Diverse toxin repertoire but limited metabolic capacities inferred from the draft genome assemblies of three Spiroplasma (Citri clade) strains associated with Drosophila.

Abstract

Spiroplasma (class Mollicutes) is a diverse wall-less bacterial genus whose members are strictly dependent on eukaryotic hosts (mostly arthropods and plants), with which they engage in pathogenic to mutualistic interactions. Spiroplasma are generally fastidious to culture in vitro, especially those that are vertically transmitted by their hosts, which include flies in the genus Drosophila. Drosophila has been invaded by at least three independent clades of Spiroplasma: Poulsonii (the best studied, contains reproductive manipulators and defensive mutualists associated with two major clades of Drosophila and has amongst the highest substitution rates within bacteria), Citri (restricted to the repleta group of Drosophila) and Ixodetis. We report the first genome drafts of Drosophila-associated Citri clade Spiroplasma: strain sMoj from Drosophila mojavensis, strain sAld-Tx from Drosophila aldrichi from Texas (newly discovered; also associated with Drosophila mulleri) and strain sHy2 from Drosophila hydei (the only Drosophila species known to naturally also harbour a Poulsonii clade strain, thereby providing an arena for horizontal gene transfer). Compared to their Poulsonii clade counterparts, we infer that the three Citri clade strains have the following: (1) equal or worse DNA repair abilities; (b) more limited metabolic capacities, which may underlie their comparatively lower titres and transmission efficiency; and (c) similar content of toxin domains, including at least one ribosome-inactivating protein, which is implicated in the Poulsonii-conferred defence against natural enemies. As a byproduct of our phylogenomic analyses and exhaustive search for certain toxin domains in public databases, we document the toxin repertoire in close relatives of Drosophila-associated Spiroplasma, and in a very divergent newly discovered lineage (i.e. 'clade X'). Phylogenies of toxin-encoding genes or domains imply substantial exchanges between closely and distantly related strains. Surprisingly, despite encoding several toxin genes and achieving relatively high prevalences in certain natural populations (sAld-Tx in this study; sMoj in prior work), fitness assays of sMoj (this study) and sAld-Tx (prior work) in the context of wasp parasitism fail to detect a beneficial effect to their hosts. Thus, how Citri clade strains persist in their Drosophila host populations remains elusive.