Chromosome-level genome assembly and population genomics unveil strigolactone-regulated growth adaptation in the mycoheterotrophic orchid <i>Gastrodia elata</i>

Mycoheterotrophic plants rely entirely on fungal symbionts for nutrients, yet the role of intraspecific genomic variation in shaping symbiotic adaptation remains unclear. <i>Gastrodia elata</i> is a mycoheterotrophic orchid with multiple cultivated varieties. Here, we generated a chromosome-level genome of <i>G. elata</i> Bl. f. <i>glauca.</i> Comparative genomic analyses with published <i>G. elata</i> assemblies revealed extensive intraspecific variation, characterized by transposon-mediated inversions occurring in 26% of syntenic regions. Notably, these regions frequently harbored orphan genes. Population genomic analysis of 150 individuals identified three genetically distinct clades: two cultivated (Clades E and G) and one hybrid (Clade I). Transcriptomic profiling uncovered clade-specific expression patterns in symbiosis-related genes, particularly within strigolactone signaling pathways. Molecular dynamics simulations and protein interaction assays demonstrated that polymorphisms in the M domain of the suppressor protein DWARF53 (GeD53) modulate strigolactone signaling by altering the stability of its interaction with the receptor (GeD14). Specifically, a Clade G-specific haplotype enhanced signaling through stabilized protein interactions, thereby influencing tuber development genes, whereas GeD14 variants had minimal functional impact. Further co-expression networks identified <i>LOL5</i>, <i>RNP1</i>, and <i>MTHD</i> as downstream effectors correlating with clade-specific tuber phenotypes and carbohydrate allocation. These findings demonstrate how intraspecific variation in strigolactone signaling components drives functional divergence in <i>G. elata</i>, providing both mechanistic insights into mycoheterotrophic adaptation and genomic resources for future research.