The Fraxinus mandshurica genome reveals a dual adaptive strategy linking rapidly evolving immune receptors and structural fortification.

Fraxinus mandshurica exhibits high tolerance to ash dieback and superior wood mechanical properties, yet the genomic basis of these dual traits remains incompletely understood. Here, we present a chromosome-scale genome assembly of the elite clone 'M8' and integrate comparative genomics with temporal transcriptomics to investigate its adaptive architecture. We show that recent tandem and proximal duplications have contributed to the diversification and candidate positive selection of the NLR immune repertoire. Transcriptomic profiling reveals a stage-associated deployment pattern, in which expressed NLR genes are enriched during the Transition Stage, consistent with reinforced immune surveillance during rapid xylem expansion. As development progresses, the Latewood Stage shifts toward phenylpropanoid metabolism, lignification-related programs, and structural reinforcement. We identify and experimentally validate a latewood-recruited FmNAC104-FmPRX1 candidate regulatory module, in which FmNAC104 binds to and activates the FmPRX1 promoter and promotes endogenous FmPRX1 expression. Formal NAC/PRX gene family analysis further supports an enlarged NAC/PRX repertoire relative to P. trichocarpa and clarifies the orthogroup status of the FmNAC104-FmPRX1 module among related ash species. Collectively, our findings support a 'fortified defense' working model in which F. mandshurica temporally coordinates immune-receptor diversification with latewood-associated structural reinforcement. This study provides a genomic resource and candidate targets for breeding programs aimed at improving wood quality and disease resilience in Fraxinus.