A critical re-evaluation of multilocus sequence typing (MLST) efforts inWolbachia

Abstract

26Wolbachia (Alphaproteobacteria, Rickettsiales) is the most common, and 27 arguably one of the most important inherited symbionts. Molecular differentiation of 28Wolbachia strains is routinely performed with a set of five multilocus sequence typing 29 (MLST) markers. However, since its inception in 2006, the performance of MLST in 30Wolbachia strain typing has not been assessed objectively. Here, we evaluate the 31 properties of Wolbachia MLST markers and compare it to 252 other single copy loci 32 present in the genome of most Wolbachia strains. Specifically, we investigated how well 33 MLST performs at strain differentiation, at reflecting genetic diversity of strains, and as 34 phylogenetic marker. We find that MLST loci are outperformed by other loci at all tasks 35 they are currently employed for, and thus that they do not reflect the properties of a 36Wolbachia strain very well. We argue that whole genome typing approaches should be 37 used for Wolbachia typing in the future. Alternatively, if few-loci-approaches are 38 necessary, we provide a characterization of 252 single copy loci for a number a criteria, 39 which may assist in designing specific typing systems or phylogenetic studies. 40