Graph-based pan-genome reveals structural and functional diversity across oil palm domestication gradients

Background Oil palm ( Elaeis guineensis Jacq.), the world’s most land‑efficient oil crop, underpins global vegetable oil supply yet faces mounting constraints from limited expansion, climate stress, and disease pressure. These challenges highlight the urgent need for genomic resources that capture species‑wide diversity to support sustainable improvement. While recent reference assemblies have advanced trait discovery, single linear genomes fail to represent the full spectrum of structural and gene‑content variation, limiting resolution of agronomic alleles. Results Here, we constructed a graph-based pan-genome from 30 diverse oil palm assemblies representing wild, semi-domesticated, and commercial accessions. We characterized structural variants, gene presence–absence variation, and copy-number gains, with focusing on functional stratification and resistance gene dynamics. The graph-based pan-genome revealed extensive structural and gene-content variation, including a large conserved core, complemented by shell and unique fractions enriched or biased toward regulatory, stress-responsive, and defense-related functions. Structural variation and duplication-derived copy-number gains contributed substantially to gene-content diversity, with semi-domesticated accessions exhibiting the greatest variability. Resistance gene repertoires showed contrasting patterns: receptor-like kinases remained comparatively stable, whereas the CNL subclass of NLR genes contributed disproportionately to shell-genome variation and duplication-associated turnover. Conclusions This graph-based pan-genome provides a curated multi-assembly reference and comparative framework for oil palm genomics. By capturing structural variants, gene-content variations, copy-number gains, and resistance gene dynamics across domestication gradients, it establishes a foundation for future pan-GWAS analysis, functional genomics, and molecular breeding strategies aimed at improving resilience and productivity in this globally important crop.