Whole-genome sequencing of Apis mellifera lamarckii: first comprehensive genomic atlas of Egyptian honeybees reveals pathogen resistance mechanisms and local adaptation signatures

This study presents the first comprehensive genomic atlas of Egypt’s native honeybee, Apis mellifera lamarckii. Along with the Morphometric Assessment, a thorough examination of A. m. lamarckii workers and taxonomical characterization was conducted. Using PacBio long-read sequencing and Hi-C scaffolding, we generated a chromosome-scale genome assembly, revealing unique adaptations underlying its resilience to pathogens and arid climates. Key genomic findings revealed a triple-copy amplification of the Defensin-1 (Def-1) gene, providing a structural basis for its natural resistance to Varroa destructor mites. Transcriptomic profiling under pesticide stress confirmed functional consequences, showing dramatic upregulation of SFCYP5 (> 110-fold) and Def-1 (> 50-fold), alongside trade-offs including ABA suppression (0.01-fold). Morphometric analysis of 120 workers confirmed distinct physical traits, including smaller body size (proboscis: 5.45–5.46 mm; hindwing length: ~6.01 mm) and reduced colony sizes compared to European subspecies. Whole-genome resequencing identified structural variants near immune loci (Def-1 and Hymenoptaecin) and detoxification genes (SFCYP family), with significant enrichment in pathogen-recognition pathways (KEGG map04626; p < 0.0001. These results resolve A. m. lamarckii’s evolutionary divergence and provide critical genomic tools for conserving its unique adaptations amid hybridization threats.