Targeted long-read Nanopore sequencing data for the complete Vitellogenin gene from 543 Apis mellifera honey bees
This dataset contains targeted long-read Nanopore sequencing data for the complete vitellogenin (vg) gene from 543 diploid Apis mellifera honey bees sampled from 21 apiaries across Europe and the USA. Raw reads were phased into two vg alleles per individual and used to generate haplotype consensus sequences for population genetic analyses of vg variation, haplogroup structure, recombination, and signatures of selection.  In honey bees (Apis mellifera), the ancient and multifunctional protein Vitellogenin (Vg) is tightly linked to colony health. Vg contributes to several key traits, including nutrient transport, immunity support, and regulation of social behavior. However, the role of selective forces in shaping natural variation in this gene is poorly understood. To address this, we use a population genetic approach based on long-read sequences to characterize full-length vg haplotype variation. Using sequences from 543 honey bees sampled in Europe and the USA, including different subspecies and multiple geographical locations and we test whether patterns of variation and divergence are compatible with selection. Our findings show that vg segregates into two main haplotype versions (haplogroups), defined by 65 common polymorphisms, which together account for 69% of the sampled haplotypes. One haplogroup is abundant in A. m. mellifera conservatory samples. At the protein level, the haplogroups differ at only seven positions, all of which are in the protein's lipid-binding cavity. This concentration at a single functional region motivates the hypothesis that haplogroup differences may affect lipid binding or transport. The remaining 58 polymorphisms are synonymous or in noncoding regions, which could influence gene expression and splicing. We further find that comparisons of variation across our samples are compatible with a history of positive selection at vg, in line with prior work. Taken together, our results document substantial vg haplotype structure across sampled honey bees and identify protein-coding differences concentrated in the lipid-binding cavity. This provides a foundation for future work linking vg genetic variation to Vg function and colony-related phenotypes.
This dataset contains targeted long-read Nanopore sequencing data for the complete vitellogenin (vg) gene from 543 diploid Apis mellifera honey bees sampled from 21 apiaries across Europe and the USA. Raw reads were phased into two vg alleles per individual and used to generate haplotype consensus sequences for population genetic analyses of vg variation, haplogroup structure, recombination, and signatures of selection.  In honey bees (Apis mellifera), the ancient and multifunctional protein Vitellogenin (Vg) is tightly linked to colony health. Vg contributes to several key traits, including nutrient transport, immunity support, and regulation of social behavior. However, the role of selective forces in shaping natural variation in this gene is poorly understood. To address this, we use a population genetic approach based on long-read sequences to characterize full-length vg haplotype variation. Using sequences from 543 honey bees sampled in Europe and the USA, including different subspecies and multiple geographical locations and we test whether patterns of variation and divergence are compatible with selection. Our findings show that vg segregates into two main haplotype versions (haplogroups), defined by 65 common polymorphisms, which together account for 69% of the sampled haplotypes. One haplogroup is abundant in A. m. mellifera conservatory samples. At the protein level, the haplogroups differ at only seven positions, all of which are in the protein's lipid-binding cavity. This concentration at a single functional region motivates the hypothesis that haplogroup differences may affect lipid binding or transport. The remaining 58 polymorphisms are synonymous or in noncoding regions, which could influence gene expression and splicing. We further find that comparisons of variation across our samples are compatible with a history of positive selection at vg, in line with prior work. Taken together, our results document substantial vg haplotype structure across sampled honey bees and identify protein-coding differences concentrated in the lipid-binding cavity. This provides a foundation for future work linking vg genetic variation to Vg function and colony-related phenotypes.
NORWEGIAN UNIVERSITY OF LIFE SCIENCES