Abstract Reductive genome evolution is commonly observed among host-associated bacteria including many important pathogens, such as Mycobacterium leprae but its molecular mechanism is not well understood 1–5 . One of the most widely accepted hypotheses to explain bacterial genome reduction is Muller’s ratchet, in which the associated bacteria tend to accumulate deleterious mutations for reduction in the absence of chromosomal recombination inside the eukaryotic host organism 1,2 . Cardinium species belong to the family Amoebophilaceae of the CFB group bacteria, which are a group of endosymbiont bacteria widely distributed among arthropods, that along with Wolbachia can cause cytoplasmic incompatibility 6,7 . In this study, we explored bacterial reductive evolution within the de novo assembled genomes of Cardinium endosymbionts in two astigmatic mites 8,9 . Our results shed light on the reduction mechanism driven by endogenous plasmids and their encoded enzymes.

Endogenous Plasmids and Reductive Genome Evolution in Host-Associated Bacteria