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Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample
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...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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F1000Research
2016
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5115224/ https://www.ncbi.nlm.nih.gov/pubmed/27928499 http://dx.doi.org/10.12688/f1000research.9912.3 |
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author | Gilks, William P. Pennell, Tanya M. Flis, Ilona Webster, Matthew T. Morrow, Edward H. |
author_facet | Gilks, William P. Pennell, Tanya M. Flis, Ilona Webster, Matthew T. Morrow, Edward H. |
author_sort | Gilks, William P. |
collection | PubMed |
description | 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 (LH (M)). 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/). |
format | Online Article Text |
id | pubmed-5115224 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | F1000Research |
record_format | MEDLINE/PubMed |
spelling | pubmed-51152242016-12-06 Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample Gilks, William P. Pennell, Tanya M. Flis, Ilona Webster, Matthew T. Morrow, Edward H. F1000Res Data Note 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 (LH (M)). 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/). F1000Research 2016-12-22 /pmc/articles/PMC5115224/ /pubmed/27928499 http://dx.doi.org/10.12688/f1000research.9912.3 Text en Copyright: © 2016 Gilks WP et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Data Note Gilks, William P. Pennell, Tanya M. Flis, Ilona Webster, Matthew T. Morrow, Edward H. Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample |
title | Whole genome resequencing of a laboratory-adapted
Drosophila melanogaster population sample |
title_full | Whole genome resequencing of a laboratory-adapted
Drosophila melanogaster population sample |
title_fullStr | Whole genome resequencing of a laboratory-adapted
Drosophila melanogaster population sample |
title_full_unstemmed | Whole genome resequencing of a laboratory-adapted
Drosophila melanogaster population sample |
title_short | Whole genome resequencing of a laboratory-adapted
Drosophila melanogaster population sample |
title_sort | whole genome resequencing of a laboratory-adapted
drosophila melanogaster population sample |
topic | Data Note |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5115224/ https://www.ncbi.nlm.nih.gov/pubmed/27928499 http://dx.doi.org/10.12688/f1000research.9912.3 |
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