Genomic and metabolomic analysis of <i>Ficus altissima</i> and <i>Ficus hirta</i>: evolutionary divergence and medicinal implications

<italic>Ficus altissima</italic> is an evergreen tree characterized by a distinctive buttress root system, which plays a crucial role in its ecosystem. <italic>Ficus hirta</italic>, a shrub to small tree, is well known for the medicinal properties of its roots. In this study, we sequenced the genomes of both species using third-generation Oxford Nanopore sequencing technology, revealing genome sizes of 355.9 Mb for <italic>F. altissima</italic> and 323.7 Mb for <italic>F. hirta</italic>. By integrating publicly available <italic>Ficus</italic> genome data, we constructed a phylogenetic tree and estimated that <italic>F. altissima</italic> and <italic>F. hirta</italic> diverged approximately 41 million years ago (Mya). In <italic>F. altissima</italic>, we identified genes involved in the auxin signaling pathway and found that members of the PIN gene family were highly expressed in buttress roots. To further investigate their role, we conducted a comprehensive analysis of the PIN gene family, including phylogenetic relationships, gene structure, conserved motifs, and protein domains. Promoter analysis revealed that the regulatory regions of 14 PIN genes contain <italic>cis</italic>-acting elements associated with light response, hormone signaling, and stress response. Additionally, through extensive targeted metabolomic analysis, we used high-performance liquid chromatography (HPLC) to detect a diverse range of secondary metabolites in the roots of <italic>F. hirta</italic>. By integrating these findings with transcriptomic data, we identified key genes involved in the psoralen biosynthetic pathway. The high-quality reference genomes and metabolomic data generated in this study provide valuable resources for advancing research on <italic>Ficus</italic> root biology and its bioactive compounds.