Erezyilmaz, D.F.; Lu, K.
Genotype-phenotype association for mate choice in progeny of Drosophila simulans backcross
Cite this dataset as:
Erezyilmaz, D.F.; Lu, K. (2022). Genotype-phenotype association for mate choice in progeny of Drosophila simulans backcross. NERC EDS Environmental Information Data Centre. https://doi.org/10.5285/8dde3529-1cf7-4b0f-907d-a1631f38afd7
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This dataset is available under the terms of the Open Government Licence
https://doi.org/10.5285/8dde3529-1cf7-4b0f-907d-a1631f38afd7
The data resource contains Drosophila simulans backcross female mate choice (phenotype) aligned with whole-genome genotypes of 784 female backcross progeny. The data were 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 incomplete or inconsistent genomes 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.
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 incomplete or inconsistent genomes 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 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) 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 progeny of Drosophila simulans backcross. NERC EDS Environmental Information Data Centre. https://doi.org/10.5285/8dde3529-1cf7-4b0f-907d-a1631f38afd7
Related
This dataset is included in the following collections
Citations
Lu, K., & Erezyilmaz, D. (2024). Two major-effect loci influence interspecific mating in females of the sibling species, Drosophila simulans and D. sechellia. In S. Macdonald (Ed.), G3: Genes, Genomes, Genetics. Oxford University Press (OUP) https://doi.org/10.1093/g3journal/jkae279
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 Downstate
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
Keywords
Funding
Natural Environment Research Council Award: NE/S010351/1
Last updated
13 January 2025 10:11