One to host them all: genomics of the diverse bacterial endosymbionts of the spider Oedothorax gibbosus

Bacterial endosymbionts of the groups <em>Wolbachia</em>, <em>Cardinium </em>and <em>Rickettsiaceae </em>are well-known for their diverse effects on their arthropod hosts, ranging from mutualistic relationships to reproductive phenotypes. Here, we analyzed a unique system in which the dwarf spider <em>Oedothorax gibbosus</em> is co-infected with up to five different endosymbionts affiliated with <em>Wolbachia</em>, ‘<em>Candidatus </em>Tisiphia’ (formerly Torix group <em>Rickettsia</em>), <em>Cardinium, </em>and <em>Rhabdochlamydia</em>. Using short-read genome sequencing data, we show that the endosymbionts are heterogeneously distributed among <em>O. gibbosus</em> populations and are frequently found co-infecting spider individuals. To study this intricate host-endosymbiont system on a genome resolved level, we used long-read sequencing to reconstruct closed genomes of the <em>Wolbachia</em>, ‘<em>Ca. </em>Tisiphia’ and <em>Cardinium </em>endosymbionts. We provide insights in the ecology and evolution of the endosymbionts and shed light on the interactions with their spider host. We detected high quantities of transposable elements in all endosymbiont genomes and provide evidence that ancestors of the <em>Cardinium</em>, ‘<em>Ca. </em>Tisiphia’ and <em>Wolbachia </em>endosymbionts have co-infected the same hosts in the past. Our findings contribute to broadening our knowledge about endosymbionts infecting one of the largest animal phyla on earth, and show the usefulness of transposable elements as an evolutionary “contact-tracing” tool.