Abstract
Flemingia macrophylla, a prominent shrub species within the Fabaceae family, is widely distributed across China and Southeast Asia. In addition to its ecological importance, it possesses notable medicinal value, with its roots traditionally used for treating rheumatism, enhancing blood circulation, and alleviating joint pain. We employed Nanopore sequencing platforms to generate a high-quality reference genome for F. macrophylla, with an assembled genome size of 1.01 Gb and a contig N50 of 59.43 Mb. A total of 33,077 protein-coding genes were predicted, and BUSCO analysis indicated a genome completeness of 99%. Phylogenomic analyses showed that F. macrophylla is most closely related to Cajanus cajan among the sampled taxa, with an estimated divergence time of 13.2-20.0 MYA. Evidence of whole-genome duplication (WGD) events was detected in F. macrophylla, C. cajan, and P. vulgaris, with these species sharing two WGD events. The unique gene families in F. macrophylla are associated with strong resistance to both abiotic and biotic stress, supporting its remarkable ecological adaptability. Furthermore, gene family expansion analysis revealed a significant enrichment of genes related to secondary metabolites biosynthesis, providing a molecular basis for its high medicinal value. In summary, this study provides a foundational genomic resource for F. macrophylla, offering valuable insights into its genetic architecture, evolutionary history, and potential applications in medecine and agriculture. The comprehensive analyses lay the groundwork for future research into the species's medicinal properties and evolutionary biology.