Recent studies have identified two genes in bacteriophage WO, cifA and cifB, that contribute to the induction of cytoplasmic incompatibility (CI)[1, 2], and one of these two genes, cifA, rescues it [3]. These findings underpin a two-by-one genetic model (Figure 1 A) that reflects current understanding of CI genetics and embraces various functional models [3](Figure 1 B). A recent article by Beckmann et al.[4] provides interesting ideas about the mechanism and evolutionary history of the CI genes. Therein, they claim that it is' clearer than ever that the CI induction and rescue stem from a toxin–antidote (TA) system', and that disputes regarding the operon status of the cif genes are semantic. They also propose a new nomenclature to describe the genes. It is important to test hypotheses and develop nomenclature carefully in the context of current data because misconceptions can sometimes become a narrative for those unfamiliar with the evidence. Here, we present and evaluate three points of criticism of the arguments related to the TA model, the operon hypothesis, and the proposed gene nomenclature. We recommend caution and nuance in interpreting current data (and lack thereof). As we will frequently note, more research will be necessary before a functional narrative should be prescribed for CI.

The TA Model The proposed TA model [4] assumes that male-derived CifB (the presumed toxin) is transferred to the host embryo during fertilization and that its associated defects are rescued upon binding to embryoderived CifA (the presumed antidote). Although CifA and CifB bind to each other in vitro [3], there is no evidence for transfer of CifB to the embryo. In fact, there is evidence to the contrary that was mentioned by the authors. Mass spectrometry and SDS-PAGE analyses indicate that CifA, but not CifB, is present in the spermatheca of females mated to infected males [5]. There are numerous technical explanations for why CifB is absent–for example, CifB protein expression levels may be below the threshold of detection–but the current evidence is consistent with a model wherein CifA, but not CifB, reaches the female reproductive tract. Therefore, it cannot be assumed that CifB from the male directly interacts with CifA in the embryo. For this reason the essential premise of the TA model is unfounded. One of several alternative hypotheses is that, instead of CifB transferring with the sperm, a host product modified by CifA and/or CifB leads to CI induction, and the host modification is then reversed by CifA in the embryo [3]. It is notable that, if supported, this model and others (Figure 1 B) would contradict the proposed TA model.