Compendium of Drosophila Genome Assemblies

Posted 28 Apr 2012 in drosophila, genome bioinformatics, high throughput sequencing

[UPDATE: The UCSD Drosophila Species Stock Center now maintains a list of information about Drosophila genome sequences: The compendium here will no longer be updated. To ensure a single, up-to-date source of information, please send suggested links to the DSSC.]

Since the publication of the Drosophila melanogaster genome, the D. pseudoobscura genome, and the remaining 10 species from the Drosophila 12 Genomes Project, a number of other Drosophila genomes have been sequenced and assembled using whole genome shotgun approaches. Periodically, I find myself needing to find versions of these assemblies from the data producer, NCBI, Flybase, or UCSC, and so to help streamline this process I’ve collected these links together into a single compendium here, along with links to the original stocks used for sequencing. Hopefully this will be of use to others as well.

Data Producer
UCSC Genome Browser
Stock Center
D. melanogaster Berkeley Drosophila Genome Project AABU00000000 dmel dm3 1522
D. simulans Washington University Genome Sequencing Center AAGH00000000 dsim droSim1 n.a.
D. simulans Andolfatto Lab n.a. n.a. n.a. 1380
D. mauritiana Schlotterer Lab n.a. n.a. n.a. E-18912
D. sechellia Broad Institute AAKO00000000 dsec droSec1 1373
D. yakuba Washington University Genome Sequencing Center AAEU00000000 dyak droYak2 1385
D. santomea Andolfatto Lab n.a. n.a. n.a. 2367
D. erecta Agencourt Biosciences AAPQ00000000 dere droEre2 1374
D. ficusphila Baylor College of Medicine Genome Center AFFG00000000 n.a. n.a. 2332
D. eugracilis Baylor College of Medicine Genome Center AFPQ00000000 n.a. n.a. 2350
D. suzukii University of Edinburgh GenePool CAKG00000000 n.a. n.a. n.a
D. biarmipes Baylor College of Medicine Genome Center AFFD00000000 n.a. n.a. 2312
D. takahashii Baylor College of Medicine Genome Center AFFI00000000 n.a. n.a. 2325
D. elegans Baylor College of Medicine Genome Center AFFF00000000 n.a. n.a. 2334
D. rhopaloa Baylor College of Medicine Genome Center AFPP00000000 n.a. n.a. 2327
D. kikkawai Baylor College of Medicine Genome Center AFFH00000000 n.a. n.a. 2330
D. bipectinata Baylor College of Medicine Genome Center AFFE00000000 n.a. n.a. 2329
D. ananassae Agencourt Biosciences AAPP00000000 dana droAna3 1368
D. pseudoobscura Baylor College of Medicine Genome Center AADE00000000 dpse dp4 1277
D. persimilis Broad Institute AAIZ00000000 dper droPer1 1369
D. miranda Bachtrog Lab AJMI00000000 n.a. n.a. n.a.
D. willistoni J. Craig Venter Institute AAQB00000000 dwil droWil1 1375
D. virilis Agencourt Biosciences AANI00000000 dvir droVir3 1371
D. americana Vieira Lab n.a. n.a. n.a. n.a.
D. mojavensis Agencourt Biosciences AAPU00000000 dmoj droMoj3 1370
D. grimshawi Agencourt Biosciences AAPT00000000 dgri droGri2 1225
D. albomicans Wang/Bachtrog Labs ACVV00000000 n.a. n.a. n.a.


  1. This is a great resource, thank you for compiling everything together in one place! We will post a link on our website.

  2. JJQ

    I want to second what the DSSC said – thanks for the list and links! I really appreciate having all of these resources in one place.

  3. Julien Roux

    Thanks for this useful post!
    Do you have any idea what is the closest outgroup genome sequence available?

    Also, after additional web and literature search, there are some new additional genome sequences available, thta you might want to add to the list:
    – D. suzukii is also available from here:
    Chiu JC, Jiang X, Zhao L, Hamm CA, Cridland JM, et al. (2013) Genome of Drosophila suzukii, the Spotted Wing Drosophila. G3: Genes|Genomes|Genetics 3: 2257-2271.
    – It seems that the Andolfatto lab is also sequencing D. teissieri, but I couldn’t find the link to the data.
    – An independent de novo genome assembly of D. mauritiana was performed for this paper: Garrigan D, Kingan SB, Geneva AJ, Vedanayagam JP, Presgraves DC (2014) Genome diversity and divergence in Drosophila mauritiana: multiple signatures of faster X evolution. Genome Biol Evol 6: 2444-2458.
    – D. affinis was sequenced by the Schlotterer Lab for this paper: Palmieri N, Kosiol C, Schlötterer C (2014) The life cycle of Drosophila orphan genes. eLife
    – This paper also used data from D. lowei available on SRA (Noor lab?):
    – The i5K project nominated 3 additional species, not sure what is their status: Drosophila hydei, Drosophila immigrans, Drosophila subobscura

    Hope this helps!

  4. caseybergman

    Dear Julien

    Thanks for the nice words and suggested links. I’ve decided not to update this page since the DSSC now maintains a similar resource, and they are interested in actively maintaining this compendium. I’ve made a note at the top of this page about this. Please send your suggested links to the DSSC, if they aren’t there already.

    Best regards,

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