Abstract

Summary Highly reduced genomes of 144–416 kilobases have been described from nutrient-provisioning bacterial symbionts of several insect lineages [1–5]. Some host insects have formed stable associations with pairs of bacterial symbionts that live in specialized cells and provide them with essential nutrients; genomic data from these systems have revealed remarkable levels of metabolic complementarity between the symbiont pairs [3, 4, 6, 7]. The mealybug Planococcus citri (Hemiptera: Pseudococcidae) contains dual bacterial symbionts existing with an unprecedented organization: an unnamed gammaproteobacteria, for which we propose the name Candidatus Moranella endobia, lives inside the betaproteobacteria Candidatus Tremblaya princeps [8]. Here we describe the complete genomes and metabolic contributions of these unusual nested symbionts. We show that whereas there is little overlap in retained genes involved in nutrient production between symbionts, several essential amino acid pathways in the mealybug assemblage require a patchwork of interspersed gene products from Tremblaya, Moranella, and possibly P. citri. Furthermore, although Tremblaya has the smallest cellular genome yet described, it contains a genomic inversion present in both orientations in individual insects, starkly contrasting with the extreme structural stability typical of highly reduced bacterial genomes [4, 9, 10].