(i) Any differences observed may be explained by the host genotype, whether they are directly linked to the ovarian phenotype or not. (ii) Because NA is triply infected whereas Pi3 is singly infected, differences could also be due to the presence or absence of wAtab1 and AZD1390 wAtab2. (iii) NA and Pi3 symbiotic individuals have differing bacterial community compositions due to the moderate antibiotic treatment of Pi3 [26]. General procedures Rearing Wasps

were allowed to parasite Wolbachia-free D. melanogaster. Insects were reared on axenic medium [27] and maintained under controlled conditions (climate chambers at 21°C, 70% relative humidity and cycle LD 12:12). Young adults (0-1 day old) were collected and anesthetized on ice before being dissected in a drop of PBS and/or stored until use at -80°C. Antibiotic treatment Because VE822 we were interested in determining the effect of symbiosis, we performed antibiotic treatments

to produce Wolbachia-free (i.e. aposymbiotic) wasps. Even though antibiotics could also affect host gene expression directly (e.g. cytotoxicity, modification of mitochondrial metabolism) or indirectly (e.g. change in gut microflora), antibiotic treatment is the only efficient method to eliminate Wolbachia from A. tabida. Aposymbiotic females are sterile, and so it is impossible to establish and maintain aposymbiotic lines. Hence, antibiotic treatments had to be administered just before the experiment to obtain aposymbiotic wasps, as described in [6]. Briefly, rifampicin 2% (Hoechst, Germany) was added to the axenic nutritive medium to reach a final concentration of 2 mg/g of standard diet. Seventy D. melanogaster eggs were deposited in this medium, and allowed to be parasitized by

three female wasps. The Gefitinib supplier developing Drosophila thus transferred the antibiotic to each of the endoparasitoid wasp larvae, rendering them aposymbiotic. As a control, the same procedure was performed without the antibiotic treatment. Bacterial challenge Because we were interested in identifying immunity-related genes, we performed a challenge by the intracellular bacteria Salmonella typhimurium (strain 12023G, Grenoble) to enhance the immune response of A. tabida (Pi3 strain). Bacteria were prepared from a 2 h-culture initially started with a 1/10 dilution of an overnight culture (LB + SN-38 mouse ampicillin, 37°C, 190 rpm). Bacteria were rinsed twice and concentrated in 1 mL of fresh LB medium. Immune challenge was performed by injecting 13.2 nL of the mother solution (corresponding to 1.8×105 bacteria) in the thorax of young (0-1 day old) females (Nanoject II injector, Drummond, Broomall, PA). As a control, 13.2 nL of fresh LB medium was injected as described above. Individuals were collected 3h, 6h and 12h after challenge (or LB injection), and stored until use at -80°C.