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I'm trying to correct low coverage parts of an assembly of these PacBio reads with Illumina data. According to PacBio they "have sequenced adult males from a subline of the ISO1 (y; cn, bw, sp) strain of D. melanogaster. This is the same stock used in the official BDGP reference assemblies since the first genome sequence release in 2000."

Unfortunately the Illumina data sequenced by the same guys (also ISO1 (y; cn, bw, sp) but 2057) "revealed significant differences" to the official reference strain. Something I found out as well.

Now I'm trying to find Illumina data for the reference strain at NCBI, but I'm pretty lost. There seem to be dozens of different strains and I can't figure out which one is the reference strain, mostly because I'm completely unfamiliar with the biological nomenclature like ISO1, (y; cn, bw, sp) and 2057 or D8, D20-C2, mbn2 and so on.

So I guess my question is: What strain exactly is the drosophila melanogaster reference strain used in BDGP and how do I find SRA data of this strain on NCBI?

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As described in File S1 of Gutzwiller et al (2015) the relationship between the sub-strain of the ISO1 reference strain used by BDGP for the original Drosophila genome proejct, and the sub-strain in the Bloomington Drosophila Stock Center is complicated:

"We investigated the cause of the discrepancy of Wolbachia sequences in the Berkeley Drosophila Genome Project (BDGP) and Bloomington Drosophila Stock Center (BDSC) ISO1 genomic data by first establishing the provenance of these lineages. As documented in the BDSC database, the BDSC ISO1 sub-strain was donated directly to the stock center by Jim Kenni- son in 1994. The ISO1 sub-strain used by the BDGP was obtained from Gerry Rubin’s lab in the late 1990’s (Roger Hoskins, personal communication). The Rubin lab ISO1 sub-strain was obtained in the mid-1990s from Jim Kennison via at least one intermediate lab (Todd Laverty, personal communication). Thus, in contrast to naive assumptions, the ISO1 sub-strain at the Bloomington Drosophila Stock Center is neither a direct descendant nor progenitor of the ISO1 sub-strain used in the D. melanogaster genome project, and these two sub-strains have had independent trajectories since at least 1994."

The PacBio dataset you refer to was generated using the BDGP sub-strain. The Illumina data you refer to was generated using the BDSC sub-strain and is available here: https://www.ncbi.nlm.nih.gov/sra/ERX645969[accn]

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  • $\begingroup$ Yes, but I'm looking for Illumina data for the BDGP sub-strain. It is exactly the problem that one of the data sets is BDGP and the other BDSC. Otherwise great background information! $\endgroup$ – BlindKungFuMaster May 3 '17 at 7:02
  • $\begingroup$ As far as I know, there is no public Illumina DNA-seq data from the BDGP sub-strain of ISO1. $\endgroup$ – C. Bergman May 3 '17 at 12:03

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