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

Gilks, William P, Pennell, Tanya M, Flis, Ilona, Webster, Matthew T and Morrow, Edward H (2016) Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample. F1000Research, 5. a2644. ISSN 2046-1402

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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.

Item Type: Article
Schools and Departments: School of Life Sciences > Evolution, Behaviour and Environment
Subjects: Q Science > Q Science (General)
Q Science > QH Natural history > QH0301 Biology > QH0426 Genetics
Q Science > QH Natural history > QH0301 Biology > QH0426 Genetics > QH0447 Genes. Alleles. Genome
Q Science > QH Natural history > QH0301 Biology
Q Science > QH Natural history > QH0301 Biology > QH0426 Genetics > QH0460 Mutations
Depositing User: William Gilks
Date Deposited: 09 Nov 2016 15:55
Last Modified: 17 Aug 2017 15:43
URI: http://sro.sussex.ac.uk/id/eprint/65392

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Project NameSussex Project NumberFunderFunder Ref
2Sexes_1Genome: Sex-specific genetic effects on fitness and human diseaseG0781EUROPEAN UNION2011-STG280632