Such sets often only include some or all of the five Multi Locus Sequence Typing (MLST) markers and the wsp gene for Wolbachia and the data is even more restricted for Spiroplasma, as no MLST markers are yet available for this symbiont. Most phylogenetic studies on Wolbachia and Spiroplasma are based on a small set of markers. Thus, we lack a true understanding of the diversity and origin of these symbionts in insects, which in turn challenges the comprehensive study of the evolution of these microbial symbioses. Yet, many host-symbiont interactions remain un-noticed. Altogether, the diversity of phenotypes associated to these symbionts, and their versatile transmission modes, have made host-symbiont associations excellent study systems for various eco-evolutionary processes. Hybridization between closely related host species may also support such horizontal transfers of the symbionts through the introgressed matriline. Studies have shown that divergent species sharing the same diet, or the same parasites, are also prone to share similar symbiotic strains. Additionally, both of these maternally inherited symbionts have been suggested to occasionally transfer horizontally between host species. One such ability revolves around the manipulation of the hosts reproductive system, this occurs in a diverse range of hosts, and more specifically in the butterflies Hypolimnas bolina for Wolbachia and Danaus chrysippus for Spiroplasma or play defensive roles against diverse parasites and pathogens of their host, including viruses, other bacteria, or parasitoids. These two symbionts owe their success to their abilities to affect their host biology and promote their own transmission to the next generation of hosts. Reports suggest that at least 40% of all insects are infected by the facultative endosymbiotic bacterium Wolbachia, while up to 10% of insect species (and up to 23% of Aranaea species) carry Spiroplasma, another facultative endosymbiotic bacterium. The ever-expanding genomic databases provide a diverse databank from which one can characterize and explore the true diversity of symbiotic entities.įacultative endosymbiotic bacteria are extremely common in insects. This highlights the usefulness of public databases to explore the hidden diversity of symbiotic entities, allowing the development of hypotheses regarding host-symbiont associations. Our results indicate that many of the host-symbiont associations remain largely unexplored, with the majority of associations we identify never being recorded before. Construction of partial symbiotic genomes and phylogenetic analyses suggested the Wolbachia strains from the supergroup B were the most prevalent type of symbionts, while Spiroplasma infections were scarce in the Lepidoptera species screened here. Of the 106 species screened, 20 (19%) and nine (8.5%) were found to be infected with either Wolbachia or Spiroplasma, respectively. We compared the performance of two screening software, Kraken2 and MetaPhlAn2, to identify the bacterial infections and using a baiting approach we reconstruct endosymbiont genome assemblies. In this study, we screened publicly available Lepidoptera genomic material for two of the most common insect endosymbionts, namely Wolbachia and Spiroplasma, in 1904 entries, encompassing 106 distinct species. Consequently, we have only a restricted idea of the true symbiont diversity in insects, which may hinder our understanding of even bigger questions in the field such as the evolution or establishment of symbiosis. Many symbionts however very often go undetected. They owe their success to their ability to promote their own transmission through various manipulations of their hosts’ life-histories. Maternally inherited bacterial symbionts are extremely widespread in insects.
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