Both are stable phylogenetic markers widely used in bacterial phylogenetics due to reduced frequency of heterologous gene exchanges [26], [27].
Alternatively, the chimeric structure of p42d might have been the result of multiple gene exchanges and rearrangements.
Intracellular bacteria may have shared an ancestral host (amoeba or an ancestral protist) where gene exchanges occurred more than one billion years ago [36].
Interestingly, Bacteroidetes species such as Algoriphagus are commonly found in association with modern choanoflagellates [41], thus providing opportunities for gene exchanges.
At some point in their evolution, the organisms specialize in different niches, and subsequently, gene exchanges decrease, and the gene repertoires undergo changes.
We assumed, as others have [13], that multiple gene exchanges or non-orthologous gene displacements have occurred during the extensive evolution between eukaryotes and viruses, thus blurring the topology.
Finally, our panorama phylogenetic analysis demonstrates that H9N2 influenza viruses have undergone extensive reassortments since 1997, particularly in China (Figure 1), suggesting that novel H9N2 reassortant viruses can be generated by gene exchanges.
Today, free-living amoeba likely have a lifestyle that is similar to that of the ancestral protists from which current intracellular pathogens may have been created after gene exchanges more than one billion years ago [4].
This high presence of TA system components, as well as bacteriophage-derived proteins, attests to our previous observations that AG (at least R. bellii) and TRG rickettsiae are linked via conjugative systems and have a pronounced presence of similar plasmid (and now phage) related ORFs, likely the end products of various lateral gene exchanges between these distantly related groups.
Gene exchanges between Rickettsia spp. and Cardinium endosymbionts of diverse arthropod species have previously been reported.
This result is in agreement with the hypothesis of multiple lateral gene exchanges with the host.
