Historic museum samples provide evidence for a recent replacement of Wolbachia types in European Drosophila melanogaster.

<p>This dataset contains the newly assembled <i>Wolbachia </i>draft genomes and assembly statistics of eight previously published historic <i>Drosophila melanogaster</i> museum samples sequenced with Illumina (Shpak et al. 2023) and of nine previously unpublished contemporary and newly assembled <i>Wolbachia </i>draft genomes that were newly sequenced with Oxford Nanopore technology. All historic samples were comprised of <i>w</i>MelCS <i>Wolbachia </i>variants collected 200-90 years ago in Sweden, Denmark and Germany. The contemporary samples consisted of <i>w</i>Mel and <i>w</i>MelCS variants from Portugal and Finland and of <i>w</i>Mel, <i>w</i>MelCS and <i>w</i>MelPop variants in long-standing <i>Drosophila</i> lab stocks.</p>