Published July 10, 2023 | Version v1
Dataset Open

Prunus armeniaca SNPs dataset

Authors/Creators

  • 1. Royal Botanic Gardens, Kew
  • 2. INRAE, Univ. Bordeaux, Biogeco
  • 3. INRAE, UMR 1332 BFP

Description

-"armeniaca.SNPs.vcf.gz": dataset including SNPs genotypes for 255 individuals of Prunus armeniaca from Central Asia, filtered from Groppi et al. 2021 (https://www.nature.com/articles/s41467-021-24283-6). 

-"P.armeniaca Q-values.xlsx": fastStructure Q-value assignment as obtained in Groppi et al. (2021) for each individual (indicated by unique labels in the first column). Q-value assignments to the two main Asian gene pools ("Northern" and "Southern" gene pools).

This dataset was prepared in association with the manuscript:

Gargiulo R., Decroocq V., González-Martínez S.C., Paz-Vinas I., Aury J-M., Lesur Kupin I., Plomion C., Schmitt S., Scotti I., Heuertz M. 2023. Estimation of contemporary effective population size in plant populations: limitations of genomic datasets. bioRxiv 2023.07.18.549323; doi: https://doi.org/10.1101/2023.07.18.549323

See the analytical workflow at: https://github.com/Ralpina/Ne-plant-genomic-datasets/blob/main/README.md (https://doi.org/10.5281/zenodo.8134169)

 

Files

Files (31.5 GB)

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md5:9d8aa9d970b208b9b702f4599f1cff68
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Additional details

References

  • Groppi, Alexis et al. (2021). Population genomics of apricots unravels domestication history and adaptive events. Nature Communications. 12, 3956.
  • Gargiulo R., Decroocq V., González-Martínez S.C., Paz-Vinas I., Aury J-M., Lesur Kupin I., Plomion C., Schmitt S., Scotti I., Heuertz M. (2023). Estimation of contemporary effective population size in plant populations: limitations of genomic datasets. bioRxiv 2023.07.18.549323; doi: https://doi.org/10.1101/2023.07.18.549323
  • Gargiulo R. (2023). Ralpina/Ne-plant-genomic-datasets: Ne-plant-genomic-datasets (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.8134169