Whole-genome sequencing of wild and ancestral Dura provides insight into genetic shifting during the domestication of oil palm (Elaeis guineensis Jacq.)

Oil palm ( Elaeis guineensis Jacq. ) is a vital global crop, and its genetic improvement benefits from comprehensive genome sequencing. This study presents the whole-genome sequencing and annotation of two key genetic resources: the wild (Eg-DCM) and ancestral (Eg-DBG) Dura accessions. Comparative analysis with the advanced breeding Dura (Eg-D1) provides insights into genome structure, gene content, and evolutionary shifts during domestication. Retroelements dominated both genomes, constituting 46.10% in Eg-DBG and 43.85% in Eg-DCM. Gene prediction found 61,256 and 53,985 genes, refined into high-confidence sets of 39,263 (Eg-DBG) and 35,298 (Eg-DCM). A decline in resistance genes (R-genes) was observed in Eg-D1, suggesting that selection pressures influenced their retention. Codon usage analysis revealed significant shifts, showing increased mutational bias, with a stronger correlation between GC content at the third (GC3) and the first and second (GC12) codon positions in Eg-D1. Moreover, the relationship between GC3 and the effective number of codons (ENC) suggests stronger selection pressure driving codon optimization, a trend commonly observed in domesticated crops. These findings highlight how artificial selection has shaped genome composition, resistance mechanisms, and translational efficiency. The assembled genomes provide essential resources for understanding oil palm evolution and optimizing breeding strategies for enhanced productivity and sustainability.