Dataset Information

A genotyping by sequencing approach can disclose Apis mellifera population genomic information contained in honey environmental DNA.

ABSTRACT: Awareness has been raised over the last years on the genetic integrity of autochthonous honey bee subspecies. Genomic tools available in Apis mellifera can make it possible to measure this information by targeting individual honey bee DNA. Honey contains DNA traces from all organisms that contributed or were involved in its production steps, including the honey bees of the colony. In this study, we designed and tested a genotyping by sequencing (GBS) assay to analyse single nucleotide polymorphisms (SNPs) of A. mellifera nuclear genome using environmental DNA extracted from honey. A total of 121 SNPs (97 SNPs informative for honey bee subspecies identification and 24 SNPs associated with relevant traits of the colonies) were used in the assay to genotype honey DNA, which derives from thousands of honey bees. Results were integrated with information derived from previous studies and whole genome resequencing datasets. This GBS method is highly reliable in estimating honey bee SNP allele frequencies of the whole colony from which the honey derived. This assay can be used to identify the honey bee subspecies of the colony that produced the honey and, in turn, to authenticate the entomological origin of the honey.

SUBMITTER: Bovo S

PROVIDER: S-EPMC9666642 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature

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A genotyping by sequencing approach can disclose Apis mellifera population genomic information contained in honey environmental DNA.

Bovo Samuele S Utzeri Valerio Joe VJ Ribani Anisa A Taurisano Valeria V Schiavo Giuseppina G Fontanesi Luca L

Scientific reports 20221115 1

Awareness has been raised over the last years on the genetic integrity of autochthonous honey bee subspecies. Genomic tools available in Apis mellifera can make it possible to measure this information by targeting individual honey bee DNA. Honey contains DNA traces from all organisms that contributed or were involved in its production steps, including the honey bees of the colony. In this study, we designed and tested a genotyping by sequencing (GBS) assay to analyse single nucleotide polymorphi ...[more]

PMID: 36379985

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Project description:BACKGROUND: Deep sequencing of viruses isolated from infected hosts is an efficient way to measure population-genetic variation and can reveal patterns of dispersal and natural selection. In this study, we mined existing Illumina sequence reads to investigate single-nucleotide polymorphisms (SNPs) within two RNA viruses of the Western honey bee (Apis mellifera), deformed wing virus (DWV) and Israel acute paralysis virus (IAPV). All viral RNA was extracted from North American samples of honey bees or, in one case, the ectoparasitic mite Varroa destructor. RESULTS: Coverage depth was generally lower for IAPV than DWV, and marked gaps in coverage occurred in several narrow regions (< 50 bp) of IAPV. These coverage gaps occurred across sequencing runs and were virtually unchanged when reads were re-mapped with greater permissiveness (up to 8% divergence), suggesting a recurrent sequencing artifact rather than strain divergence. Consensus sequences of DWV for each sample showed little phylogenetic divergence, low nucleotide diversity, and strongly negative values of Fu and Li's D statistic, suggesting a recent population bottleneck and/or purifying selection. The Kakugo strain of DWV fell outside of all other DWV sequences at 100% bootstrap support. IAPV consensus sequences supported the existence of multiple clades as had been previously reported, and Fu and Li's D was closer to neutral expectation overall, although a sliding-window analysis identified a significantly positive D within the protease region, suggesting selection maintains diversity in that region. Within-sample mean diversity was comparable between the two viruses on average, although for both viruses there was substantial variation among samples in mean diversity at third codon positions and in the number of high-diversity sites. FST values were bimodal for DWV, likely reflecting neutral divergence in two low-diversity populations, whereas IAPV had several sites that were strong outliers with very low FST. CONCLUSIONS: This initial survey of genetic variation within honey bee RNA viruses suggests future directions for studies examining the underlying causes of population-genetic structure in these economically important pathogens.

Project description:BackgroundThe molecular mechanisms underlying the post-mating behavioral and physiological transitions undergone by females have not been explored in great detail. Honey bees represent an excellent model system in which to address these questions because they exhibit a range of "mating states," with two extremes (virgins and egg-laying, mated queens) that differ dramatically in their behavior, pheromone profiles, and physiology. We used an incompletely-mated mating-state to understand the molecular processes that underlie the transition from a virgin to a mated, egg-laying queen. We used same-aged virgins, queens that mated once but did not initiate egg-laying, and queens that mated once and initiated egg-laying.ResultsDifferences in the behavior and physiology among groups correlated with the underlying variance observed in the top 50 predictive genes in the brains and the ovaries. These changes were correlated with either a behaviorally-associated pattern or a physiologically-associated pattern. Overall, these results suggest that the brains and the ovaries of queens are uncoupled or follow different timescales; the initiation of mating triggers immediate changes in the ovaries, while changes in the brain may require additional stimuli or take a longer time to complete. Comparison of our results to previous studies of post-mating changes in Drosophila melanogaster identified common biological processes affected by mating, including stress response and alternative-splicing pathways. Comparison with microarray data sets related to worker behavior revealed no obvious correlation between genes regulated by mating and genes regulated by behavior/physiology in workers.ConclusionStudying the underlying molecular mechanisms of post-mating changes in honey bee queens will not only give us insight into how molecular mechanisms regulate physiological and behavioral changes, but they may also lead to important insights into the evolution of social behavior. Post-mating changes in gene regulation in the brains and ovaries of honey bee queens appear to be triggered by different stimuli and may occur on different timescales, potentially allowing changes in the brains and the ovaries to be uncoupled.

Dataset Information

A genotyping by sequencing approach can disclose Apis mellifera population genomic information contained in honey environmental DNA.

Publications

A genotyping by sequencing approach can disclose Apis mellifera population genomic information contained in honey environmental DNA.

Similar Datasets

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