Future application potential of Ormosia plant shown by chromosome-level genome of the rare Ormosia henryi

Background. Ormosia henryi , an endemic tree species in China. Its wood is characterized by a distinctive fragrance, dense texture, and high hardness, has substantial economic worth. However, wild O. henryi are continuously affected from illegal logging and over-exploitation. Compounded by its inherently slow growth rate, low natural seed set, difficulties in seed germination and habitat fragmentation, its wild populations experienced drastic decline. Methods. We present the chromosome-level genome assembly of the endangered timber tree Ormosia henryi (2.64 Gb, Contig N50 = 39.17 Mb, Scaffold N50 = 338.40 Mb), integrating comparative genomics to elucidate its adaptive evolution and utilization potential. Results. Genome annotation revealed 83.89% repetitive sequences and 39,017 protein-coding genes, of which 99.32% are functionally annotated. Phylogenetic analysis identified Lupinus albus as the closest relative (divergence time ~ 53.82 million years ago). Two whole-genome duplication events (Ks peaks at 0.47 and 2.26) and significant gene family expansion (276 families) were detected, alongside 122 positively selected genes enriched in photosynthesis, phenylpropanoid biosynthesis, and DNA repair pathways, demonstrating enhanced intrinsic adaptability. This evidence indicates that the endangerment of O. henryi may primarily stem from overexploitation rather than that by genetic vulnerability. This genomic resource enables molecular breeding (e.g., growth-regulating tree height using regulating ATP-dependent DNA helicase PIF1), conservation strategies, and sustainable industrial applications (high-value wood processing, medicinal resource development, ecological restoration).