Genome Resequencing of the Honeybee Apis mellifera jemenetica (Hymenoptera: Apidae): A Key Tool towards Characterization, Conservation, and Genomic Selection

Abstract

We report the whole-genome sequence of the Arabian honeybee (Apis mellifera jemenetica). Seven A. m. jemenetica samples were sequenced representing three distinct subpopulations. Generated sequence reads were mapped to the reference honeybee Apis mellifera genome (Amel_HAv3.1). Data revealed genome-wide patterns of genetic variation which can be useful in the characterization and assessment of positive selection of the Arabian honeybee using different genetic markers. In total, 75.16 Gb of clean bases were generated, and the GC content of samples ranged between 31.9 and 35.3%. The effective reference genome size is 223,937,270 bp. The mapping rate of samples varied from 88.97% to 96.19%, and the effective mapping depth was between 41.80 and 48.84X. Single-nucleotide polymorphisms (SNPs) among sequenced individuals ranged between 2379499 and 2396116 with respect to the reference A. mellifera genome (Amel_HAv3.1), and 2% of the SNPs were nonsynonymous. Genome Analysis Toolkit (GATK) detected 1097962–1109829 InDels and 10090–11962 structural variations (SV) from which 22.1 to 33.8% were in the form of deletions. Copy number variation (CNV) ranged between 550 and 2824, and 45–91% of them were downregulated. These variations among interbreeding individuals or groups of the same species may reflect an adaptive environmental response and fitness among different subpopulations and can be very useful for subspecies characterization, conservation, and selection of the Arabian honeybee.