The delayed flower bud opening of Lonicera japonica ‘Huajin 6’ extends its harvest window and enhances agricultural value, yet the underlying molecular basis remains unclear. Here, we assembled a chromosome-level genome of ‘Huajin 6’ using PacBio sequencing and high-throughput chromosome conformation capture scaffolding (824.72 Mb, scaffold N50 = 91.2 Mb). Comparative genomic analyses revealed a subfamily-specific contraction of lipoxygenase (LOX) genes, particularly within the 9-LOX clade, which is associated with a reduced jasmonate biosynthetic capacity during floral development. Transcriptomic and hormone profiling showed coordinated suppression of jasmonic acid (JA) biosynthesis-related genes and a marked reduction of JA and its bioactive derivatives during the transition from the complete white stage to flower opening. A JA-responsive co-expression module enriched in cell wall modification genes exhibited attenuated activation in ‘Huajin 6’. Functional assays further demonstrated that exogenous JA restored timely flower bud opening in both ‘Huajin 6’ and L. macranthoides, while heterologous expression of Lonicera LOX genes enhanced jasmonate accumulation in Arabidopsis. Together, these findings are consistent with a jasmonate threshold model in which LOX gene contraction constrains JA accumulation during floral transition, contributing to delayed flower bud opening and highlighting how genome structural variation influences hormone-dependent flowering dynamics.

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