Rapid evolution ofWolbachiain cherry fruit flies
Authors: Bruzzese Daniel J. , Schuler Hannes , Yee Wee L. , Holzschuh Aurel , Feder Jeffrey L. 
Published: January 2025

AbstractWolbachiais a widespread bacterial endosymbiont in arthropods known for its ability to manipulate host reproduction through cytoplasmic incompatibility (CI), thereby promoting its spread. However,Wolbachiaharbors an array of mobile genetic elements (MGEs) that can rapidly alter its genomic structure and content, including thecifloci responsible for CI. At the phylogenetic scale,Wolbachiagenomes are shown to be dynamic with MGEs causing widespread genome rearrangements. But on ecological time scales, the evolution ofWolbachiaremains largely unknown. In this study, we leverage the natural history ofWolbachiain cherry-infesting fruit flies in theRhagoletis cingulatasibling species group. Members of this species group share a commonWolbachiastrain,wCin2, and their divergence spans from 1,000 to 150,000 years ago. We utilized Nanopore sequencing to characterizewCin2Wolbachiagenome divergence across recent to more distant evolutionary timescales. We report rapid evolution of population-level differences in gene content (includingcifloci and MGEs) and genome structure, with differentiation increasing with time since host divergence. Notably, structural variants were the first to appear both between and amongwCin2 populations. Our results also indicated that the CI phenotype previously attributed to a distinctWolbachiastrain,wCin3, that coinfects flies in the southwestern USA and Mexico, may instead be caused bycifgenes that were horizontally transferred intowCin2. Finally, we discovered a novelWolbachiastrain,wInd, which appears to have been recently horizontally acquired by cherry fly populations in the Pacific Northwest of the USA. Our findings underscore the fluidity and rapid genome evolution ofWolbachia, with significant implications forcifgene dynamics and potential impacts on host evolutionary trajectories.Author SummaryIn our study, we explore the genome evolution ofWolbachia, a common bacterial endosymbiont found in many insects that can manipulate its hosts’ reproduction to help it spread more effectively.Wolbachia’sgenome is shown to change dramatically over long evolutionary periods due to mobile genetic elements. However, little is known about howWolbachia’sgenome evolves over shorter ecological timeframes. Here, we utilized cherry-infesting fruit flies and theirWolbachiastrain known aswCin2, both of which have spread across North America for the past 150,000 years. Using long-read sequencing, we assembled multiplewCin2Wolbachiagenomes from across North America and made comparisons betweenwCin2Wolbachiagenomes that have recently diverged and comparisons to those that have been isolated for over 150,000 years. Our findings reveal thatWolbachia’sgenome can evolve swiftly, with differences in gene content and most prominently genome structure arising between recently separatedWolbachiapopulations and increasing as populations diverge over time. Interestingly, these changes also impact the key genes responsible forWolbachia’sreproductive manipulation. This research highlights the rapid and dynamic nature ofWolbachiagenome evolution across different evolutionary timescales and offers insights into endosymbiont-host relationships as well as their potential impact on host speciation and vector control.