title: Whole genome resequencing of a laboratory-adaptedDrosophila melanogasterpopulation sample.
abstract: As part of a study into the molecular genetics of sexually dimorphic complex traits, we used high-throughput sequencing to obtain data on genomic variation in an outbred laboratory-adapted fruit fly (Drosophila melanogaster) population. We successfully resequenced the whole genome of 220 hemiclonal females that were heterozygous for the same Berkeley reference line genome (BDGP6/dm6), 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 (Accession number SRP058502). We used Haplotype Caller to discover and genotype 1,726,931 small genomic variants (SNPs and indels, <200bp). Additionally we detected and genotyped 167 large structural variants (1-100Kb in size) using GenomeStrip/2.0. Sequence and genotype data are publicly-available at the corresponding NCBI databases: Short Read Archive, dbSNP and dbVar (BioProject PRJNA282591). We have also released the unfiltered genotype data, and the code and logs for data processing and summary statistics ( https://zenodo.org/communities/sussex_drosophila_sequencing/).
authors.affiliation: Evolution, Behaviour and Environment Group, School of Life Sciences, John Maynard Smith Building, University of Sussex, Falmer, UK.
authors.forename: William P
authors.initials: WP
authors.lastname: Gilks
authors.affiliation: Evolution, Behaviour and Environment Group, School of Life Sciences, John Maynard Smith Building, University of Sussex, Falmer, UK.
authors.forename: Tanya M
authors.initials: TM
authors.lastname: Pennell
authors.affiliation: Evolution, Behaviour and Environment Group, School of Life Sciences, John Maynard Smith Building, University of Sussex, Falmer, UK.
authors.forename: Ilona
authors.initials: I
authors.lastname: Flis
authors.affiliation: Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
authors.forename: Matthew T
authors.initials: MT
authors.lastname: Webster
authors.affiliation: Evolution, Behaviour and Environment Group, School of Life Sciences, John Maynard Smith Building, University of Sussex, Falmer, UK.
authors.forename: Edward H
authors.initials: EH
authors.lastname: Morrow
keywords: data; dimorphic traits; drosophila; sequencing