Insights into Drosophila-Wolbachia interactions: cryptic Wolbachia strains in closely related species

Wolbachia is a widespread group of endosymbiotic bacteria of arthropods that have diverse and complex effects on their host biology. Among them, are the protection against viruses and the mostly known reproductive effects including Cytoplasmic Incompatibility, male-killing, induction of parthenogenesis and feminization. Owing to its effects, Wolbachia are considered to be great candidates for their biocontrol potential. Between Drosophila species, Wolbachia are extremely common and include strains with variable phenotypic effects. Here we report on the genome sequencing of the Wolbachia endosymbiont “wSuzi” from the invasive pest Drosophila suzukii. The final assembly yielded approximately 1.35 Mbp in 110 contigs, with an average depth of coverage 60X. We found wSuzi to be closely related to the widespread D. simulans’ wRi strain. The two strains proved to be identical on the basis of the existing typing systems, including Multiple Locus Sequence Typing (MLST) and the most recently Multiple Locus VNTR Analysis (MLVA). However, several structural variations such as InDels and genomic rearrangements were able to discriminate the two strains. Based on the differences between wRi and wSuzi, we identified variable regions that were able to recognize different strains in different populations of D. suzukii and in the sister species of D. suzukii. Our results show that the currently used marker systems for Wolbachia lack the resolution to discriminate and identify potential cryptic strains. This could lead to an underestimation of the true biodiversity of Wolbachia bacteria but could also affect the design of applied control strategies and subsequent monitoring procedures