Cotesia sesamiae populations targeted capture

The African parasitoid wasp Cotesia sesamiae is a generalist species structured in locally adapted populations showing differences in host range. The recent discovery of C. typhae, a specialist, sister species to C. sesamiae, further provides a good framework to study the genetic determinants of parasitoid host range. To investigate the genomic bases of divergence between these populations and species, we used a targeted sequencing approach on 24 samples. We targeted the bracovirus genomic region encoding virulence genes involved in the interaction with the lepidopteran hosts of the wasps. High sequencing coverage was obtained for all samples allowing the study of genetic variations between wasp populations and species. By combining population genetic estimations, such as diversity (π), relative differentiation (FST) and absolute differentiation (dxy), with branch-site dN/dS measures, we identified six out of 98 bracovirus genes showing significant divergence and impacted by positive selection. These genes belonging to different gene families are potentially involved in host adaptation and in the specialization process. Fine scale analyses of the genetic variations also revealed deleterious mutations and large deletions on certain genes inducing pseudogenization and loss of function. These results highlight the crucial role of the bracovirus in the molecular interactions between the wasp and its hosts and in the evolutionary processes of specialization.