Strain-specific and pooled genome sequences for populations of <i>Drosophila melanogaster</i> from three continents.

Casey M. Bergman; Penelope R. Haddrill

doi:10.12688/f1000research.6090.1

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Data Note

Strain-specific and pooled genome sequences for populations of Drosophila melanogaster from three continents.

[version 1; peer review: 3 approved]

Casey M. Bergman¹, Penelope R. Haddrill²

PUBLISHED 29 Jan 2015

Author details Author details

¹ Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
² Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK

OPEN PEER REVIEW

REVIEWER STATUS

This article is included in the Data: Use and Reuse collection.

Abstract

To contribute to our general understanding of the evolutionary forces that shape variation in genome sequences in nature, we have sequenced genomes from 50 isofemale lines and six pooled samples from populations of Drosophila melanogaster on three continents. Analysis of raw and reference-mapped reads indicates the quality of these genomic sequence data is very high. Comparison of the predicted and experimentally-determined Wolbachia infection status of these samples suggests that strain or sample swaps are unlikely to have occurred in the generation of these data. Genome sequences are freely available in the European Nucleotide Archive under accession ERP009059. Isofemale lines can be obtained from the Drosophila Species Stock Center.

Keywords

Drosophila melanogaster, Wolbachia pipientis, population genomics, population genetics, pool-seq, DNA-seq

Corresponding author: Casey M. Bergman

Competing interests: No competing interests were disclosed.

Grant information: This work was supported by Human Frontier Science Program Young Investigator grant RGY0093/2012 to CMB and National Environmental Research Council grant NE/G013195/1 to PRH.
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Copyright: © 2015 Bergman CM and Haddrill PR. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Data associated with the article are available under the terms of the Creative Commons Zero "No rights reserved" data waiver (CC0 1.0 Public domain dedication).

How to cite: Bergman CM and Haddrill PR. Strain-specific and pooled genome sequences for populations of Drosophila melanogaster from three continents. [version 1; peer review: 3 approved]. F1000Research 2015, 4:31 (https://doi.org/10.12688/f1000research.6090.1) First published: 29 Jan 2015, 4:31 (https://doi.org/10.12688/f1000research.6090.1) Latest published: 29 Jan 2015, 4:31 (https://doi.org/10.12688/f1000research.6090.1)

Introduction

Whole genome shotgun sequences can now be generated easily using short-read sequencing technology for most organisms. Hundreds of resequenced genomes now exist for Drosophila melanogaster that can be used for population and genomic analysis in this model insect species (Lack et al., 2014). To contribute to the worldwide sampling of population genomic data in D. melanogaster, we have sequenced genomes of multiple isofemale lines from three populations collected on different continents reported in Verspoor & Haddrill (2011): Montpellier, France (FR, n=20), Athens, Georgia, USA (GA, n=15) and Accra, Ghana (GH, n=15). Pools of these same isofemale lines were also sequenced to be able compare results based on strain-specific sequencing to pooled sequencing. Strains sequenced here were chosen because isofemale lines exist in the Drosophila Species Stock Center and because their infection status for the Wolbachia pipientis bacterial endosymbiont had previously been determined (Verspoor & Haddrill, 2011).

Materials and methods

Isofemale strains were selected randomly from the full population samples reported in Verspoor & Haddrill (2011). Genomic DNA for isofemale lines was prepared by snap freezing females in liquid nitrogen, then extracting DNA using a standard phenol-chloroform extraction protocol with ethanol and ammonium acetate precipitation. DNA samples were generated for each isofemale lines using 50, 25, and 25 adult females for the FR, GA and GH populations, respectively.

For pooled samples, single adult females from each isofemale line were used to construct two samples for each population. The first pooled sample contains one fly from each of the same strains that were sequenced as isofemale lines (FR_pool_20, GA_pool_15, GH_pool_15). The second pooled sample contains one fly from all isofemale lines sampled for each population reported in Verspoor & Haddrill (2011) (FR_pool_39, GA_pool_30, GH_pool_32).

500 bp short-insert libraries using the Illumina Paired-End Sample Prep Kit (Part # 1005063) were constructed and 90 bp paired-end reads were generated using an Illumina HiSeq 2000 to an estimated coverage of ~50× per strain by BGI-Hong Kong. Forty-one samples were sequenced in single lanes shared typically with two other samples on a single run and 15 samples were sequenced using the same layout on two runs, generating 71 pairs of fastq files for the 56 samples. Data were generated over a total of seven sequencing runs. Raw data was filtered by BGI to remove read pairs where either read contained adapters or greater than 50% of bases with a quality value <= 5. No other trimming or filtering of the raw data was performed prior to submission using original filenames provided by BGI to the European Nucleotide Archive.

Dataset validation

To validate the quality of the raw sequence data, forward and reverse reads were analyzed using fastQC (version 0.11.2) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Forward and reverse read files for all runs had PASS status for most fastQC statistics. Per base sequence quality gave FAIL status for forward or reverse read files for all of the GA samples (which were sequenced together on one run) because of poor quality scores in the terminal 1–5 bp of the read. These poor quality termini can be easily trimmed and do not affect mappability, as the percent of reads mapped for these runs is very high (see Dataset 1).

Run	SampleName	PercentMapped	WolbachiaDepth	WolbachiaBreadth	PredictedInfectionStatus	ExperimentalInfectionStatus	NumRead1	LengthRead1	BasicStatisticsRead1	PerBaseSequenceQualityRead1	PerTileSequenceQualityRead1	PerSequenceQualityScoresRead1	PerBaseSequenceContentRead1	PerSequenceGCContentRead1	PerBaseNContentRead1	SequenceLengthDistributionRead1	SequenceDuplicationLevelsRead1	OverrepresentedSequencesRead1	AdapterContentRead1	KmerContentRead1	NumRead2	LengthRead2	BasicStatisticsRead2	PerBaseSequenceQualityRead2	PerTileSequenceQualityRead2	PerSequenceQualityScoresRead2	PerBaseSequenceContentRead2	PerSequenceGCContentRead2	PerBaseNContentRead2	SequenceLengthDistributionRead2	SequenceDuplicationLevelsRead2	OverrepresentedSequencesRead2	AdapterContentRead2	KmerContentRead2
ERR705945	FR23	98.23	157.2661506	1	infected	y	43632996	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	43632996	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705946	FR24	98.26	253.4116299	1	infected	y	43346106	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	43346106	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705947	FR25	98.03	0.153247956	0.136415409	uninfected	n	43752189	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	43752189	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705948	FR26	98.07	0.089912146	0.080452318	uninfected	n	44941659	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	44941659	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705949	FR28	97.99	243.9421572	1	infected	y	43685595	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	43685595	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705950	FR29	97.87	0.081407529	0.07185147	uninfected	n	42950484	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	42950484	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705951	FR30	98.23	0.002058714	0.002058714	uninfected	n	42649081	90	PASS	PASS	WARN	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	42649081	90	PASS	PASS	WARN	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705952	FR31	98.02	0.009130119	0.003469051	uninfected	n	42446188	90	PASS	PASS	WARN	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	42446188	90	PASS	PASS	WARN	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705953	FR32	98.15	0.011783572	0.010895406	uninfected	n	43804532	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	43804532	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705954	FR33	98.19	0.032124608	0.030857829	uninfected	n	44688030	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	44688030	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705955	FR34	98	0.077131557	0.067549468	uninfected	n	43183556	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	43183556	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705956	FR35	98.3	315.1657004	1	infected	y	42738121	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	42738121	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705957	FR37	98.09	0.005362121	0.003086493	uninfected	n	43621725	90	PASS	PASS	FAIL	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	43621725	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705958	FR38	98.11	0.00454179	0.003613397	uninfected	n	42989610	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	42989610	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705959	FR39	97.53	0.02486153	0.002581674	uninfected	n	43653460	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	43653460	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705960	FR42	98.13	0.149636136	0.13461226	uninfected	n	43513827	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	43513827	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705961	FR44	98.25	176.3625032	1	infected	y	43999930	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	43999930	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705962	FR45	98.08	231.0189465	1	infected	y	43534574	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	43534574	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705963	FR46	98.25	194.166927	1	infected	y	43032033	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	43032033	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705964	FR48	98.31	183.7333295	1	infected	y	44173007	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	44173007	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705965	FRpool20	98.06	98.83144421	1	infected	na	44255580	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	44255580	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705966	FRpool39	97.86	111.5827327	1	infected	na	43945723	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	FAIL	43945723	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	FAIL
ERR705967	GA01	98.18	150.1729217	0.999719195	infected	y	44032050	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	44032050	90	PASS	FAIL	WARN	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705968	GA02	97.95	215.2846917	1	infected	y	43935045	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	43935045	90	PASS	FAIL	WARN	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705969	GA03	97.97	209.1012232	0.999730238	infected	y	43868793	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	43868793	90	PASS	FAIL	WARN	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705970	GA04	98.01	147.6178483	0.999727082	infected	y	43288985	90	PASS	PASS	WARN	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	43288985	90	PASS	FAIL	FAIL	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705971	GA05	97.77	0.101011057	0.090340453	uninfected	n	43348545	90	PASS	PASS	WARN	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	43348545	90	PASS	FAIL	FAIL	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705972	GA06	97.98	0.007450808	0.007387705	uninfected	n	43688990	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	43688990	90	PASS	PASS	WARN	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	FAIL
ERR705973	GA07	97.94	0.074818068	0.071163654	uninfected	n	43503291	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	43503291	90	PASS	FAIL	FAIL	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705974	GA08	98.1	182.8769394	0.999798861	infected	n	36815786	90	PASS	PASS	FAIL	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	36815786	90	PASS	FAIL	FAIL	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705975	GA08	97.9	14.52127022	0.999612709	infected	n	3132551	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	3132551	90	PASS	PASS	FAIL	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705976	GA09	98.07	188.2177543	0.999725505	infected	y	42739085	90	PASS	FAIL	FAIL	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	42739085	90	PASS	FAIL	FAIL	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705977	GA10	97.85	122.3655108	1	infected	y	42490121	90	PASS	FAIL	FAIL	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	42490121	90	PASS	FAIL	FAIL	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705978	GA11	97.95	246.9037461	0.999725505	infected	y	42911088	90	PASS	FAIL	FAIL	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	42911088	90	PASS	FAIL	WARN	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705979	GA12	97.96	197.0479893	0.999730238	infected	y	41533830	90	PASS	FAIL	FAIL	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	41533830	90	PASS	FAIL	WARN	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705980	GA13	98.15	168.4276705	0.999719983	infected	y	43339064	90	PASS	FAIL	WARN	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	43339064	90	PASS	FAIL	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705981	GA15	98	0.11221882	0.105207362	uninfected	n	43191678	90	PASS	FAIL	WARN	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	43191678	90	PASS	FAIL	WARN	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705982	GA17	98.02	0.116029412	0.108342759	uninfected	n	43375446	90	PASS	FAIL	WARN	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	43375446	90	PASS	FAIL	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705983	GApool15	98.1	60.85875647	1	infected	na	22168996	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	22168996	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705984	GApool15	98.1	60.83926259	1	infected	na	22205575	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	22205575	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705985	GApool30	98.08	52.71559543	1	infected	na	22154884	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	22154884	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705986	GApool30	98.08	52.71422611	1	infected	na	22185750	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	22185750	90	PASS	PASS	WARN	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705987	GH01	97.49	0.025129715	0.023159344	uninfected	n	22063039	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	22063039	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705988	GH01	97.49	0.022915612	0.021481611	uninfected	n	22097255	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	22097255	90	PASS	PASS	WARN	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705989	GH02	97.24	0.014733606	0.009604175	uninfected	n	22077514	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	22077514	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705990	GH02	97.24	0.014497761	0.008524336	uninfected	n	22109134	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	22109134	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705991	GH04	97.44	0.022074773	0.020114657	uninfected	n	22221140	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	22221140	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705992	GH04	97.44	0.021787657	0.019542003	uninfected	n	22253515	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	22253515	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705993	GH05	96.84	0.013619061	0.009383317	uninfected	n	22143765	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	22143765	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705994	GH05	96.85	0.014468576	0.00899366	uninfected	n	22170215	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	22170215	90	PASS	PASS	WARN	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705995	GH06	97.24	0.014600302	0.009973323	uninfected	n	22259211	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	22259211	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705996	GH06	97.23	0.011142294	0.00801794	uninfected	n	22287021	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	22287021	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705997	GH08	97.22	0.010342472	0.006264484	uninfected	n	22223535	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	22223535	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705998	GH08	97.22	0.008726264	0.006128814	uninfected	n	22160305	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	22160305	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR705999	GH09	97.36	0.005674477	0.004113483	uninfected	n	22217543	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	22217543	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR706000	GH09	97.35	0.00659025	0.00413478	uninfected	n	22150945	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	22150945	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR706001	GH10	97.35	0.009387261	0.004999282	uninfected	n	22258559	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	22258559	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR706002	GH10	97.34	0.008257729	0.003450909	uninfected	n	22189787	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	22189787	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR706003	GH11	97.49	0.007382184	0.007095068	uninfected	n	22202208	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	22202208	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR706004	GH11	97.48	0.007166847	0.00646089	uninfected	n	22122521	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	22122521	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR706005	GH12	97.49	0.006886042	0.006856857	uninfected	n	22103525	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	22103525	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR706006	GH12	97.48	0.006885253	0.006671494	uninfected	n	22030025	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	22030025	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR706007	GH14	97.3	0.008649752	0.005751778	uninfected	n	22276314	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	22276314	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR706008	GH14	97.28	0.010572796	0.008571663	uninfected	n	22209150	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	22209150	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR706009	GH15	97.48	59.98279515	0.999712884	infected	y	22233167	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	22233167	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR706010	GH15	97.48	60.15407617	0.999720772	infected	y	22163376	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	22163376	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR706011	GH16	97.11	0.012396453	0.006327586	uninfected	n	44096323	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	44096323	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR706012	GH17	97.55	0.003690698	0.003533731	uninfected	n	44519157	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	44519157	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR706013	GH18	97.24	0.025455481	0.016151831	uninfected	n	44409433	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	44409433	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS
ERR706014	GHpool15	97.35	9.322955366	0.99934768	infected	na	44828941	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS	44828941	90	PASS	PASS	PASS	PASS	WARN	PASS	PASS	PASS	PASS	PASS	PASS	PASS

Dataset 1.Descriptive statistics for validation of Drosophila melanogaster genome sequence data.

The PercentMapped column is obtained from the output of samtools flagstat using BAM files of mapped reads generated by bowtie2. The WolbachiaDepth, WolbachiaBreadth and PredictedInfectionStatus columns are obtained from the output of bedtools genomecov using BAM files of mapped reads generated by bowtie2. The ExperimentalInfectionStatus column is obtained from the results of Verspoor & Haddrill (2011). All other columns are obtained from the output of fastQC on the raw, unmapped reads.

To validate that the majority of the DNA sequenced is from the focal organism(s), untrimmed reads for each sample were mapped in paired-end mode using Bowtie (version 2.2.4) (Langmead & Salzberg, 2012) with default options to a “hologenome” reference generated by concatenating genome sequences for D. melanogaster (Genbank accession GCA_000001215.4) (Hoskins et al., 2015) and W. pipientis (Genbank accession AE017196) (Wu et al., 2004). Mapping to a hologenome was performed since many of these strains are known to be infected with Wolbachia (Verspoor & Haddrill, 2011). Unfiltered BAM files were used to estimate the proportion of reads in each sample that mapped to the expected target organisms using samtools flastat (version 0.1.19-44428cd) (Li et al., 2009). Greater than 96.8% of all reads in each run were mapped to the hologenome reference, indicating low levels of contaminating DNA in these data (Dataset 1).

Mapping to a hologenome also allowed us to verify if strain or sample swaps occurred in the process of producing these genome sequences by comparing predicted Wolbachia infection status with previously determined PCR-based infection status (Verspoor & Haddrill, 2011). Wolbachia infection status was predicted from genome sequences for each strain following a modified protocol from Richardson et al. (2012). Briefly, strains were predicted as "infected" when breadth of mapped read coverage was greater than 90% of the Wolbachia genome and mean depth of coverage was greater than one. Here, we compute breadth of coverage directly from the bedtools genomecov (version v2.22.0) (Quinlan & Hall, 2010) output rather than from a consensus sequence, as was done previously by Richardson et al. (2012). Predicted Wolbachia infection status matched experimentally determined infection status for 55/56 samples (98.2% concordance), indicating that strain or sample swaps are unlikely to have occurred during the generation of this dataset (Dataset 1). The only exception observed was for line GA08 from the Georgia population, which the WGS data indicates is infected while PCR data indicates it is uninfected. This observation can be explained by either PCR amplification failure for the GA08 stock in Verspoor & Haddrill (2011) or infection of the GA08 stock after data collection for Verspoor & Haddrill (2011). Further analysis of the Wolbachia infection status of this stock is warranted prior to use.

Data availability

Raw sequence data for the 56 samples reported here can be found in the European Nucleotide Archive (http://www.ebi.ac.uk/ena) under accession ERP009059. Isofemale lines can be obtained from the Drosophila Species Stock Center (https://stockcenter.ucsd.edu) under accessions 14021-0231.139, 14021-0231.140, 14021-0231.141, 14021-0231.142, 14021-0231.143, 14021-0231.144, 14021-0231.145, 14021-0231.146, 14021-0231.147, 14021-0231.148, 14021-0231.149, 14021-0231.150, 14021-0231.151, 14021-0231.152, 14021-0231.153, 14021-0231.154, 14021-0231.155, 14021-0231.156, 14021-0231.157, 14021-0231.158, 14021-0231.183, 14021-0231.184, 14021-0231.185, 14021-0231.186, 14021-0231.187, 14021-0231.188, 14021-0231.189, 14021-0231.190, 14021-0231.191, 14021-0231.192, 14021-0231.193, 14021-0231.194, 14021-0231.195, 14021-0231.196, 14021-0231.197, 14021-0231.163, 14021-0231.164, 14021-0231.165, 14021-0231.166, 14021-0231.167, 14021-0231.168, 14021-0231.170, 14021-0231.172, 14021-0231.174, 14021-0231.176, 14021-0231.177, 14021-0231.178, 14021-0231.180, 14021-0231.181 and 14021-0231.182..

Descriptive statistics for validation of each run can be found in Dataset 1, DOI: 10.5256/f1000research.6090.d42636 (Bergman & Haddrill, 2014).

Author contributions

CMB and PRH conceived the study. CMB and PRH designed the experiments. PRH conducted the experiments. CMB conducted the data analysis. CMB prepared the first draft of the manuscript. All authors were involved in the revision of the draft manuscript and have agreed to the final content.

Competing interests

No competing interests were disclosed.

Grant information

This work was supported by Human Frontier Science Program Young Investigator grant RGY0093/2012 to CMB and National Environmental Research Council grant NE/G013195/1 to PRH.

I confirm that the funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Acknowledgments

We thank BGI-Hong Kong for assistance with genome sequencing and initial data quality control analysis and Daniel Halligan for assistance with data management.

References

Bergman CM, Haddrill PR: Dataset 1 in “Strain-specific and pooled genome sequences for populations of Drosophila melanogaster from three continents”. F1000Research. 2014. Data Source
Hoskins RA, Carlson JW, Wan KH, et al.: The Release 6 reference sequence of the Drosophila melanogaster genome. Genome Res. 2015. PubMed Abstract | Publisher Full Text
Lack J, Cardeno C, Crepeau M, et al.: The Drosophila Genome Nexus: a population genomic resource of 623 Drosophila melanogaster genomes, including 197 genomes from a single ancestral range population. Genetics. 2015. Publisher Full Text
Langmead B, Salzberg SL: Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012; 9(4): 357–359. PubMed Abstract | Publisher Full Text | Free Full Text
Li H, Handsaker B, Wysoker A, et al.: The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16): 2078–9. PubMed Abstract | Publisher Full Text | Free Full Text
Quinlan AR, Hall IM: BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010; 26(6): 841–2. PubMed Abstract | Publisher Full Text | Free Full Text
Richardson MF, Weinert LA, Welch JJ, et al.: Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster. PLoS Genet. 2012; 8(12): e1003129. PubMed Abstract | Publisher Full Text | Free Full Text
Verspoor RL, Haddrill PR: Genetic diversity, population structure and Wolbachia infection status in a worldwide sample of Drosophila melanogaster and D. simulans populations. PLoS One. 2011; 6(10): e26318. PubMed Abstract | Publisher Full Text | Free Full Text
Wu M, Sun LV, Vamathevan J, et al.: Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements. PLoS Biol. 2004; 2(3): E69. PubMed Abstract | Publisher Full Text | Free Full Text

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¹ Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
² Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK

Competing interests

No competing interests were disclosed.

Grant information

This work was supported by Human Frontier Science Program Young Investigator grant RGY0093/2012 to CMB and National Environmental Research Council grant NE/G013195/1 to PRH.
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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© 2015 Bergman CM and Haddrill PR. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Data associated with the article are available under the terms of the Creative Commons Zero "No rights reserved" data waiver (CC0 1.0 Public domain dedication).

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Bergman CM and Haddrill PR. Strain-specific and pooled genome sequences for populations of Drosophila melanogaster from three continents. [version 1; peer review: 3 approved]. F1000Research 2015, 4:31 (https://doi.org/10.12688/f1000research.6090.1)

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Reviewer Report 06 Mar 2015

Sergey Nuzhdin, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA

Joyce Kao, New York University, New York, NY, USA

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https://doi.org/10.5256/f1000research.6521.r7868

The authors have presented a succinct, but detailed description of sequence data for several populations that will certainly be useful to the Drosophila community. I see no major flaws in the manuscript. However, as a minor suggestion, it may be ... Continue reading

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Reviewer Report 18 Feb 2015

Ian Dworkin, Department of Biology, McMaster University, Hamilton, ON, Canada

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https://doi.org/10.5256/f1000research.6521.r7634

This article primarily summaries the generation of a large set of resequenced Drosophila strains from three populations (Ghana, France and the US). Sequencing was done both individually for each isofemale strain, as well as in sequenced pools for each of ... Continue reading

This article primarily summaries the generation of a large set of resequenced Drosophila strains from three populations (Ghana, France and the US). Sequencing was done both individually for each isofemale strain, as well as in sequenced pools for each of three populations. While the primary goal of this research appears to be to provide the community with these additional genomic resources, the researchers were also particularly interested in examining Wolbachia infection status in the strains. Given that all raw data has been made available, it is likely that will provide an important useful resource for genomic analyses.

A few minor comments:
Some comparison of mapping quality for the pooled sequences (as compared to the individual isofemale strains) would have been useful.

Some explanation as to why the number of individuals used for the three different sequencing pools differed would have also been helpful to understand the provenance of the data.

Competing Interests: No competing interests were disclosed.

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Reviewer Report 03 Feb 2015

John E. Pool, Laboratory of Genetics, University of Wisconsin - Madison, Madison, WI, USA

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https://doi.org/10.5256/f1000research.6521.r7534

The authors' data will add value to Drosophila population genomic resources. I see no technical flaws in the manuscript. If the authors see fit, they could a bit more context to the data. For example, they could note that a ... Continue reading

The authors' data will add value to Drosophila population genomic resources. I see no technical flaws in the manuscript. If the authors see fit, they could a bit more context to the data. For example, they could note that a mosaic of homozygous and heterozygous regions may be expected from the isofemale line genomes. Optionally, they could also briefly put these three populations in historical context (i.e. that the species originated from sub-Saharan Africa but perhaps not western Africa specifically, that it expanded out of sub-Saharan Africa with a population bottleneck, and that North American populations are thought to have both European and African ancestry). The France and Ghana samples sequenced here may prove useful for identifying population ancestry in North American and other admixed populations.

Trivial edits:

Methods paragraph 1:
“each isofemale lines” (delete final “s”)

References - from title of Lack et al. 2015, delete second “genomes”. Update precise author information.

Competing Interests: No competing interests were disclosed.

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

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Joyce Kao, New York University, New York, USA

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Sergey Nuzhdin, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA

Joyce Kao, New York University, New York, NY, USA

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Approved

The authors have presented a succinct, but detailed description of sequence data for several populations that will certainly be useful to the Drosophila community. I see no major flaws in the manuscript. However, as a minor suggestion, it may be useful for readers if the authors update their Introduction to not only place the populations in the context of migration history, but perhaps to also briefly list the geographical areas covered by other sequence resources to clearly illustrate how their dataset adds onto the currently available resources.

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Ian Dworkin, Department of Biology, McMaster University, Hamilton, ON, Canada

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Approved

This article primarily summaries the generation of a large set of resequenced Drosophila strains from three populations (Ghana, France and the US). Sequencing was done both individually for each isofemale strain, as well as in sequenced pools for each of three populations. While the primary goal of this research appears to be to provide the community with these additional genomic resources, the researchers were also particularly interested in examining Wolbachia infection status in the strains. Given that all raw data has been made available, it is likely that will provide an important useful resource for genomic analyses.

A few minor comments:
Some comparison of mapping quality for the pooled sequences (as compared to the individual isofemale strains) would have been useful.

Some explanation as to why the number of individuals used for the three different sequencing pools differed would have also been helpful to understand the provenance of the data.

Competing Interests

No competing interests were disclosed.

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

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John E. Pool, Laboratory of Genetics, University of Wisconsin - Madison, Madison, WI, USA

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Approved

The authors' data will add value to Drosophila population genomic resources. I see no technical flaws in the manuscript. If the authors see fit, they could a bit more context to the data. For example, they could note that a mosaic of homozygous and heterozygous regions may be expected from the isofemale line genomes. Optionally, they could also briefly put these three populations in historical context (i.e. that the species originated from sub-Saharan Africa but perhaps not western Africa specifically, that it expanded out of sub-Saharan Africa with a population bottleneck, and that North American populations are thought to have both European and African ancestry). The France and Ghana samples sequenced here may prove useful for identifying population ancestry in North American and other admixed populations.

Trivial edits:

Methods paragraph 1:
“each isofemale lines” (delete final “s”)

References - from title of Lack et al. 2015, delete second “genomes”. Update precise author information.

Competing Interests

No competing interests were disclosed.

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

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[1] Bergman CM, Haddrill PR: Dataset 1 in “Strain-specific and pooled genome sequences for populations of Drosophila melanogaster from three continents”. F1000Research. 2014. Data Source

[2] Hoskins RA, Carlson JW, Wan KH, et al.: The Release 6 reference sequence of the Drosophila melanogaster genome. Genome Res. 2015. PubMed Abstract | Publisher Full Text

[3] Lack J, Cardeno C, Crepeau M, et al.: The Drosophila Genome Nexus: a population genomic resource of 623 Drosophila melanogaster genomes, including 197 genomes from a single ancestral range population. Genetics. 2015. Publisher Full Text

[4] Langmead B, Salzberg SL: Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012; 9(4): 357–359. PubMed Abstract | Publisher Full Text | Free Full Text

[5] Li H, Handsaker B, Wysoker A, et al.: The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16): 2078–9. PubMed Abstract | Publisher Full Text | Free Full Text

[6] Quinlan AR, Hall IM: BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010; 26(6): 841–2. PubMed Abstract | Publisher Full Text | Free Full Text

[7] Richardson MF, Weinert LA, Welch JJ, et al.: Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster. PLoS Genet. 2012; 8(12): e1003129. PubMed Abstract | Publisher Full Text | Free Full Text

[8] Verspoor RL, Haddrill PR: Genetic diversity, population structure and Wolbachia infection status in a worldwide sample of Drosophila melanogaster and D. simulans populations. PLoS One. 2011; 6(10): e26318. PubMed Abstract | Publisher Full Text | Free Full Text

[9] Wu M, Sun LV, Vamathevan J, et al.: Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements. PLoS Biol. 2004; 2(3): E69. PubMed Abstract | Publisher Full Text | Free Full Text

Strain-specific and pooled genome sequences for populations of Drosophila melanogaster from three continents.

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