As part of ongoing efforts to characterize complete genome sequences of microbial symbioints of Drosophila species, the Bergman Lab has been involved in mining complete genomes of the Wolbachia endosymbiont from whole-genome shotgun sequences of D. melanogaster. This work is inspired by Steve Salzberg and colleagues’ pioneering paper in 2005 showing that Wolbachia genomes can be extracted from the whole-genome shotgun sequence assemblies of Drosophila species. We have adapted this technique to utilize short-read next generation sequencing data from population genomics projects in D. melanogaster, together with the reference Wolbachia genome published by Wu et al. (2005).
Currently we have identified infection status and extracted nearly-complete genomes from the two major resequencing efforts in D. melanogaster: the Drosophila Genetic Reference Panel (DGRP) and Drosophila Population Genomics Project (DPGP). We employ a fairly standard BWA/SAMtools pipeline, with a few tricks that are essential for getting good quality assemblies and consensus sequences. Our first iteration of this pipeline was used to predict infection status in the DGRP strains. These results have been published in the DGRP main paper published in early 2012, and can be found in Supplemental Table 9 of the DGRP paper or more usefully in a comma-separated file at the DGRP website.
We have now applied an update version of our pipeline to both the DGRP and DPGP datasets and have used these “essentially complete” genome sequences to study the recent evolutionary history of Wolbachia in D. melanogaster. In the process of generating these data we received several inquiries about the status of this project so, in the spirit of Open Science that makes genomics such a productive field, we have released the consensus sequences and alignments of 179 Wolbachia and 290 mitochondrial genomes from the DGRP and DPGP prior to publication of our manuscript.
Since we are not the primary data producer for these assemblies, it is not approporiate to employ a data release policy based on the NHGRI guidelines. Instead, we have chosen to release these data under a Creative Commons Attribution 3.0 Unported License. If you use these assemblies or alignments in your projects, please cite the main DGRP and DPGP papers for the raw data and cite the following reference for the mtDNA or Wolbachia assemblies:
Richardson, M.F., L.A. Weinert, J.J. Welch, R.S. Linheiro, M.M. Magwire, F.M. Jiggins & C.M. Bergman (2012) Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster. PLOS Genetics 8:e1003129.
A tar.gz archive contaning a reference-based multiple sequence alignment of release 1.0 of the complete D. melanogaster mtDNA and Wolbachia assemblies can be obtained here. If you have questions about the methods used to produce these assemblies, any associated meta-data from these assemblies, or the content of our manuscript please contact Casey Bergman for details.