Gall induction in gall wasps (Cynipidae s. lat.) : Insights from comparative genomics

Cynipidae are a family of wasps (Hymenoptera), whose larval stages develop inside plant galls, that is, abnormal plant structures formed in response to the presence of foreign organisms. Most cynipids are gall inducers and are often capable of notable levels of host manipulation. Others are inquilines, meaning they are dependent on other species for the initiation of the gall. Their larvae then develop inside the gall, often killing the original inducer and modifying the gall in the process. The biochemical mechanism of gall induction is still shrouded in mystery. In this thesis, various approaches are implemented to try to shed some light on the process. In Paper I, we used shotgun sequencing to investigate the bacterial association of larvae of different species inhabiting the bedeguar gall on roses, and showed that neither the inquiline nor the gall inducer inhabiting this gall are associated with symbiotic bacteria that are likely to be involved in gall induction, despite earlier speculations to that effect. In Paper II, I used comparative genomic analysis of a recently evolved gall inducer in the genus Synergus and three related inquilines to identify candidate genes involved in gall initiation. Specifically, I used a new method relying on genome-wide analyses to control for confounding factors, implemented in the software Bayescode. Then, I used Gene Onthology (GO) analysis to show that the candidate genes are associated with specific functions, such as “egg follicle development” and “neural development”. In paper III, we used genomic and transcriptomic data to infer the phylogeny of the family. The analysis confirmed that the phytophagous Cynipidae fall into two distinct lineages, as suggested by a recent phylogenomic analysis based on ultraconserved elements. We propose that these families be recognized as Cynipidae s. str. (oak gallers and relatives) and Diplolepididae (rose gallers and relatives). Finally, in paper IV, I applied the same methods as in Paper II to genomes of the Cynipidae s. str. to identify candidate genes associated with gall secondary structures. I inferred that these genes are often associated with GO terms relative to egg development and cell movement. In conclusion, the data presented here can provide a useful starting point for future research on cynipids