[UPDATE: The UCSD Drosophila Species Stock Center now maintains a list of information about Drosophila genome sequences: https://stockcenter.ucsd.edu/info/genomeresources. 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.
This is a great resource, thank you for compiling everything together in one place! We will post a link on our website.
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.
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:
http://spottedwingflybase.oregonstate.edu/
http://www.ncbi.nlm.nih.gov/nuccore/AWUT00000000.1
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. http://genomics.princeton.edu/AndolfattoLab/research3.html
– 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.
http://trace.ddbj.nig.ac.jp/DRASearch/study?acc=SRP012053
– 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?):
https://trace.ddbj.nig.ac.jp/DRASearch/study?acc=SRP007802
– The i5K project nominated 3 additional species, not sure what is their status: Drosophila hydei, Drosophila immigrans, Drosophila subobscura
Hope this helps!
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,
Casey