An AT mutational bias in the tiny GC-rich endosymbiont genome of Hodgkinia

The fractional guanine p cytosine (GC) contents of sequenced bacterial genomes range from 13% to 75%. Despite several decades of research aimed at understanding this wide variation, the forces controlling GC content are not well understood. Recent work has suggested that a universal adenine + thymine (AT) mutational bias exists in all bacteria and that the elevated GC contents found in some bacterial genomes is due to genome-wide selection for increased GC content. These results are generally consistent with the low GC contents observed in most strict endosymbiotic bacterial genomes, where the loss of DNA repair mechanisms combined with the population genetic effects of small effective population sizes and decreased recombination should lower the efficacy of selection and shift the equilibrium GC content in the mutationally favored AT direction. Surprisingly, the two smallest bacterial genomes, Candidatus Hodgkinia cicadicola (144 kb) and Candidatus Tremblaya princeps (139 kb), have the unusual combination of highly reduced genomes and elevated GC contents, raising the possibility that these bacteria may be exceptions to the otherwise apparent universal bacterial AT mutational bias. Here, using population genomic data generated from the Hodgkinia genome project, we show that Hodgkinia has a clear AT mutational bias. These results provide further evidence that an AT mutational bias is universal in bacteria, even in strict endosymbionts with elevated genomic GC contents.