Rapid molecular evolution of Spiroplasma symbionts of Drosophila

<i>Spiroplasma</i> is a genus of <i>Mollicutes</i> whose members include plant pathogens, insect pathogens and endosymbionts of animals. <i>Spiroplasma</i> phenotypes have been repeatedly observed to be spontaneously lost in <i>Drosophila</i> cultures, and several studies have documented a high genomic turnover in <i>Spiroplasma</i> symbionts and plant pathogens. These observations suggest that <i>Spiroplasma</i> evolves quickly in comparison to other insect symbionts. Here, we systematically assess evolutionary rates and patterns of <i>Spiroplasma poulsonii</i>, a natural symbiont of <i>Drosophila</i>. We analysed genomic evolution of <i>s</i>Hy within flies, and <i>s</i>Mel within <i>in vitro</i> culture over several years. We observed that <i>S. poulsonii</i> substitution rates are among the highest reported for any bacteria, and around two orders of magnitude higher compared with other inherited arthropod endosymbionts. The absence of mismatch repair loci <i>mutS</i> and <i>mutL</i> is conserved across <i>Spiroplasma</i>, and likely contributes to elevated substitution rates. Further, the closely related strains <i>s</i>Mel and <i>s</i>Hy (>99.5 % sequence identity in shared loci) show extensive structural genomic differences, which potentially indicates a higher degree of host adaptation in <i>s</i>Hy, a protective symbiont of <i>Drosophila hydei</i>. Finally, comparison across diverse <i>Spiroplasma</i> lineages confirms previous reports of dynamic evolution of toxins, and identifies loci similar to the male-killing toxin Spaid in several <i>Spiroplasma</i> lineages and other endosymbionts. Overall, our results highlight the peculiar nature of <i>Spiroplasma</i> genome evolution, which may explain unusual features of its evolutionary ecology.