Unlike intracellular bacterial parasites, intracellular symbionts have a mutual or commensal relationship with their hosts . Mutualism describes a relationship where both species receive a fitness gain, and commensalism is where one gains but the other is not significantly harmed . However, living together allows symbiotic species to genetically coevolve in a way that can benefit both . Thus, symbiosis is regularly referred to as mutualism [88, 89].
Given that many organisms share symbiotic relationships, there is an opportunity for evolutionary change. Hence, researchers have begun to evaluate gene transfer among these species. A primitive example is the early eukaryotic (plant) symbiotic relationship with free-living photosynthetic bacteria. Algae were believed to engulf chloroplasts from these bacteria over a billion years ago, leaving the plants with a powerful photosynthesis ability and the bacteria with the possibility for reductive genome evolution towards an obligate intracellular lifestyle [90, 91].
Genetic exchanges in endosymbionts commonly affect host coevolution . The genome of a Buchnera g-proteobacterium symbiont of a pea aphid (also known as plant lice), although small in size and relying on the aphid for nutrients due to its intracellular compartmentalization, contains genes and pathways responsible for synthesizing essential amino acids that are missing in the aphid . Wolbachia, the most common symbiont of arthropods, infecting an estimated 17-76% of all insect species, has attracted special attention because of their impact on host reproduction and evolutionary processes . The main reproductive alterations found in Wolbachia-infected arthropods are cytoplasmic incompatibility (infected males become unable to reproduce with uninfected or infected females), parthenogenesis induction (reproduction of infected females without males), feminiza-tion of genetic males (infected males become fertile or infertile females), death of infected males and oogenesis completion . A single Wolbachia strain can produce different phenotypes in different hosts [94, 95], suggesting rampant horizontal gene transfer and divergent evolution. Indeed, intergenic recombination has frequently been identified throughout the Wolbachia genomes, including the housekeeping genes . Another example where gene transfer underlies pheno-typic change comes from Parachlamydia, an amoeba symbiont and opportunistic pathogen of humans . The family Parachlamydiaceae is in the order Chlamydiales because of its Chlamydiaceae-like developmental cycle. Like Wolbachia, strains of Parachlamydia that reside in dissimilar tissues and hosts exhibit dissimilar phe-notypes , suggesting horizontal transfer and divergent evolution. For example, Parachlamydia have acquired numerous virulence factors similar to Chlamydiaceae, including type III secretion for communication/infection with host cells, ATP/ADP translocase for energy import and surface proteins for diversity [6, 97]. In addition, genomic islands have also been identified . Surprisingly, Parachlamydia acantha-moebae, unlike Chlamydiaceae, contains the tra genes that are essential for the F-like conjugative transfer system [6, 98]. In this transfer system, the tra genes are responsible for sex pilus movement and mating pair stabilization, and thus likely facilitate DNA uptake . Consequently, the similarity and dissimilarity between Parachlamydiaceae and Chlamydiaceae implies the shared common ancestor and evolutionary divergence of each family to suit a specific niche .
As with the intracellular bacterial parasites, gene transfer within species and with other intracellular species is also possible when multiple infections occur. An example of intraspecies recombination in Wolbachia occurs for the gene encoding surface proteins such as wsp, in which recombination results in different surface recognition or host interaction due to altered antigenicity [92, 96]. Based on various recombination detection programs such as MaxChi and Geneconv, intragenic recombination, although occurring less frequently compared to intergenic transfer, has been detected among various genes including the housekeeping gene gltA .
Phylogenetic clustering of different strains of Wolbachia that reside in distantly related host ranges also emphasizes horizontal transfer during some period of the evolutionarily process . For cross-species gene transfer among intracellular symbionts, sequencing analysis identified DNA exchange between Wolbachia pipien-tis and Trichogramma karkai that exhibited multiple infections in the same host egg . Indeed, the genetic data highlighted interspecies recombination and gene transfer for many genes, including glt, wsp and several other housekeeping and surface encoding genes . Further, the data supported the phylogenetic tree topologies for Wolbachia and Trichogramma .
Evidence of gene transfer from the intracellular symbionts to their host organisms has also been described. Indeed, horizontal gene transfer from organelles, which can be occupied by intracellular microorganisms, to the eukaryotic nucleus is common . The traditional example with regard to the presence of eubacterial genes in eukaryotes is the mitochondrial endosymbiont, which may have originated from Rickettsia . As another example of gene transfer to the host, approximately 11 kb of DNA from Wolbachia was identified in the chromosome of the symbiotic bean beetle . Genome-wide studies have also reported that an average of 18% of the Arabidopsis genome may have been derived from intracellular symbiotic bacteria . Furthermore, genome-wide studies reported that more than 50% of the yeast Saccharomyces cerevisiae genome was transferred from a variety of bacteria, including a cyanobacterium (Synechocystis 6803), a proteobacterium (E. coli) and a methanogen (Methanococcus jannaschii) .
Phages and transposons have also been identified in Wolbachia and Parachlamy-dia [6, 93]. For instance, a lytic phage named WO was discovered in insect- and nematode-infecting Wolbachia. WO induces five reproductive alterations in the Wolbachia-infected arthropods . Several repetitive DNA and mobile elements denoted in these microorganisms also support the possibility of high genome flux [104, 105]. Disrupted synteny also infers inversion and translocation that may be a result of genetic recombination . These findings support the importance of horizontal transfer and transduction among symbionts.
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