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Background  The evolution of the  Alphaproteobacteria  and origin of the mitochondria are topics of considerable debate. Most studies have placed the mitochondria ancestor within the  Rickettsiales  order. Ten years ago, the bacterium  Odyssella thessalonicensis  was isolated from  Acanthamoeba spp ., and the 16S rDNA phylogeny placed it within the  Rickettsiales . Recently, the whole genome of  O. thessalonicensis  has been sequenced, and 16S rDNA phylogeny and more robust and accurate phylogenomic analyses have been performed with 65 highly conserved proteins.    Methodology/Principal Findings  The results suggested that the  O. thessalonicensis  emerged between the  Rickettsiales  and other  Alphaproteobacteria . The mitochondrial proteins of the  Reclinomonas americana  have been used to locate the phylogenetic position of the mitochondrion ancestor within the  Alphaproteobacteria  tree. Using the K tree score method, nine mitochondrion-encoded proteins, whose phylogenies were congruent with the  Alphaproteobacteria  phylogenomic tree, have been selected and concatenated for Bayesian and Maximum Likelihood phylogenies. The  Reclinomonas americana  mitochondrion is a sister taxon to the free-living bacteria  Candidatus Pelagibacter ubique , and together, they form a clade that is deeply rooted in the  Rickettsiales  clade.    Conclusions/Significance  The  Reclinomonas americana  mitochondrion phylogenomic study confirmed that mitochondria emerged deeply in the  Rickettsiales  clade and that they are closely related to  Candidatus Pelagibacter ubique .

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Phylogenomic Analysis of Odyssella thessalonicensis Fortifies the Common Origin of Rickettsiales, Pelagibacter ubique and Reclimonas americana Mitochondrion