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Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample

View ORCID ProfileWilliam P. Gilks, Tanya M. Pennell, Ilona Flis, Matthew T. Webster, View ORCID ProfileEdward H. Morrow
doi: https://doi.org/10.1101/081554
William P. Gilks
1Evolution, Behaviour and Environment Group, School of Life Sciences, John Maynard Smith Building, University of Sussex, Falmer, BN1 9QG, United Kingdom,
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Tanya M. Pennell
1Evolution, Behaviour and Environment Group, School of Life Sciences, John Maynard Smith Building, University of Sussex, Falmer, BN1 9QG, United Kingdom,
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Ilona Flis
1Evolution, Behaviour and Environment Group, School of Life Sciences, John Maynard Smith Building, University of Sussex, Falmer, BN1 9QG, United Kingdom,
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Matthew T. Webster
2Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, PO Box 582, Uppsala Universitet, SE-751 23 Uppsala, Sweden.
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Edward H. Morrow
1Evolution, Behaviour and Environment Group, School of Life Sciences, John Maynard Smith Building, University of Sussex, Falmer, BN1 9QG, United Kingdom,
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Abstract

As part of a study into the molecular genetics of sexually dimorphic complex traits, we used next-generation sequencing to obtain data on genomic variation in an outbred laboratory-adapted fruit fly (Drosophila melanogaster) population. We successfully resequenced the whole genome of 2 females from the Berkeley reference line (BDGP6/dm6), and 220 hemiclonal females that were heterozygous for the same reference line genome, and a unique haplotype from the outbred base population (LHM). The use of a static and known genetic background enabled us to obtain sequences from whole-genome phased haplotypes. We used a BWA-Picard-GATK pipeline for mapping sequence reads to the dm6 reference genome assembly, at a median depth-of coverage of 31X, and have made the resulting data publicly-available in the NCBI Short Read Archive (BioProject PRJNA282591). Haplotype Caller discovered and genotyped 1,726,931 genetic variants (SNPs and indels, <200bp). Additionally, we used GenomeStrip/2.0 to discover and genotype 167 large structural variants (1-100Kb in size). Sequence data and quality-filtered genotype data are publicly-available at NCBI (Short Read Archive, dbSNP and dbVar). We have also released the unfiltered genotype data, and the code and logs for data processing, summary statistics, and graphs, via the research data repository, Zenodo, (https://zenodo.org/, ’Sussex Drosophila Sequencing’ community).

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted October 17, 2016.
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Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample
William P. Gilks, Tanya M. Pennell, Ilona Flis, Matthew T. Webster, Edward H. Morrow
bioRxiv 081554; doi: https://doi.org/10.1101/081554
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Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample
William P. Gilks, Tanya M. Pennell, Ilona Flis, Matthew T. Webster, Edward H. Morrow
bioRxiv 081554; doi: https://doi.org/10.1101/081554

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