0a1129e7-549c-42f8-8b9b-a57a3104e5fd_9912_-_william_gilks_v3.pdf (6.12 MB)
Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample
Version 2 2023-06-12, 08:34
Version 1 2023-06-09, 03:59
journal contribution
posted on 2023-06-12, 08:34 authored by William P Gilks, Tanya M Pennell, Ilona Flis, Matthew T Webster, Ted MorrowAs 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.
Funding
2Sexes_1Genome: Sex-specific genetic effects on fitness and human disease; G0781; EUROPEAN UNION; 2011-STG280632
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- Published
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- Published version
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F1000ResearchISSN
2046-1402Publisher
F1000ResearchExternal DOI
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5Article number
a2644Department affiliated with
- Evolution, Behaviour and Environment Publications
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- Yes
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- Yes
Legacy Posted Date
2016-11-09First Open Access (FOA) Date
2016-11-09First Compliant Deposit (FCD) Date
2016-11-09Usage metrics
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