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

## TL;DR

This study provides the first detailed genome of the Egyptian honeybee, revealing how it resists pathogens and adapts to harsh environments.

## Contribution

The first chromosome-scale genome assembly of Apis mellifera lamarckii, uncovering pathogen resistance and adaptation mechanisms.

## Key findings

- A triple-copy amplification of the Defensin-1 gene contributes to resistance against Varroa destructor mites.
- Transcriptomic profiling shows significant upregulation of SFCYP5 and Def-1 under pesticide stress.
- Genomic variants near immune and detoxification genes are enriched in pathogen-recognition pathways.

## Abstract

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.

The online version contains supplementary material available at 10.1186/s12864-025-12435-7.