Genomic islands in <i>Wolbachia</i> prophages drive amplification and diversification of cytoplasmic incompatibility genes in <i>Culex pipiens</i>

Abstract Wolbachia are maternally inherited endosymbiotic bacteria widespread among arthropods. They manipulate their host reproduction to enhance their prevalence in host populations. The most common manipulation is cytoplasmic incompatibility (CI), which causes embryonic death in crosses between infected males and uninfected females, or between individuals carrying incompatible Wolbachia strains. CI patterns are highly complex in the mosquito Culex pipiens, where the causal genes cidA and cidB are amplified and diversified, forming a “cid repertoire” within each Wolbachia wPip genome. Despite their central role in CI, the genomic mechanisms underlying such cid amplification and diversification remain poorly understood. This knowledge gap is largely due to the difficulty of assembling wPip’s genomes due to highly repeated genes and mobile elements, especially in WO prophages. Here, we directly annotated Illumina-corrected Nanopore sequences to investigate the genomic flanking context of cid genes in 3 distinct wPip lineages. We assembled WO prophage regions of substantial length containing the entire cid repertoire previously described in these bacterial lineages. Within these WO regions, cid genes are consistently embedded in modular and rearrangeable islands composed of MutL, rnhA, and small mobile elements, all displaying hyperconserved nucleotide identity across islands. These genomic islands are probably drivers for major rearrangement and recombination events responsible for the amplification and diversification of cidwPip genes within and between the wPip genomes, leading to CI complexity in C. pipiens.