Compilation of Genome Resources

Species

Species Group

Lab/Genome Project

Reference

WGS Project

Stock Number

Assembly Version - Method

Coverage

D. affinis obscura C. Schlotterer (Vetmeduni Vienna, Austria) Palmieri et al. (2014) D. affinis Genome Release 1.0 14012-0141.02 CLC Genomics Workbench 4.6  

D. albomicans

immigrans

Kunming Institute of Zoology, Chinese Academy of Sciences

Zhou et al (2012).

ACVV01 - Reference Genome

KM55-5

DroAlb_1.0 - SOAPdenovo v. 1.04

100.0x

D. americana virilis Schlotterer, Vieira, Fonseca

H5 & W11
ABYSS (1.2.6), SSPACE, Minimus2
 

D. ananassae

melanogaster

Drosophila 12 Genomes Consortium

Drosophila 12 Genomes Consortium (2007)

AAPP01 – Reference Genome

14024-0371.13

dana_caf1 - CAF1

8.9x

D. arizonae repleta

T.A. Markow (LANGEBIO/UCSD)

Sanchez-Flores et al. (2016) ASM16502v1 15081-1271.41 AllPaths-LG 52x

D. biarmipes

melanogaster

Baylor College of Medicine

modENCODE Drosophila reference genome sequencing

AFFD02 - Reference Genome

14023-0361.10

Dbia_2.0 - Celera Assembler v. 6.1; BWA v. 0.6.0; Samtools v. 0.1.14; GATK v. 1.1-9; Indel_call_and_upgrade.pl v. 1.0

186.9x

D. bipectinata

melanogaster

Baylor College of Medicine

modENCODE Drosophila reference genome sequencing

AFFE02 – Reference Genome

14024-0381.19

Dbip_2.0 - Celera Assembler v. 6.1; BWA v. 0.6.0; Samtools v. 0.1.14; GATK v. 1.1-9; Indel_call_and_upgrade.pl v. 1.0

266.3x

D. busckii busckii D. Bachtrog (UC Berkeley) Vicoso & Bachtrog (2015) ASM101435v1   SOAPdenovo  

D. elegans

melanogaster

Baylor College of Medicine

modENCODE Drosophila reference genome sequencing

AFFF02 - Reference Genome

14027-0461.03

Dele_2.0 - Celera Assembler v. 6.1; BWA v. 0.6.0; Samtools v. 0.1.14; GATK v. 1.1-9; Indel_call_and_upgrade.pl v. 1.0

204.9x

D. erecta

melanogaster

Drosophila 12 Genomes Consortium

Drosophila 12 Genomes Consortium (2007)

AAPQ01 – Reference Genome

14021-0224.01 

dere_caf1 – CAF1

10.6x

D. eugracilis

melanogaster

Baylor College of Medicine

modENCODE Drosophila reference genome sequencing

AFPQ02 – Reference Genome

14026-0451.10

Deug_2.0 - Celera Assembler v. 6.1; BWA v. 0.6.0; Samtools v. 0.1.14; GATK v. 1.1-9; Indel_call_and_upgrade.pl v. 1.0

218.1x

D. ficusphila

melanogaster

Baylor College of Medicine

modENCODE Drosophila reference genome sequencing

AFFG02 - Reference Genome

14025-0441.05

Dfic_2.0 - Celera Assembler v. 6.1; BWA v. 0.6.0; Samtools v. 0.1.14; GATK v. 1.1-9; Indel_call_and_upgrade.pl v. 1.0

208.7x

D. grimshawi

grimshawi

Drosophila 12 Genomes Consortium

Drosophila 12 Genomes Consortium (2007)

AAPT01 - Reference Genome

15287-2541.00

dgri_caf1 - CAF1

7.9x

D. kikkawai

melanogaster

Baylor College of Medicine

modENCODE Drosophila reference genome sequencing

AFFH02 - Reference Genome

14028-0561.14

Dkik_2.0 - Celera Assembler v. 6.1; BWA v. 0.6.0; Samtools v. 0.1.14; GATK v. 1.1-9; Indel_call_and_upgrade.pl v. 1.0

181.7x

D. lowei obscura   Palmieri et al. (2014)

  CLC Genomics Workbench 4.6 using SRX091466 and SRX091467  

D. mauritiana

melanogaster

C. Schlotterer (Vetmeduni Vienna, Austria)

Nolte et al. (2013)

Drosophila mauritiana Genome Release 1.0

14021-0241.151 (MS17)

CLC Assembly Cell v. 3.1.0 beta2

50x

   
Garrigan et al. (2014) SRP012053 14021-0241.60 ABYSS 72-130x

D. melanogaster

melanogaster

Berkeley Drosophila Genome Project

Adams et al. (2000)

AABU01 - Reference Genome

14021-0231.36

Release 5

 

 

 

C.  Bergman (U. of Manchester, UK)

Haddrill & Bergman (2015)

Resequenced 50 D. melanogaster lines from France, USA, and Ghana

14021‑0231.139- 14021‑0231.197

 

 

D. miranda

obscura

D. Bachtrog (UC Berkeley)

Zhou & Bachtrog (2012)

AJMI02 - Reference Genome

14011-0101.21 (MSH22)

DroMir_2.2 - SOAPdenovo v. 1.04

~30x

D. mojavensis

repleta

Drosophila 12 Genomes Consortium

Drosophila 12 Genomes Consortium (2007)

AAPU01 - Reference Genome

15081-1352.22

dmoj_caf1 - CAF1

8.2x

D. navojoa repleta T.A. Markow (LANGEBIO/UCSD) Sanchez-Flores et al. (2016) ASM165401v1 15081-1374.12 AllPaths-LG 81x

D. persimilis

obscura

Drosophila 12 Genomes Consortium

Drosophila 12 Genomes Consortium (2007)

AAIZ01 - Reference Genome

14011-0111.49

dper_caf1 – CAF1

4.1x

D. pseudoobscura

obscura

Drosophila 12 Genomes Consortium

Drosophila 12 Genomes Consortium (2007)

AADE01

14011-0121.94

dpse_3.0 - PBJelly v. 12.8.2; Atlas genome assembly

9.7x Sanger; 24x PacBio

 

 

Delcher,A., Pop,M. and Salzberg,S.

 

AAFSO1

MV2-25

ASM14949v1 - Info. N/A

Info. N/A

D. rhopaloa

melanogaster

Baylor College of Medicine

modENCODE Drosophila reference genome sequencing

AFPP02 – Reference Genome

14029-0021.01

Drho_2.0 - Celera Assembler v. 6.1; BWA v. 0.6.0; Samtools v. 0.1.14; GATK v. 1.1-9; Indel_call_and_upgrade.pl v. 1.0

214.5x

D. santomea melanogaster P. Andolfatto (Princeton University)     14021-0271.01   ~10x

D. sechellia

melanogaster

Drosophila 12 Genomes Consortium

Drosophila 12 Genomes Consortium (2007)

AAKO01 - Reference Genome

14021-0248.25

dsec_caf1 – CAF1

4.9x

D. simulans

melanogaster

Drosophila 12 Genomes Consortium

Drosophila 12 Genomes Consortium (2007)

AAGH01 - Part of the Reference Genome mosaic with 6 other D. simulans lines.

14021-0251.195 (w501)

dsim_caf1- CAF1

4x

 

 

The Genome Institute (Washington University)

 

AASR01

14021-0251.199 (C167.4)

ASM18091v1

1x

 

 

The Genome Institute (Washington University)

 

AASS01

14021-0251.196 (MD106TS)

ASM18087v1

1x

 

 

The Genome Institute (Washington University)

 

AAST01

14021-0251.197 

(MD199S)

ASM18085v1

1x

 

 

The Genome Institute (Washington University)

 

AASU01

14021-00251.198 (New Caledonia 48S)

ASM18093v1

1x

 

 

The Genome Institute (Washington University)

 

AASV01

14021-0251.216 (SIM4)

ASM18097v1

1x

 

 

The Genome Institute (Washington University)

 

AASW01

14021-0251.194 (SIM6)

ASM18095v1

1x

    P. Andolfatto (Princeton University) Hu et al. (2013) SRA055460

14021-0251.195

(w501)

dsimV2 - Velvet 75X
    K. Thornton (UC Irvine) Rogers et al. (2014) SRP040290 & SRP029453  14021-0251.293 - 14021-0251.311   50-150x
D. subobscura obscura M. Noor (Duke University) Mittleman et al. (in press) PRJNA345020

14011-0131.12 & 14011-0131.13

   

D. suzukii

melanogaster

D. Begun (UC Davis)

Chiu et al. (2013)

AWUT01 – Reference Genome

14023-0311.03

Dsuzukii.v01 - SOAPdenovo v. 2

195x

 

 

O. Stabelli (IASMA Research and Innovation Center, Italy)

Stabelli et al. (2013)

CAKG01

N/A

ASM32968v1 – info. N/A

 

D. takahashii

melanogaster

Baylor College of Medicine

modENCODE Drosophila reference genome sequencing

AFFI02  - Reference Genome

14022-0311.13

Dtak_2.0 - Celera Assembler v. 6.1; BWA v. 0.6.0; Samtools v. 0.1.14; GATK v. 1.1-9; Indel_call_and_upgrade.pl v. 1.0

242.1x

D. virilis

virilis

Drosophila 12 Genomes Consortium

Drosophila 12 Genomes Consortium (2007)

AANI01 - Reference Genome

15010-1051.87

Dvir_caf1 - CAF1

8.0x

 

 

Washington University

Leung et al. (2010)

CM000831 - Chromosome 6 only

15010-1051.88

ASM412v1 – Info. N/A

Info. N/A

D. willistoni

willistoni

Drosophila 12 Genomes Consortium

Drosophila 12 Genomes Consortium (2007)

AAQB01 - Reference Genome

14030-0811.24

dwil_caf1 – CAF1

8.4x

D. yakuba

melanogaster

Drosophila 12 Genomes Consortium

Drosophila 12 Genomes Consortium (2007)

AAEU02

14021-0261.01 (Tai18E2)

dyak_caf1 - CAF1

9.1x

    K. Thornton (UC Irvine) Rogers et al. (2014) SRP040290 &SRP029453 14021-0261.38 - 14021-0261.54   50-150x

Scaptodrosophila

lebanonensis

victoria D. Bachtrog (UC Berkeley) Vicoso & Bachtrog (2015) ASM101444v1 SOAPdenovo  

Drosophila Species Stock Center Staff are dedicated to keeping this page up to date but we need help from the community in this endeavor. If you have updates or corrections please email Maxi Richmond (mrichmond@ucsd.edu). Last updated 1Aug2016.