Recombination, truncation and horizontal transfer shape the diversity of cytoplasmic incompatibility patterns.

are endosymbiotic bacteria inducing various reproductive manipulations of which cytoplasmic incompatibility (CI) is the most common. CI leads to reduced embryo viability in crosses between males carrying and uninfected females or those carrying an incompatible symbiont strain. In the mosquito , the Pip causes highly complex crossing patterns. This complexity is linked to the amplification and diversification of the CI causal genes, and , with polymorphism located in the CidA-CidB interaction regions. We previously showed correlations between the identity of gene variants and CI patterns. However, these correlations were limited to specific crosses, and it is still unknown whether id gene polymorphism in males' and females' can explain and predict the wide range of crossing types observed in . Taking advantage of a new method enabling full-gene acquisition, we sequenced complete repertoires from 45 Pip strains collected worldwide. We demonstrated that the extensive diversity of genes arises from recombination and horizontal transfers. We uncovered further polymorphism outside the interface regions and strongly correlated with CI patterns. Most importantly, we showed that in every Pip genome, all but one variant are truncated. Truncated s located in palindromes are partially or completely deprived of their deubiquitinase domain, crucial for CI. The identity of the sole full-length variant seems to dictate CI patterns, irrespective of the truncated present. Truncated CidBs exhibit reduced toxicity and stability in cells, which potentially hinders their loading into sperm, essential for CI induction.