Chromosome‐level genome assembly of the mangrove associate <i>Derris trifoliata</i> provides insights into adaptive evolution and rotenoid biosynthesis

Abstract Derris trifoliata Lour. is a common mangrove‐associated legume important for coastal ecosystem stability and serves as a natural source of rotenoids. However, the lack of high‐quality reference genomes has hindered the investigation of its evolutionary history and key functional traits. Here, we present a high‐quality, chromosome‐level genome assembly for D. trifoliata , representing the first reported genome resource for rotenoid‐producing legumes. The assembled genome spans 811 Mb across 11 chromosomes, with a BUSCO completeness of 98.3% and all telomeres and centromeres identified. Evolutionary analysis revealed two rounds of whole‐genome duplication event shared with Papilionoideae. The more recent event, along with lineage‐specific tandem and proximal duplications, drove the expansion of genes involved in stress responses and secondary metabolism, facilitating adaptation to extreme intertidal environments. Metabolomic profiling identified four major rotenoids predominantly accumulated in roots, which likely provide effective chemical defense against the belowground stress in mangrove habitats. By integrating transcriptomic and metabolomic data, we reconstructed the rotenone biosynthesis pathway and identified candidate enzymes and transcription factors. Notably, the potential tandem expansion and functional evolution of the key biosynthesis genes 2ODD s offer clues to the evolution of specialized biosynthesis pathways. This high‐quality genome, combined with multi‐omics analyses, provides insight into the environmental adaptation and specialized metabolism of D. trifoliata , establishing a valuable foundation for broader evolutionary research and future biotechnological applications of rotenoid‐producing legumes.