Data from: Complex population structure and haplotype patterns in Western Europe honey bee from sequencing a large panel of haploid drones
Creators
- 1. GenPhySE, Université de Toulouse, INRAE, INPT, INP-ENVT, 31326 Castanet Tolosan, France
- 2. INRAE, UR 406 Abeilles et Environment, UMT PrADE, 84914 Avignon, France
- 3. GeT-PlaGe, Genotoul, INRAE, Castanet Tolosan, France
- 4. Bee Research Institute, F.-Engels-Straße 32, 16540 Hohen Neuendorf, Germany
- 5. National Research Institute of Horticulture, Apiculture Division, 24–100 Puławy, Poland
- 6. CREA Research Centre for Agriculture and Environment, via di Saliceto 80, Bologna, Italy
- 7. University of Maribor, Faculty of Agriculture and Life Sciences, Pivola, Slovenia
- 8. Department of Agroecology, Science and Technology, Aarhus University, Slagelse, Denmark
- 9. Agroscope, Swiss Bee Research Centre, Bern, Switzerland
- 10. Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Bragança, Portugal
- 11. GABI, INRAE, AgroParisTech, Université Paris-Saclay, 78352 Jouy-en-Josas, France
Description
This vcf file contains 7.023.689 SNPs and 870 honey bee samples, as described in the paper "Complex population structure and haplotype patterns in Western Europe honey bee from sequencing a large panel of haploid drones" by Wragg et al., available at https://doi.org/10.1101/2021.09.20.460798 as preprint.
Eight hundred and seventy haploid drone samples from several honey bee subspecies hybrids were sequenced and aligned to the HAv3.1 reference genome. Sequence read alignment and genotyping quality filters were used to obtain a selection of 7.023.689 high-quality SNPs. The file Diversity_Study_629_Samples.txt corresponds to the 629 unique samples that were used for the diversity study described in the paper and can be used to recreate the restricted diversity dataset using bcftools or an equivalent software.
Having sequenced haploid drones, heterozygous SNPs resulting from duplicated regions could be filtered out and the data is phased.
Files
Diversity_Study_629_Samples.txt
Files
(26.7 GB)
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Additional details
Related works
- Is supplement to
- Working paper: 10.1101/2021.09.20.460798 (DOI)
References
- Wragg D, Eynard SE, Basso B, Canale-Tabet K, Labarthe E, Bouchez O, et al. Complex population structure and haplotype patterns in Western Europe honey bee from sequencing a large panel of haploid drones [Internet]. Genetics; 2021 Sep. Available from: http://biorxiv.org/lookup/doi/10.1101/2021.09.20.460798