Evolutionary genetics of cytoplasmic incompatibility genes cifA and cifB in prophage WO of Wolbachia

The bacterial endosymbiont Wolbachia manipulates arthropod reproduction to facilitate its maternal spread through populations. The most common manipulation is cytoplasmic incompatibility (CI): Wolbachia-infected males produce modified sperm that cause embryonic mortality, unless rescued by eggs harboring the same Wolbachia. The genes underlying CI, cifA and cifB, were recently identified in the eukaryotic association module of Wolbachias prophage WO. Here, we use transcriptomic and genomic approaches to address three important evolutionary facets of these genes. First, we assess whether or not cifA and cifB comprise a classic toxin-antitoxin operon, and show they do not form an operon in strain wMel. They coevolve but exhibit strikingly distinct expression across host development. Second, we provide new domain and functional predictions across homologs within Wolbachia, and we show amino acid sequences vary substantially across the genus. Lastly, we investigate conservation of cifA and cifB and find degradation and loss of the genes is common in strains that no longer induce CI. Taken together, we find no evidence for the operon hypothesis in wMel, provide functional annotations that broaden the potential mechanisms of CI induction, illuminate recurrent erosion of cifA and cifB in non-CI strains, and advance an understanding of the most widespread form of reproductive parasitism.