Haplotype-Resolved Chromosome-Scale Genome Assembly of Lonicera macranthoides Hand.-Mazz. Reveals Genetic Determinants of Bioactive Compound Biosynthesis and Phytohormone-Mediated Metabolic Regulation

Lonicera macranthoides is a traditional Chinese medicinal herb valued for its chlorogenic acid (CGA) and triterpenoid saponins. To elucidate the genetic basis of these medicinal properties, we generated a haplotype-resolved chromosome-scale genome assembly combining PacBio long-read sequencing and High-throughput Chromosome Conformation Capture (Hi-C) data. The assembly comprises two haplomes, LmacA (857.17 Mb, contig N50 = 31.19 Mb) and LmacB (824.65 Mb, contig N50 = 27.17 Mb), representing the most contiguous genomic resource for the genus to date. Comparative genomic analyses identified species-specific gene families enriched in triterpenoid biosynthesis, phenylpropanoid metabolism, and stress-response pathways. Integrated GWAS, transcriptomic, and metabolomic analyses identified key genes regulating CGA and triterpenoid saponin biosynthesis, including a UGT cluster, an HCT cluster, and MYB transcription factors. We further found evidence that jasmonic acid and isopentenyl adenine dynamically balance floral organ development and secondary metabolite accumulation via MYB/bHLH transcription factors and MAPK signaling. This study establishes the first biosynthetic pathways for CGA and saponins in L. macranthoides, reveals regulatory mechanisms driven by haplotype structural variations (notably a Chr7 inversion), and provides genomic resources for molecular breeding and bioactive compound exploitation.