Erezyilmaz, D.F.; Lu, K.
Genotype-phenotype association for mate choice in a Drosophila simulans-sechellia backcross population
Cite this dataset as:
Erezyilmaz, D.F.; Lu, K. (2022). Genotype-phenotype association for mate choice in a Drosophila simulans-sechellia backcross population. NERC EDS Environmental Information Data Centre. https://doi.org/10.5285/871c537d-2a84-432f-8597-7e895e0ffdcb
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This dataset is available under the terms of the Open Government Licence
https://doi.org/10.5285/871c537d-2a84-432f-8597-7e895e0ffdcb
The data resource contains Drosophila simulans-sechellia backcross female mate choice (phenotype) aligned with whole-genome genotypes of 692 female backcross progeny. The data was generated in a laboratory at Stony Brook University New York and each test was conducted in 28.5 x 95mm plastic vials. Phenotype data was collected in 2015 and the final analysis was completed in 2021. Illumina libraries were sequenced at University of Oregon G3 Genomics Center, and the multiplexed shotgun genotyping (MSG) software was run at Janelia Research Campus Virginia.
The experiments were conducted to align the genotype of females with behavioural phenotype, female preference. Three test females were allowed to choose from three males of either species. ‘Choice’ was determined by copulation, and the species of ‘chosen’ male was recorded before gDNA was extracted from the female.
Standard molecular biology was used to generate Illumina libraries from individual backcross females for sequencing. Deniz Erezyilmaz was responsible for data collection and interpretation. Those genomes with ambiguous genotypes at more than 25% of markers due to sparse reads/coverage were eliminated from the analysis.
The research was funded through NERC grant NE/S010351/1. Investigating the dual role of mate choice genes in behavioural isolation and hybridization.
The experiments were conducted to align the genotype of females with behavioural phenotype, female preference. Three test females were allowed to choose from three males of either species. ‘Choice’ was determined by copulation, and the species of ‘chosen’ male was recorded before gDNA was extracted from the female.
Standard molecular biology was used to generate Illumina libraries from individual backcross females for sequencing. Deniz Erezyilmaz was responsible for data collection and interpretation. Those genomes with ambiguous genotypes at more than 25% of markers due to sparse reads/coverage were eliminated from the analysis.
The research was funded through NERC grant NE/S010351/1. Investigating the dual role of mate choice genes in behavioural isolation and hybridization.
Publication date: 2022-04-13
View numbers valid from 01 June 2023 Download numbers valid from 20 June 2024 (information prior to this was not collected)
Format
Comma-separated values (CSV)
Provenance & quality
The Drosophila simulans-sechellia backcross genotypes were obtained by Multiplexed Shotgun Genotyping (Andolfatto et al, 2011), and the files were thinned using David Stern’s (Janelia Research Campus) script, pull_thin (github.com/dstern/pull_thin) were obtained by two-choice assay, females choosing between D. simulans and D. sechellia males.
Standard molecular biology was used to generate Illumina libraries from individual backcross females for sequencing, as described in: Andolfatto, P., Davison, D., Erezyilmaz, D., Hu, T.T., Mast, J., Sunayama-Morita, T., & Stern, D.L. (2011). Multiplexed shotgun genotyping for rapid and efficient genetic mapping. In Genome Research (Vol. 21, Issue 4, pp. 610–617). Cold Spring Harbor Laboratory. https://doi.org/10.1101/gr.115402.110
Standard molecular biology was used to generate Illumina libraries from individual backcross females for sequencing, as described in: Andolfatto, P., Davison, D., Erezyilmaz, D., Hu, T.T., Mast, J., Sunayama-Morita, T., & Stern, D.L. (2011). Multiplexed shotgun genotyping for rapid and efficient genetic mapping. In Genome Research (Vol. 21, Issue 4, pp. 610–617). Cold Spring Harbor Laboratory. https://doi.org/10.1101/gr.115402.110
Licensing and constraints
This dataset is available under the terms of the Open Government Licence
Cite this dataset as:
Erezyilmaz, D.F.; Lu, K. (2022). Genotype-phenotype association for mate choice in a Drosophila simulans-sechellia backcross population. NERC EDS Environmental Information Data Centre. https://doi.org/10.5285/871c537d-2a84-432f-8597-7e895e0ffdcb
Related
This dataset is included in the following collections
Supplemental information
Andolfatto, P., Davison, D., Erezyilmaz, D., Hu, T.T., Mast, J., Sunayama-Morita, T., & Stern, D.L. (2011). Multiplexed shotgun genotyping for rapid and efficient genetic mapping. In Genome Research (Vol. 21, Issue 4, pp. 610–617). Cold Spring Harbor Laboratory.
Correspondence/contact details
Authors
Lu, K.
State University of New York
Other contacts
Rights holder
University of Oxford
Custodian
NERC EDS Environmental Information Data Centre
info@eidc.ac.uk
Publisher
NERC EDS Environmental Information Data Centre
info@eidc.ac.uk
Additional metadata
Funding
Natural Environment Research Council Award: NE/S010351/1
Last updated
27 February 2024 16:22