Data from: Two male-killing Wolbachia from Drosophila birauraia that are closely related but distinct in genome structure

<p><a>Insects </a>harbour diverse maternally inherited bacteria and viruses, some of which have evolved to kill the male progeny of their hosts (male killing: MK). The fly species <em>Drosophila biauraria</em> carries a maternally transmitted MK-inducing partiti-like virus, but it was unknown if it carries other MK-inducing endosymbionts. Here, we identified two male-killing <em>Wolbachia</em> strains (<em>w</em>Biau1 and <em>w</em>Biau2) from <em>D. biauraria</em> and compared their genomes to elucidate their evolutionary processes. The two strains were genetically closely related but had exceptionally different genome structures with considerable rearrangements compared with combinations of other <em>Wolbachia</em> strains. Despite substantial changes in the genome structure, the two <em>Wolbachia</em> strains did not experience gene losses that would disrupt the male-killing expression or persistence in the host population. The two <em>Wolbachia</em>-infected matrilines carried distinct mitochondrial haplotypes, suggesting that <em>w</em>Biau1 and <em>w</em>Biau2 have invaded <em>D. biauraria</em> independently and undergone considerable genome changes owing to unknown selective pressures in evolutionary history. This study demonstrated the presence of three male-killers from two distinct origins in one fly species and highlighted the diverse and rapid genome evolution of MK <em>Wolbachia </em>in the host.</p>