserved across the Moraceae. These findings provide valuable insights into the genetic mechanisms underlying fruit development, specialized metabolite biosynthesis, and stress tolerance in F. carica, offering potential applications for crop improvement and advancing our understanding of genome evolution and environmental adaptability in the Moraceae family.