- Population genomics (targeted sequencing and RAD-Seq analysis)
- Genomics (genome assembly, mapping, annotation)
- Transcriptomics (RNA-Seq analysis)
Molecular Biology (RNA and DNA extractions, PCR, qPCR, sequencing preparation)
Parasitic wasps lay their eggs into eggs, larvae or pupae of other insects. The genus Cotesia comprises several species that parasitize caterpillars. They are widely studied for their high agronomical interest. The larvae of these wasps grow inside their host and have to overcome host defences. In our lab, we study the original strategy developed by these wasps: the domestication of viruses, named bracoviruses (BVs). These bracoviruses have been stably integrated in the genome of the wasps and play a crucial role in the wasp life cycle. It allows the wasps to produce virus particles containing virulence genes. These virus particles are introduced simultaneously with the wasp eggs in the host and the bracovirus virulence genes are expressed, induce immunosuppression and allow wasp larval development and parasitism success. In the genome of the wasp, the bracovirus comprises two parts: the nudiviral genes producing the particles and the proviral segments encoding virulence genes packaged in the particles.
From an evolutionary point of view, the bracovirus is a fascinating entity and the goal of my thesis is to better understand its role in the mechanisms of adaptation and speciation of these wasps. To achieve this, I combine population genetics and genomic approaches.
Cotesia sesamiae is an African species and parasitize over twenty lepidopteran stem borer species. Various studies have shown that genes of BV (eg CrV1) were directly related to parasitic success on some hosts and therefore specialization. Nonetheless, other BV genes could be involved in wasp local adaptation or specialization to their lepidopteran hosts. To investigate this, we realized a targeted sequence capture focused on the BV genome on different African C. sesamiae populations.
Thanks to population genetic tools (genetic diversity and differentiation), we have shown that BV is truly behaving like an "island of divergence" with different genes involved in the adaptation.
However, this study focused on the BV does not give a global vision of the selection traces in the whole wasp genome. Other traits and other genes may therefore be involved in the adaptation. To answer that, we made a RAD-Sequencing approach on many samples from different populations.
Otherwise, in order to refine our knowledge on the organization of the bracovirus sequences in the wasp genome, we sequenced, in collaboration with the Genoscope, our laboratory strain of Cotesia congregata using a combined Next-Generation Sequencing (NGS) approaches (454 and Illumina). The quality of this genome is similar to that of reference genomes (Apis mellifera and Nasonia vitripennis).
In addition, we realize a RNA-Sequencing approach focused on the wasp ovaries at different nymphal stages, which will allow the functional and temporal characterization of the bracovirus particle production. Moreover, these data, completed with other RNA-Seq data, will be used to annotate the genome.
This genome sheds light on genetic exchange that exists between the wasp genome and the bracovirus (Transposable Elements, wasp gene transfers) but also will serve as a reference genome for a large comparative genomic study.