Structurally reorganized Wmk lineage with distinct genomic context and restricted distribution in Wolbachia.

Patterns of diversity in symbiont effector genes provide crucial insight into evolutionary processes shaping their diversification, particularly those arising from host-symbiont interactions. In the widespread symbiont genus Wolbachia, the male-killing candidate gene wmk encodes a putative transcriptional regulator with at least five known phylogenetic types based on sequence divergence. However, additional wmk homologs characterized by large in-frame deletions, and protein reorganization suggest that diversity extends far beyond sequence variation alone. Yet, the full extent of structural diversification in wmk effectors remains poorly understood. In this study, I analyzed homologous proteins from 251 Wolbachia genomes using comparative sequence and structure-informed approaches to comprehensively characterize wmk effector diversity. These results demonstrate that sequence and structural diversification largely follow similar patterns, with one newly identified lineage standing 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 reveal 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, providing new insights into the evolutionary forces governing effector gene diversification in this important symbiont system.