Abstract
Wolbachia (Alphaproteobacteria, Rickettsiales) is the most common, and arguably one of the most important inherited symbionts. Molecular differentiation of Wolbachia strains is routinely performed with a set of five multilocus sequence typing (MLST) markers. However, since its inception in 2006, the performance of MLST in Wolbachia strain typing has not been assessed objectively. Here, we evaluate the properties of Wolbachia MLST markers and compare it to 252 other single copy loci present in the genome of most Wolbachia strains. Specifically, we investigated how well MLST performs at strain differentiation, at reflecting genetic diversity of strains, and as phylogenetic marker. We find that MLST loci are outperformed by other loci at all tasks they are currently employed for, and thus that they do not reflect the properties of a Wolbachia strain very well. We argue that whole genome typing approaches should be used for Wolbachia typing in the future. Alternatively, if few loci approaches are necessary, we provide a characterisation of 252 single copy loci for a number a criteria, which may assist in designing specific typing systems or phylogenetic studies.
Highlights
Wolbachia is a genus of maternally inherited intracellular Alphaproteobacteria that is found in arthropod and nematode hosts (Werren et al 2008)
multilocus sequence typing (MLST) analyses are widely used in the community of Wolbachia researchers and a large database for comparative studies is available
They are too conserved to allow reliable and fine-scaled strain differentiation, they do not reflect genome wide divergence rates well, and they are poor phylogenetic markers at shallow or deep divergence levels. They are outcompeted at all of these tasks by other loci. These properties make the definition of a strain in the genus Wolbachia per MLST very problematic and we recommend that this practice is discontinued
Summary
Wolbachia is a genus of maternally inherited intracellular Alphaproteobacteria that is found in arthropod and nematode hosts (Werren et al 2008). Host specificity and type of symbiosis differs between major lineages of Wolbachia, which are currently classified into 16 supergroups named with capital letters from A–F and H–Q, consecutively in the order of their description (Glowska et al 2015; Gerth 2016). Supergroups A and B are found in arthropods, representing the vast majority of described Wolbachia lineages. Many different types of symbioses, including reproductive parasitism, facultative mutualism, and obligate mutualism have been found for these lineages (Zug & Hammerstein 2015). Supergroups C and D are restricted to filarial nematodes, with which they share a close relationship that can be described as obligate mutualism (Makepeace & Gill 2016)
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