Whole genome sequencing of Wolbachia variants

DNA sequencing of D. melanogaster ovaries (DrosDel w1118 isogenic background) infected with different Wolbachia wMel variants. For each of the 9 fly lines, 20 females were anaesthetized under CO2 and washed in 50% bleach solution for 3 min. Females were then briefly washed in distilled water and dissected under a microscope. The two ovaries of the 20 females were pooled for DNA extraction. DNA was extracted using the Gentra Puregene DNA Purification kit according to the manufacturer's protocol, including an RNase A treatment. Library preparation and sequencing were performed at the Eastern Sequence and Informatics Hub (Cambridge, UK). 75 bp paired-end libraries were prepared with an insert size of 300 bp and sequenced in one lane of HiSeq2000 (Illumina). Base calling was performed using the Offline Basecaller (version 1.9.3) from Illumina, and demultiplexing was handled by bespoke Eastern Sequence and Informatics Hub software.