Comparative Chloroplast Genomics and Maternal Lineage Diversity in Oil Palm (Elaeis guineensis)

Background Oil palm ( Elaeis guineensis ) is the world’s most important source of vegetable oil, yet comparative studies of its chloroplast genomes remain limited, particularly for African accessions. Understanding plastome diversity and maternal lineage variation is critical for tracing domestication history and developing molecular markers for breeding and conservation. Results We report the first complete chloroplast genomes from Tanzanian Dura and Pisifera, Cameroonian Dura, and the ancestral Deli Dura from Indonesia, analyzed alongside 44 additional plastomes. Comparative analyses revealed highly conserved genome organization and gene content, with subtle differences in IR–SC boundaries and intergenic spacers. Simple sequence repeat (SSR) profiling confirmed the dominance of A/T mononucleotide repeats but highlighted lineage-specific variation, including a markedly reduced genic SSR density in Pisifera-Tz, while total SSR counts remained stable across accessions (≈ 859–860; Supplementary Table S3). Phylogenetic reconstruction clustered Pisifera-Tz with Dura-Cmr, while Dura-Tz and Dura-BBG formed distinct clades, reflecting multiple maternal lineages. Haplotype network analysis identified 14 distinct haplotypes, revealing moderate but structured plastome diversity. Benchmarking of sequencing platforms demonstrated complementary strengths: MGI provided deep coverage, while PacBio improved assembly contiguity and resolution of repetitive regions. Conclusion This study expands plastome resources for E. guineensis , generating the first Tanzanian and Cameroonian chloroplast genomes and uncovering lineage-specific SSR variation. Integration of comparative genomics, phylogenetics, and haplotype analysis advances understanding of oil palm domestication and supports the development of plastome-based molecular markers for breeding, conservation, and genetic resource management.