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 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/).
Highlights
As part of a study on the molecular genetics of sexually dimorphic complex traits, we used hemiclonal analysis in conjunction with next-generation sequencing to characterise molecular genetic variation across the genome, from an outbred laboratory-adapted population of Drosophila melanogaster, LHM1,2
The 220 hemiclone females that were sequenced in the present study have a maternal haplotype, from the dm[6] reference assembly strain (BDGP6+ISO1 mito/dm[6], Bloomington Drosophila Stock Center no. 2057)[4,5], and have a different paternal genome each, sampled using cytogenetic cloning from the LHM base population
Previous studies indicate that the limits for DNA quantity in next-generation sequencing are 50–500ng[6]
Summary
As part of a study on the molecular genetics of sexually dimorphic complex traits, we used hemiclonal analysis in conjunction with next-generation sequencing to characterise molecular genetic variation across the genome, from an outbred laboratory-adapted population of Drosophila melanogaster, LHM1,2. The hemiclone experimental design allows the repeated phenotyping of multiple individuals, each with the same unrecombined haplotype on a different random genetic background This method has been used to investigate standing genetic variation and intersexual genetic correlations for quantitative traits[1] and gene expression[3], but it has not yet been used to obtain genomic data. We have made the mapped sequencing data, and genotype data publicly-available on NCBI, and have made the metadata, analysis code and logs publicly-available on Zenodo This is the first report of a study which uses methods for detecting both SNPs, indels and structural variants (deletions and duplications >1Kb in length), genome-wide in next-generation sequencing data, and the first report of whole genome resequencing in hemiclonal individuals
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