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of permission SGPA/DGVS/04568/11.""The advances in genome sequencing and the development of metagenomic methods have been critical for our knowledge of the bacterial world. Now that complete genomes from closely related species or even from different strains of the same species are available, numerous studies have focused on the diversity of gene repertoire and genome rearrangements (Abby and Daubin, 2007). Horizontal gene transfer (HGT), S6 Kinase transposition and intragenomic recombination are known to be important sources of evolutionary novelties, being responsible for bacterial huge metabolic diversity and adaptive potential, which are remarkable among free-living bacteria (Casjens, 1998; Rocha, 2008). However, the analysis of bacteria that have acquired an intracellular host-dependent life-style revealed important constrains to these evolutionary mechanisms. During the last 15 years, the complete genomes of many endosymbionts (i.e., obligate symbiotic bacteria that live inside eukaryotic cells) have become available. The best studied cases of endosymbiosis involve mutualistic associations with insects. Comparative genomics has allowed the identification of several commonalities among them, which are related with the stage of integration of the bacteria with their respective hosts (Moya et al., 2008; McCutcheon and Moran, 2012). Generally, intracellular bacteria have smaller genomes than their free-living relatives, mostly due to a reduction in their gene content (McCutcheon and Moran, 2012). Gene losses affect loci performing functions that are unnecessary in an intracellular environment or that can be provided by the host. Thus, highly reduced genomes (i.e., those from endosymbionts that have maintained a long relationship with their hosts) have typically lost most genes involved in DNA recombination and repair, present almost no gene duplications, lack transposable elements and prophages and present high levels of structural stability. Many insects maintain obligate mutualistic symbiosis with more than one bacterial species, so that two evolutionary outcomes are possible: complementation through the establishment of a bacterial consortium or replacement of one endosymbiont by another (Moya et al., 2009). Mealybugs (Hemiptera: Pseudococcidae) are phloem-feeding insects that have been classified in subfamilies Phenacoccinae and Pseudococcinae (Hardy et al., 2008), and present an intricate variety of endosymbiotic relationships. Based on phylogenetic analysis, it has been suggested that a betaproteobacterial ancestor of ��Ca. Tremblaya�� infected a mealybug ancestor before the split of the two subfamilies. In subfamily Phenacoccinae, ��Ca. Tremblaya phenacola�� is the obligate endosymbiont in most tested mealybug species, excluding the tribe Rhizoecini and the genus Rastrococcus, where it has been replaced by different Bacteroidetes (Gruwell et al., 2010; Husnik et al., 2013). In subfamily Pseudococcinae, the obligate endosymbiont ��Ca.