Structural reorganization and genomic context define a divergent lineage of the Wolbachia male-killing gene wmk

Patterns of diversity in symbiont effector genes provide insight into the evolutionary processes that shape their diversification, particularly those arising from host-symbiont interactions. In one of the most widespread symbiont genera, Wolbachia, the male-killing candidate gene wmk encodes a putative transcriptional regulator. Sequence divergence of this effector gene from a limited number of strains has revealed at least five phylogenetic types. However, additional wmk variants characterized by a large inframe deletion and protein reorganization suggest that diversity in wmk extends beyond sequence variation alone. To gain further insight into wmk effector diversity, homologous proteins from 251 Wolbachia genomes were analyzed using comparative sequence and structure-informed approaches. The results show that sequence and structural diversification largely follow similar patterns; however, one lineage newly identified in this analysis stands out due to pronounced structural reorganization. The distinct genomic neighborhood of this divergent lineage, relative to other wmk lineages, suggests additional diversity at the regulatory level. Together, these findings demonstrate that variation in protein structure and genomic context complements sequence-level polymorphism in shaping wmk effector diversity in Wolbachia. Further analyses indicate that symbiont supergroup and host taxonomic order constrain the distribution of the divergent wmk lineage.