BACKGROUND
symbiosis between prokaryotic and eukaryotic cells is a globally important phenomenon that influences the physiology, ecology, and evolution of virtually every organism on this planet  <cit> .
eukaryotic hosts expand their ecological niches through symbiosis with these metabolically diverse bacteria and archaea.
an illustrative case is that of the chemosynthetic endosymbionts, which enable their hosts to populate and thrive in challenging environments such as deep-sea hydrothermal vents and cold seeps  <cit> .
in these environments, reduced inorganic compounds are generated either biotically  or abiotically .
chemosynthetic symbionts use the energy derived from the oxidation of these molecules to fix inorganic carbon  <cit> .
benefits for both partners in chemosynthetic symbioses are evident.
the bacteria gain further access to the energy substrates they require from both oxic and anoxic habitats while the animals are provided with much, if not all, of their nutritional requirements  <cit> .
the intimate structural and metabolic coupling often found in chemosynthetic symbioses underscores the importance of these relationships to host survival.
the vesicomyid clams are one of the better studied chemosynthetic symbioses and exist at hydrothermal vents, hydrocarbon seeps, and other chemically reduced environments.
they are also relatively young as a group, as vesicomyid fossils date the formation of the symbiosis to the cretaceous, between 50– <dig> ma ago  <cit> .
these clams have a greatly reduced gut and feeding groove  <cit>  and, based on isotopic evidence, are thought to depend almost entirely on their endosymbionts for their carbon  <cit> .
with respect to the animal host, the association is essential – no living vesicomyids have been found devoid of symbionts.
furthermore, these symbionts have not yet been found outside the host, have never been cultured in the laboratory, and are thought to be predominantly maternally transmitted each generation via the egg  <cit> .
previous studies of other bacterial symbionts suggest that symbiont transmission strategy is a predominant factor governing nutritional symbiont genome evolution.
bacterial symbionts transferred to the next host generation via the egg  experience population bottlenecks upon transmission and few opportunities for recombination  <cit> .
because of the underlying deletion bias in bacterial genome evolution, and the limited amount of gene flow available to these symbionts, their genomes are minimized.
for example, the genomes of the vertically transmitted, mutualistic insect endosymbionts buchnera, baumannia, blochmannia, and wigglesworthia are all reduced in size and content  <cit> , exhibiting few chromosomal rearrangements, or horizontal gene transfer events  <cit> .
however, these insect nutritional symbionts retain the genomic repetoire needed to provide key metabolic intermediates, vitamins, and amino acids often missing from their hosts' specialized diets  <cit> , suggesting that host nutritional needs might select for retention of specific biosynthetic pathways.
conversely, those pathways redundant with host capabilities or nutrition are often lost completely  <cit> .
in contrast to the strictly vertically transmitted symbionts, those that undergo occasional environmental or horizontal transmission  tend to have slightly larger genomes that exhibit evidence of recombination.
for example, wolbachia pipientis, the ubiquitous insect reproductive parasite, may be laterally transmitted  <cit> , and their genomes are littered with mobile genetic elements, prophages and harbor clear evidence of past recombination events  <cit> .
it must be noted, however, that transmission strategy for many symbionts cannot be distinctly or clearly demarcated; depending on the association, symbionts are perpetuated via a spectrum from strict vertical transmission to lateral acquisition.
the insect reproductive parasites  are vertically transmitted but occasionally laterally acquired.
indeed, there is also some phylogenetic evidence, in the form of incongruent host and symbiont trees, against strict vertical transmission of the vesicomyid symbionts  <cit> .
more recently, two different strains of the vesicomyid symbionts have been found within the same host, corroborating the lateral acquisition hypothesis suggested by the phylogenetic evidence above  <cit> .
however, the vesicomyid symbionts are found in host primary oocytes  <cit>  and their genomes are reduced, and exhibit a high a+t content  <cit> , suggesting that although occasional lateral transmission may occur, the predominant transmission strategy used by the vesicomyids is vertical.
this mixed transmission strategy suggested for the vesicomyid symbionts has the potential to influence the genomic evolution of these bacteria.
research on the comparative evolutionary genomics of insect symbionts  <cit>  suggests that symbionts with strictly vertical transmission strategies would lose genetic material redundant with host capabilities and retain metabolic pathways necessary for host survival.
occasional lateral transmission might offer the opportunity for recombination and horizontal gene transfer, possibly mitigating the negative effects associated with a reduction in population size.
indeed, some evidence of recombination has been found in the vesicomyid symbiont genomes, suggesting that genomic evolution of these bacteria may not be as straightforward as in strictly vertically transmitted symbionts  <cit> .
we chose a comparative framework, utilizing both genomic and heterologous microarray data, to investigate genome evolution in the vesicomyid chemosynthetic symbionts.
the genomes of the two fully sequenced vesicomyid symbionts, ruthia magnifica, isolated from hydrothermal vents, and vesicomyosocious okutanii, isolated from cold seeps  <cit>  were compared to each other and to that of thiomicrospira crunogena, a free-living chemoautotroph isolated from hydrothermal vents and the closest sequenced relative of the vesicomyid symbionts  <cit> .
the availability of sequenced vesicomyid symbiont genomic data allowed us to develop microarrays for genome-scale analyses of conserved gene content in other vesicomyid symbionts.
indeed, the great amount of genetic conservation and synteny between the two sequenced vesicomyid symbiont genomes  <cit>  suggests that the use of cross-species microarrays in the vesicomyid symbionts may be particularly informative.
affymetrix microarrays based on the r. magnifica genome were constructed and hybridized to genomic dna from two other related vesicomyid symbionts, those of vesicomya sp.
mt-ii and calyptogena kilmeri.
vesicomya sp.
mt-ii is part of a cryptic species complex which includes the clam formerly known as calytogena pacifica  <cit> .
a sampling strategy was chosen to illuminate possible effects of phylogenetic relationships and host geochemical environment on vesicomyid symbiont genome evolution.
these four symbionts include representatives from each major clade of the vesicomyid symbiont lineage  and therefore allow us to estimate a vesicomyid symbiont core genome.
the symbionts investigated here also live within hosts inhabiting two distinct chemosynthetic environments: cold seeps and hydrothermal vents.
these habitats differ in their geochemistry with regards to the quantity of oxygen, nitrate and redox state of sulfur available for the symbioses.
the data presented here suggest a tremendous amount of genomic stasis and conserved gene content in the vesicomyid symbiont lineage; in the 50– <dig> ma that the symbionts have been host associated, their genomes have changed surprisingly little.
these data also support existing evidence for lateral acquisition of the vesicomyid symbionts  <cit> .
these results underscore the importance of the symbionts' chemoautotrophic metabolism within their hosts; they emphasize the extent to which host metabolic needs have contributed to genomic evolution in this endosymbiont lineage.
RESULTS
four chemosynthetic symbiont genomes were compared in this study, two sequenced genomes  and gene content for two other strains  based on heterologous microarray hybridizations .
the r. magnifica genome was used to build microarrays for heterologous hybridization to other vesicomyid symbionts.
heterologous microarray hybridization is especially useful when comparing strain-level variation as arrays designed based on one of the strains are likely to hybridize to the dna of other strains  <cit> .
below, differences between the sequenced genomes are first discussed with reference to a free-living chemoautotroph, thiomicrospira crunogena.
although t. crunogena is not part of the direct lineage of the vesicomyid symbionts, it is the closest sequenced relative of the chemosynthetic symbionts and provides us with some perspective as to the gene content necessary to be a functional chemoautotroph.
we then discuss chemosynthetic symbiont metabolism and evolution based on both sequence and microarray analyses.
as expected based on their maternal transmission, when compared to t. crunogena  <cit> , these symbiont genomes are reduced in size and g + c content .
the vesicomyid symbiont genomes are about half the size of t. crunogena's genome; of the  <dig>  proteins in the t. crunogena genome, the symbionts encode ~40%.
the t. crunogena genome encodes enzymes and structures lacking from many intracellular bacteria  but many of t. crunogena's metabolic capabilities are found in the vesicomyid symbiont genomes .
indeed, there are proteins unique to the vesicomyid symbionts when compared to t. crunogena and a few of these may increase the symbionts' functional potential within their hosts.
for example, the symbiont sulfur oxidation pathway includes both the sox  and the dsr  enzymes  <cit> , and therefore appears to be more complex than that of t. crunogena, which encodes the sox system exclusively  <cit> .
thus, these symbiont genomes encode for many of the metabolic pathways of free-living chemoautotrophs despite being reduced in size.
*percentage of the genome predicted to encode proteins
the sequenced vesicomyid symbiont genomes are quite similar to each other in both gene content and order.
of  <dig> and  <dig> proteins encoded in the r. magnifica and v. okutanii genomes respectively,  <dig> orthologs are conserved across both, which share a relatively high  amino acid identity.
the v. okutanii and r. magnifica genomes also share an extraordinary amount of synteny, as clear from a lagan analysis by kuwahara et al.,  <dig>  here, an analysis of synteny using mummer revealed that a total of 82% of genes in r. magnifica remain in the same genomic context and relative location in v. okutanii, with a single inversion  <cit> .
this  <dig>  kb inversion is comprised of  <dig> genes including those involved in cofactor biosynthesis , potassium uptake , regulation of nitrogen utilization , and chaperonins  .
the inversion did not truncate any of the genes in the region and their orientation does not seem to obviously affect gene function as no operons are disrupted.
there is a striking similarity between these two vesicomyid symbiont genomes, but a few substantial differences stand out.
genes unique to r. magnifica and v. okutanii are largely in the cell envelope and energy metabolism role categories, respectively .
the r. magnifica genome has a large region comprised of  <dig> open reading frames lacking in v. okutanii's genome .
this region primarily encodes proteins predicted to be involved in the biosynthesis of polysaccharides and peptidoglycan, components of the cell envelope.
the lack of this region in v. okutanii suggests that perhaps the vesicomyid symbiont intracellular lifestyle does not require the synthesis of peptidoglycan.
conversely, the r. magnifica genome lacks v. okutanii's dissimilatory nitrate reductase operon , which encodes energy metabolism proteins similar to the membrane-bound, respiratory nitrate reductase  found in escherichia coli and other proteobacteria  <cit> .
this operon may enable v. okutanii to utilize nitrate as a terminal electron acceptor and may reduce competition between host and symbiont for oxygen, although this has yet to be demonstrated.
this ability – which may have significant implications for the association's capacity to exploit hypoxic niches – may represent a significant functional difference between these two symbionts.
the heterologous microarray hybridizations of v. sp mt-ii and c. kilmeri symbiont genomic dna to the r. magnifica array confirm the genomic stasis suggested by the sequence comparisons with v. okutanii.
indeed, all of the microarray features hybridized to the c. kilmeri symbiont gdna, indicating that this symbiont contains at least the genomic repertoire of r. magnifica , while 92% of probed genes did not hybridize to the v. sp.
mt-ii gdna .
of this  <dig> % of proteins putatively absent from the v. sp.
mt-ii symbiont genome, the majority  are of unknown function and it is therefore difficult to predict how symbiont metabolism and host interaction might be affected.
a total of  <dig> proteins are shared by all four vesicomyid symbiont genomes and this core genome encodes pathways for sulfur oxidation, nitrogen assimilation and carbon fixation, as well as synthesizing the  <dig> amino acids and  <dig> vitamins and cofactors, pathways central to their chemoautotrophic metabolism.
data based on genomics, microarray hybridization results, and validated by polymerase chain reaction and slot blot dna hybridizations.
*lower estimates of genomic content based on microarray hybridization results and validation methods.
**total conserved gene content = genes shared by all four vesicomyid symbionts included in this study
interestingly, neither reducing environment nor phylogenetic position correlated strongly with genomic content.
the genomes of the two vent clam symbionts  did not share any gene content to the exclusion of the two symbionts isolated from seep clams  and vice versa.
in fact, based on the comparative genomic hybridization results, the c. kilmeri seep clam symbiont is more similar to the vent clam symbiont r. magnifica than to v. okutanii.
this is a surprising result as the c. kilmeri symbiont clades with v. okutanii in 16s rrna phylogenetic trees .
also, the vent clam symbiont v. sp.
mt-ii seems to share genomic excisions with the seep clam symbiont v. okutanii in comparison to r. magnifica; the same polysaccharide biosynthesis region absent from v. okutanii is also missing from the v. sp.
mt-ii genome.
these results are inconsistent with predictions of symbiont genomic content based on strict vertical transmission and instead support a mixed transmission strategy for these bacteria  <cit> .
occasional lateral transmission events, bringing two distinct bacterial symbionts together in the same host background, would provide the necessary opportunity for recombination in this lineage leading to this observed result: a mosaic of evolutionary histories throughout the genome  <cit> .
these four symbionts share a large fraction of their genomic repertoires, such that the total conserved genomic content within each functional role category remains comparatively high .
when functional differences between these symbionts are mapped onto a circular representation based on the sequenced chromosomes, two large regions were found to be universally conserved across all four symbiont genomes .
one segment, near the origin of replication, contains nearly all of the enzymes necessary for cytochrome  biosynthesis and the calvin-benson-bassham cycle .
it also harbors enzymes necessary for sulfur oxidation  as well as energy conservation .
the second segment, at  <dig>  bp, encodes genes involved in nitrogen metabolism , heme biosynthesis  and ubiquinone biosynthesis.
thus, many of the genes encoding enzymes thought to be fundamental to the symbioses are well conserved across four vesicomyid symbiont strains.
based on the sequence and microarray data, a reconstruction of the minimal gene set for the vesicomyid symbionts' last common symbiotic ancestor  is proposed .
genes present in at least one of the symbiont genomes were assumed to have been present in the lcsa.
below, we detail the commonalities and differences between the symbiont genomes with regards to the chemosynthetic metabolisms thought to be important to the symbiosis.
the chemosynthetic symbionts are autotrophic bacteria but there is some question as to whether they are obligately autotrophs or acquire some carbon from the host.
the genomic and microarray results from these four vesicomyid symbionts suggest they all have a complete calvin cycle utilizing a form ii rubisco and that fixed carbon can enter intermediary metabolism as phosphoglyceraldehyde.
however, the vesicomyid symbionts intermediary metabolism lacks alpha-ketoglutarate dehydrogenase, a condition thought to be an indicator of obligate autotrophy  <cit> .
the lack of a sugar phosphotransferase  system in these symbionts plus the lack of organic carbon transporters corroborates this idea.
to ameliorate the effects of an incomplete tca cycle, a glyoxylate bypass is hypothesized for r. magnifica, v. sp.
mt-ii, and c. kilmeri symbionts but this key enzyme  is missing from the v. okutanii genome  <cit>  making regeneration of succinate in v. okutanii inexplicable .
the v. okutanii genome is also lacking genes for malate dehydrogenase and fumarate reductase, suggesting significant reduction in comparison to r. magnifica.
perhaps v. okutanii employs the single citrate transporter  to take up tca intermediates from the host.
this putative sugar transporter  could theoretically function to move tca cycle intermediates between host and symbiont.
based on this evidence, the lcsa of the vesicomyid symbionts is predicted to have been an obligate autotroph.
however, unlike many free-living obligate autotrophs, the vesicomyid symbionts do not have carboxysomes, polyhedral shaped "organelles" that contain rubisco and carbonic anhydrase  <cit> .
these structures are thought to be involved in dehydration of bicarbonate to provide carbon dioxide  to rubisco.
although the carboxysome operon seen in other autotrophs is missing from the symbiont genomes, all four vesicomyid symbionts encode putative carbonic anhydrases.
it may be that the host bacteriocyte environment maintains a high concentration of co <dig> limiting the need for carobxysomes .
as is known from the riftia chemosynthetic symbiosis, the host animals might actively trap carbon intracellularly as bicarbonate, limiting the need for carboxysomes in the vesicomyid symbionts  <cit> .
indeed, the vesicomyid symbionts contain a form ii rubisco, the form with low affinity for co <dig>  known from organisms that exist in high concentrations of carbon dioxide  <cit> .
the lcsa for the vesicomyid symbionts is predicted to have derived its energy for carbon dioxide fixation from sulfur oxidation.
sulfur oxidation in all four vesicomyid symbionts is predicted to proceed via the sox  and dsr  genes.
however, the v. okutanii genome encodes dsrjnrs while r. magnifica's does not.
because this gene is lacking from the r. magnifica genome, it was not queried in the v. sp.
mt-ii or c. kilmeri symbiont genomes.
while the role of these genes in sulfur oxidation is unclear, they are thought to encode a triheme periplasmic cytochrome , a gene for biosynthesis of siroamide , and cytoplasmic proteins of unknown function   <cit> .
it is therefore unknown how symbiont metabolic function might be affected by the retention of these genes.
two distinct terminal electron acceptors , are predicted to have been used by the lcsa.
based on sequence data, r. magnifica is predicted to rely exclusively on oxygen as a terminal electron acceptor while v. okutanii might use either oxygen or nitrate.
the v. okutanii genome nitrate reductase operon consists of upstream molybdenum cofactor biosynthesis proteins  followed by narg and h, encoding the alpha and beta subunits of nitrate reductase, narj, the delta subunit which inserts the molybdenum cofactor into nitrate reductase, and nari, the gamma subunit which is a b-type cytochrome that accepts electrons from quinone to transfer to the alpha subunit  <cit> .
when we aligned the v. okuanii and r. magnifica genomes, we found evidence of this pathway's prior existence in the r. magnifica genome.
a degenerate pseudogene of the alpha subunit of v. okutanii's nitrate reductase sharing 70/ <dig> amino acids remained in the analogous position in the r. magnifica genome .
this evidence suggests that the lcsa was also capable of dissimilatory nitrate reduction.
the fact that this pathway has been lost from the r. magnifica genome is surprising, given the concentrations of nitrate  that exist in deep ocean waters  <cit> .
the loss of the dissimilatory nitrate reductase in r. magnifica and retention of the pathway in v. okutanii may reflect differences in host geochemical ecology.
the c. okutanii specimen for the v. okutanii genome project was collected off hatsushima island, in the sagami bay seep sites  <cit> .
the vesicomyid hosts found at sagami bay keep their feet buried deep within the silty sediment to access sulfide and may spend the majority of their time in anoxic conditions, where nitrate may be the more abundant oxidant  <cit> .
as the eukaryotic host must use oxygen as a terminal electron acceptor, perhaps the retention of the nitrate reductase in the seep clam symbionts reflects a means of reducing competition for oxygen between host and symbiont.
however, it is possible that the amount of oxygen available to the symbiosis in different environments may not translate to distinct microenvironments inside the bacteriocytes; the host hemoglobins  <cit>  may somehow buffer the symbionts against extreme anoxic conditions.
further research on the metabolic capabilities of the seep versus vent vesicomyids is needed to determine if ecological differences have contributed to the retention of the dissimilatory nitrate reductases.
a remarkable number of amino acid and cofactor biosynthesis pathways are conserved across all four chemosynthetic symbionts:  <dig> amino acids and  <dig> vitamints and cofactors.
although the sequenced symbiont genomes lack the gene encoding homoserine kinase , an enzyme normally utilized in the threonine biosynthetic pathway, there are kinases in all four genomes that could theoretically provide this function.
similarly, only a single cofactor biosynthesis pathway was incomplete; both sequenced symbiont genomes lack the ubid/x gene for ubiquinone biosynthesis from chorismate.
because ubiquinone is required for their energy metabolism, however, it is clear that they either must synthesize this cofactor or obtain it from the host.
thus, the extant vesicomyid symbionts, and therefore their lcsa, are capable of providing all the amino acids and prosthetic groups needed by the host.
mechanisms for nutrient transport between host and symbiont are not obvious based on the genomic data.
although all four vesicomyid symbionts encode a sec protein export system and the sec-independent tat system, the use of these pathways for transport of proteins to the host would be energetically costly for the symbiont as the terminal sequences would be wasted with each export.
few known transporters for sugars, amino acids, or vitamin/cofactors were found and instead the symbionts encode ammonium permeases, nitrate/nitrite transporters, and a sulfate exporter; transport mechanisms needed for their chemosynthetic metabolism.
of relevance to the symbiont host interaction is an abc transporter system found in the r. magnifica, v. sp.
mt-ii and c. kilmeri symbiont genomes.
this putative hemolysin transporter  is missing in v. okutanii without any trace of pseudogenes and, in other organisms, is implicated in pathogenesis  <cit> .
experimental data are needed to determine what its role may be in the vesicomyid symbionts.
the lack of transporters in the sequenced genomes and the high levels of lysozyme in calyptogena magnifica gill tissue  <cit>  has been cited as evidence that the hosts are actively, intracellularly digesting their symbionts.
however, many molluscs maintain high levels of lysozyme in their gills as a protective mechanism against pathogenesis  <cit> , and also the reduced peptidoglycan biosynthesis pathways in these genomes would make lysozyme-based digestion unnecessary.
it may be that the host utilizes other mechanisms for the digestion of the symbionts such as proteases or reactive oxygen species.
CONCLUSIONS
symbiosis is a ubiquitous and important ecological strategy for bacteria and eukaryotes, allowing the partners to inhabit environments that neither would be capable of alone.
however, for bacterial intracellular symbionts, sequestration within a eukaryotic lineage through vertical transmission can drastically affect symbiont genome evolution, leading to a reduction in gene content and metabolic capabilities.
the vesicomyid symbionts may use a mixed strategy for transmission with predominant vertical transmission punctuated by occasional lateral acquisition events  <cit> .
these rare events may give the vesicomyid symbionts the opportunity for recombination and horizontal gene transfer, allowing them to reacquire genes lost through genome reduction  <cit> .
indeed, in contrast to other sequenced symbiont genomes, the chemosynthetic symbionts of vesicomyid clams have relatively large chromosomes with an extraordinary amount of encoded metabolic capability.
based on genome sizes of free-living autotrophs , the genome of the vesicomyid clam symbionts is only reduced by half.
proteins shared by all four vesicomyid symbiont genomes  include the complete pathways necessary for chemoautotrophic metabolism.
as is clear from analyses between v. okutanii and r. magnifica, the symbionts also share a large extent of conserved synteny.
few functional differences were detected in the comparative genomic analysis; indeed the only difference likely to have ramifications for the symbiont metabolism is the ability to use nitrate as an electron acceptor.
the last common symbiotic ancestor is predicted to have been an obligate chemoautotroph, utilizing either nitrate or oxygen for the oxidation of reduced sulfur compounds.
invertebrates are able to thrive at hydrothermal vents due to the metabolic capabilities of their symbionts.
the vesicomyids, and indeed many hosts of chemosynthetic bacteria, have evolved small guts and reduced feeding mechanisms and rely primarily on their symbionts for carbon and other nutrients.
the data presented here suggest a tremendous degree of conserved gene content in the vesicomyid symbiont lineage, as these symbioses date to 50– <dig> mya.
this great extent of host dependency may be pressuring symbionts to retain the necessary metabolic pathways needed by the host.

 symbiosis between prokaryotic and eukaryotic cells is a globally important phenomenon that influences the physiology, ecology, and evolution of virtually every organism on this planet. eukaryotic hosts expand their ecological niches through symbiosis with these metabolically diverse bacteria and archaea. an illustrative case is that of the chemosynthetic endosymbionts, which enable their hosts to populate and thrive in challenging environments such as deep-sea hydrothermal vents and cold seeps. in these environments, reduced inorganic compounds are generated either biotically or abiotically. chemosynthetic symbionts use the energy derived from the oxidation of these molecules to fix inorganic carbon. benefits for both partners in chemosynthetic symbioses are evident. the bacteria gain further access to the energy substrates they require from both oxic and anoxic habitats while the animals are provided with much, if not all, of their nutritional requirements. the intimate structural and metabolic coupling often found in chemosynthetic symbioses underscores the importance of these relationships to host survival. the vesicomyid clams are one of the better studied chemosynthetic symbioses and exist at hydrothermal vents, hydrocarbon seeps, and other chemically reduced environments. they are also relatively young as a group, as vesicomyid fossils date the formation of the symbiosis to the cretaceous, between 50– ma ago. these clams have a greatly reduced gut and feeding groove and, based on isotopic evidence, are thought to depend almost entirely on their endosymbionts for their carbon. with respect to the animal host, the association is essential – no living vesicomyids have been found devoid of symbionts. furthermore, these symbionts have not yet been found outside the host, have never been cultured in the laboratory, and are thought to be predominantly maternally transmitted each generation via the egg. previous studies of other bacterial symbionts suggest that symbiont transmission strategy is a predominant factor governing nutritional symbiont genome evolution. bacterial symbionts transferred to the next host generation via the egg experience population bottlenecks upon transmission and few opportunities for recombination. because of the underlying deletion bias in bacterial genome evolution, and the limited amount of gene flow available to these symbionts, their genomes are minimized. for example, the genomes of the vertically transmitted, mutualistic insect endosymbionts buchnera, baumannia, blochmannia, and wigglesworthia are all reduced in size and content, exhibiting few chromosomal rearrangements, or horizontal gene transfer events. however, these insect nutritional symbionts retain the genomic repetoire needed to provide key metabolic intermediates, vitamins, and amino acids often missing from their hosts' specialized diets, suggesting that host nutritional needs might select for retention of specific biosynthetic pathways. conversely, those pathways redundant with host capabilities or nutrition are often lost completely. in contrast to the strictly vertically transmitted symbionts, those that undergo occasional environmental or horizontal transmission tend to have slightly larger genomes that exhibit evidence of recombination. for example, wolbachia pipientis, the ubiquitous insect reproductive parasite, may be laterally transmitted, and their genomes are littered with mobile genetic elements, prophages and harbor clear evidence of past recombination events. it must be noted, however, that transmission strategy for many symbionts cannot be distinctly or clearly demarcated; depending on the association, symbionts are perpetuated via a spectrum from strict vertical transmission to lateral acquisition. the insect reproductive parasites are vertically transmitted but occasionally laterally acquired. indeed, there is also some phylogenetic evidence, in the form of incongruent host and symbiont trees, against strict vertical transmission of the vesicomyid symbionts. more recently, two different strains of the vesicomyid symbionts have been found within the same host, corroborating the lateral acquisition hypothesis suggested by the phylogenetic evidence above. however, the vesicomyid symbionts are found in host primary oocytes and their genomes are reduced, and exhibit a high a+t content, suggesting that although occasional lateral transmission may occur, the predominant transmission strategy used by the vesicomyids is vertical. this mixed transmission strategy suggested for the vesicomyid symbionts has the potential to influence the genomic evolution of these bacteria. research on the comparative evolutionary genomics of insect symbionts suggests that symbionts with strictly vertical transmission strategies would lose genetic material redundant with host capabilities and retain metabolic pathways necessary for host survival. occasional lateral transmission might offer the opportunity for recombination and horizontal gene transfer, possibly mitigating the negative effects associated with a reduction in population size. indeed, some evidence of recombination has been found in the vesicomyid symbiont genomes, suggesting that genomic evolution of these bacteria may not be as straightforward as in strictly vertically transmitted symbionts. we chose a comparative framework, utilizing both genomic and heterologous microarray data, to investigate genome evolution in the vesicomyid chemosynthetic symbionts. the genomes of the two fully sequenced vesicomyid symbionts, ruthia magnifica, isolated from hydrothermal vents, and vesicomyosocious okutanii, isolated from cold seeps were compared to each other and to that of thiomicrospira crunogena, a free-living chemoautotroph isolated from hydrothermal vents and the closest sequenced relative of the vesicomyid symbionts. the availability of sequenced vesicomyid symbiont genomic data allowed us to develop microarrays for genome-scale analyses of conserved gene content in other vesicomyid symbionts. indeed, the great amount of genetic conservation and synteny between the two sequenced vesicomyid symbiont genomes suggests that the use of cross-species microarrays in the vesicomyid symbionts may be particularly informative. affymetrix microarrays based on the r. magnifica genome were constructed and hybridized to genomic dna from two other related vesicomyid symbionts, those of vesicomya sp. mt-ii and calyptogena kilmeri. vesicomya sp. mt-ii is part of a cryptic species complex which includes the clam formerly known as calytogena pacifica. a sampling strategy was chosen to illuminate possible effects of phylogenetic relationships and host geochemical environment on vesicomyid symbiont genome evolution. these four symbionts include representatives from each major clade of the vesicomyid symbiont lineage and therefore allow us to estimate a vesicomyid symbiont core genome. the symbionts investigated here also live within hosts inhabiting two distinct chemosynthetic environments: cold seeps and hydrothermal vents. these habitats differ in their geochemistry with regards to the quantity of oxygen, nitrate and redox state of sulfur available for the symbioses. the data presented here suggest a tremendous amount of genomic stasis and conserved gene content in the vesicomyid symbiont lineage; in the 50– ma that the symbionts have been host associated, their genomes have changed surprisingly little. these data also support existing evidence for lateral acquisition of the vesicomyid symbionts. these results underscore the importance of the symbionts' chemoautotrophic metabolism within their hosts; they emphasize the extent to which host metabolic needs have contributed to genomic evolution in this endosymbiont lineage.  four chemosynthetic symbiont genomes were compared in this study, two sequenced genomes and gene content for two other strains based on heterologous microarray hybridizations. the r. magnifica genome was used to build microarrays for heterologous hybridization to other vesicomyid symbionts. heterologous microarray hybridization is especially useful when comparing strain-level variation as arrays designed based on one of the strains are likely to hybridize to the dna of other strains. below, differences between the sequenced genomes are first discussed with reference to a free-living chemoautotroph, thiomicrospira crunogena. although t. crunogena is not part of the direct lineage of the vesicomyid symbionts, it is the closest sequenced relative of the chemosynthetic symbionts and provides us with some perspective as to the gene content necessary to be a functional chemoautotroph. we then discuss chemosynthetic symbiont metabolism and evolution based on both sequence and microarray analyses. as expected based on their maternal transmission, when compared to t. crunogena, these symbiont genomes are reduced in size and g + c content. the vesicomyid symbiont genomes are about half the size of t. crunogena's genome; of the proteins in the t. crunogena genome, the symbionts encode ~40%. the t. crunogena genome encodes enzymes and structures lacking from many intracellular bacteria but many of t. crunogena's metabolic capabilities are found in the vesicomyid symbiont genomes. indeed, there are proteins unique to the vesicomyid symbionts when compared to t. crunogena and a few of these may increase the symbionts' functional potential within their hosts. for example, the symbiont sulfur oxidation pathway includes both the sox and the dsr enzymes, and therefore appears to be more complex than that of t. crunogena, which encodes the sox system exclusively. thus, these symbiont genomes encode for many of the metabolic pathways of free-living chemoautotrophs despite being reduced in size. *percentage of the genome predicted to encode proteins the sequenced vesicomyid symbiont genomes are quite similar to each other in both gene content and order. of and proteins encoded in the r. magnifica and v. okutanii genomes respectively, orthologs are conserved across both, which share a relatively high amino acid identity. the v. okutanii and r. magnifica genomes also share an extraordinary amount of synteny, as clear from a lagan analysis by kuwahara et al., here, an analysis of synteny using mummer revealed that a total of 82% of genes in r. magnifica remain in the same genomic context and relative location in v. okutanii, with a single inversion. this kb inversion is comprised of genes including those involved in cofactor biosynthesis, potassium uptake, regulation of nitrogen utilization, and chaperonins. the inversion did not truncate any of the genes in the region and their orientation does not seem to obviously affect gene function as no operons are disrupted. there is a striking similarity between these two vesicomyid symbiont genomes, but a few substantial differences stand out. genes unique to r. magnifica and v. okutanii are largely in the cell envelope and energy metabolism role categories, respectively. the r. magnifica genome has a large region comprised of open reading frames lacking in v. okutanii's genome. this region primarily encodes proteins predicted to be involved in the biosynthesis of polysaccharides and peptidoglycan, components of the cell envelope. the lack of this region in v. okutanii suggests that perhaps the vesicomyid symbiont intracellular lifestyle does not require the synthesis of peptidoglycan. conversely, the r. magnifica genome lacks v. okutanii's dissimilatory nitrate reductase operon, which encodes energy metabolism proteins similar to the membrane-bound, respiratory nitrate reductase found in escherichia coli and other proteobacteria. this operon may enable v. okutanii to utilize nitrate as a terminal electron acceptor and may reduce competition between host and symbiont for oxygen, although this has yet to be demonstrated. this ability – which may have significant implications for the association's capacity to exploit hypoxic niches – may represent a significant functional difference between these two symbionts. the heterologous microarray hybridizations of v. sp mt-ii and c. kilmeri symbiont genomic dna to the r. magnifica array confirm the genomic stasis suggested by the sequence comparisons with v. okutanii. indeed, all of the microarray features hybridized to the c. kilmeri symbiont gdna, indicating that this symbiont contains at least the genomic repertoire of r. magnifica, while 92% of probed genes did not hybridize to the v. sp. mt-ii gdna. of this % of proteins putatively absent from the v. sp. mt-ii symbiont genome, the majority are of unknown function and it is therefore difficult to predict how symbiont metabolism and host interaction might be affected. a total of proteins are shared by all four vesicomyid symbiont genomes and this core genome encodes pathways for sulfur oxidation, nitrogen assimilation and carbon fixation, as well as synthesizing the amino acids and vitamins and cofactors, pathways central to their chemoautotrophic metabolism. data based on genomics, microarray hybridization results, and validated by polymerase chain reaction and slot blot dna hybridizations. *lower estimates of genomic content based on microarray hybridization results and validation methods. **total conserved gene content = genes shared by all four vesicomyid symbionts included in this study interestingly, neither reducing environment nor phylogenetic position correlated strongly with genomic content. the genomes of the two vent clam symbionts did not share any gene content to the exclusion of the two symbionts isolated from seep clams and vice versa. in fact, based on the comparative genomic hybridization results, the c. kilmeri seep clam symbiont is more similar to the vent clam symbiont r. magnifica than to v. okutanii. this is a surprising result as the c. kilmeri symbiont clades with v. okutanii in 16s rrna phylogenetic trees. also, the vent clam symbiont v. sp. mt-ii seems to share genomic excisions with the seep clam symbiont v. okutanii in comparison to r. magnifica; the same polysaccharide biosynthesis region absent from v. okutanii is also missing from the v. sp. mt-ii genome. these results are inconsistent with predictions of symbiont genomic content based on strict vertical transmission and instead support a mixed transmission strategy for these bacteria. occasional lateral transmission events, bringing two distinct bacterial symbionts together in the same host background, would provide the necessary opportunity for recombination in this lineage leading to this observed result: a mosaic of evolutionary histories throughout the genome. these four symbionts share a large fraction of their genomic repertoires, such that the total conserved genomic content within each functional role category remains comparatively high. when functional differences between these symbionts are mapped onto a circular representation based on the sequenced chromosomes, two large regions were found to be universally conserved across all four symbiont genomes. one segment, near the origin of replication, contains nearly all of the enzymes necessary for cytochrome biosynthesis and the calvin-benson-bassham cycle. it also harbors enzymes necessary for sulfur oxidation as well as energy conservation. the second segment, at bp, encodes genes involved in nitrogen metabolism, heme biosynthesis and ubiquinone biosynthesis. thus, many of the genes encoding enzymes thought to be fundamental to the symbioses are well conserved across four vesicomyid symbiont strains. based on the sequence and microarray data, a reconstruction of the minimal gene set for the vesicomyid symbionts' last common symbiotic ancestor is proposed. genes present in at least one of the symbiont genomes were assumed to have been present in the lcsa. below, we detail the commonalities and differences between the symbiont genomes with regards to the chemosynthetic metabolisms thought to be important to the symbiosis. the chemosynthetic symbionts are autotrophic bacteria but there is some question as to whether they are obligately autotrophs or acquire some carbon from the host. the genomic and microarray results from these four vesicomyid symbionts suggest they all have a complete calvin cycle utilizing a form ii rubisco and that fixed carbon can enter intermediary metabolism as phosphoglyceraldehyde. however, the vesicomyid symbionts intermediary metabolism lacks alpha-ketoglutarate dehydrogenase, a condition thought to be an indicator of obligate autotrophy. the lack of a sugar phosphotransferase system in these symbionts plus the lack of organic carbon transporters corroborates this idea. to ameliorate the effects of an incomplete tca cycle, a glyoxylate bypass is hypothesized for r. magnifica, v. sp. mt-ii, and c. kilmeri symbionts but this key enzyme is missing from the v. okutanii genome making regeneration of succinate in v. okutanii inexplicable. the v. okutanii genome is also lacking genes for malate dehydrogenase and fumarate reductase, suggesting significant reduction in comparison to r. magnifica. perhaps v. okutanii employs the single citrate transporter to take up tca intermediates from the host. this putative sugar transporter could theoretically function to move tca cycle intermediates between host and symbiont. based on this evidence, the lcsa of the vesicomyid symbionts is predicted to have been an obligate autotroph. however, unlike many free-living obligate autotrophs, the vesicomyid symbionts do not have carboxysomes, polyhedral shaped "organelles" that contain rubisco and carbonic anhydrase. these structures are thought to be involved in dehydration of bicarbonate to provide carbon dioxide to rubisco. although the carboxysome operon seen in other autotrophs is missing from the symbiont genomes, all four vesicomyid symbionts encode putative carbonic anhydrases. it may be that the host bacteriocyte environment maintains a high concentration of co limiting the need for carobxysomes. as is known from the riftia chemosynthetic symbiosis, the host animals might actively trap carbon intracellularly as bicarbonate, limiting the need for carboxysomes in the vesicomyid symbionts. indeed, the vesicomyid symbionts contain a form ii rubisco, the form with low affinity for co known from organisms that exist in high concentrations of carbon dioxide. the lcsa for the vesicomyid symbionts is predicted to have derived its energy for carbon dioxide fixation from sulfur oxidation. sulfur oxidation in all four vesicomyid symbionts is predicted to proceed via the sox and dsr genes. however, the v. okutanii genome encodes dsrjnrs while r. magnifica's does not. because this gene is lacking from the r. magnifica genome, it was not queried in the v. sp. mt-ii or c. kilmeri symbiont genomes. while the role of these genes in sulfur oxidation is unclear, they are thought to encode a triheme periplasmic cytochrome, a gene for biosynthesis of siroamide, and cytoplasmic proteins of unknown function. it is therefore unknown how symbiont metabolic function might be affected by the retention of these genes. two distinct terminal electron acceptors, are predicted to have been used by the lcsa. based on sequence data, r. magnifica is predicted to rely exclusively on oxygen as a terminal electron acceptor while v. okutanii might use either oxygen or nitrate. the v. okutanii genome nitrate reductase operon consists of upstream molybdenum cofactor biosynthesis proteins followed by narg and h, encoding the alpha and beta subunits of nitrate reductase, narj, the delta subunit which inserts the molybdenum cofactor into nitrate reductase, and nari, the gamma subunit which is a b-type cytochrome that accepts electrons from quinone to transfer to the alpha subunit. when we aligned the v. okuanii and r. magnifica genomes, we found evidence of this pathway's prior existence in the r. magnifica genome. a degenerate pseudogene of the alpha subunit of v. okutanii's nitrate reductase sharing 70/ amino acids remained in the analogous position in the r. magnifica genome. this evidence suggests that the lcsa was also capable of dissimilatory nitrate reduction. the fact that this pathway has been lost from the r. magnifica genome is surprising, given the concentrations of nitrate that exist in deep ocean waters. the loss of the dissimilatory nitrate reductase in r. magnifica and retention of the pathway in v. okutanii may reflect differences in host geochemical ecology. the c. okutanii specimen for the v. okutanii genome project was collected off hatsushima island, in the sagami bay seep sites. the vesicomyid hosts found at sagami bay keep their feet buried deep within the silty sediment to access sulfide and may spend the majority of their time in anoxic conditions, where nitrate may be the more abundant oxidant. as the eukaryotic host must use oxygen as a terminal electron acceptor, perhaps the retention of the nitrate reductase in the seep clam symbionts reflects a means of reducing competition for oxygen between host and symbiont. however, it is possible that the amount of oxygen available to the symbiosis in different environments may not translate to distinct microenvironments inside the bacteriocytes; the host hemoglobins may somehow buffer the symbionts against extreme anoxic conditions. further research on the metabolic capabilities of the seep versus vent vesicomyids is needed to determine if ecological differences have contributed to the retention of the dissimilatory nitrate reductases. a remarkable number of amino acid and cofactor biosynthesis pathways are conserved across all four chemosynthetic symbionts: amino acids and vitamints and cofactors. although the sequenced symbiont genomes lack the gene encoding homoserine kinase, an enzyme normally utilized in the threonine biosynthetic pathway, there are kinases in all four genomes that could theoretically provide this function. similarly, only a single cofactor biosynthesis pathway was incomplete; both sequenced symbiont genomes lack the ubid/x gene for ubiquinone biosynthesis from chorismate. because ubiquinone is required for their energy metabolism, however, it is clear that they either must synthesize this cofactor or obtain it from the host. thus, the extant vesicomyid symbionts, and therefore their lcsa, are capable of providing all the amino acids and prosthetic groups needed by the host. mechanisms for nutrient transport between host and symbiont are not obvious based on the genomic data. although all four vesicomyid symbionts encode a sec protein export system and the sec-independent tat system, the use of these pathways for transport of proteins to the host would be energetically costly for the symbiont as the terminal sequences would be wasted with each export. few known transporters for sugars, amino acids, or vitamin/cofactors were found and instead the symbionts encode ammonium permeases, nitrate/nitrite transporters, and a sulfate exporter; transport mechanisms needed for their chemosynthetic metabolism. of relevance to the symbiont host interaction is an abc transporter system found in the r. magnifica, v. sp. mt-ii and c. kilmeri symbiont genomes. this putative hemolysin transporter is missing in v. okutanii without any trace of pseudogenes and, in other organisms, is implicated in pathogenesis. experimental data are needed to determine what its role may be in the vesicomyid symbionts. the lack of transporters in the sequenced genomes and the high levels of lysozyme in calyptogena magnifica gill tissue has been cited as evidence that the hosts are actively, intracellularly digesting their symbionts. however, many molluscs maintain high levels of lysozyme in their gills as a protective mechanism against pathogenesis, and also the reduced peptidoglycan biosynthesis pathways in these genomes would make lysozyme-based digestion unnecessary. it may be that the host utilizes other mechanisms for the digestion of the symbionts such as proteases or reactive oxygen species.  symbiosis is a ubiquitous and important ecological strategy for bacteria and eukaryotes, allowing the partners to inhabit environments that neither would be capable of alone. however, for bacterial intracellular symbionts, sequestration within a eukaryotic lineage through vertical transmission can drastically affect symbiont genome evolution, leading to a reduction in gene content and metabolic capabilities. the vesicomyid symbionts may use a mixed strategy for transmission with predominant vertical transmission punctuated by occasional lateral acquisition events. these rare events may give the vesicomyid symbionts the opportunity for recombination and horizontal gene transfer, allowing them to reacquire genes lost through genome reduction. indeed, in contrast to other sequenced symbiont genomes, the chemosynthetic symbionts of vesicomyid clams have relatively large chromosomes with an extraordinary amount of encoded metabolic capability. based on genome sizes of free-living autotrophs, the genome of the vesicomyid clam symbionts is only reduced by half. proteins shared by all four vesicomyid symbiont genomes include the complete pathways necessary for chemoautotrophic metabolism. as is clear from analyses between v. okutanii and r. magnifica, the symbionts also share a large extent of conserved synteny. few functional differences were detected in the comparative genomic analysis; indeed the only difference likely to have ramifications for the symbiont metabolism is the ability to use nitrate as an electron acceptor. the last common symbiotic ancestor is predicted to have been an obligate chemoautotroph, utilizing either nitrate or oxygen for the oxidation of reduced sulfur compounds. invertebrates are able to thrive at hydrothermal vents due to the metabolic capabilities of their symbionts. the vesicomyids, and indeed many hosts of chemosynthetic bacteria, have evolved small guts and reduced feeding mechanisms and rely primarily on their symbionts for carbon and other nutrients. the data presented here suggest a tremendous degree of conserved gene content in the vesicomyid symbiont lineage, as these symbioses date to 50– mya. this great extent of host dependency may be pressuring symbionts to retain the necessary metabolic pathways needed by the host. 
to examine the genomic evolution of the vesicomyid symbionts, a comparative genomics framework, including the existing genomic data combined with heterologous microarray hybridization results, was used to analyze conserved gene content in four vesicomyid symbiont genomes. the fact that these symbionts appear to be metabolically capable autotrophs underscores the extent to which the host depends on them for nutrition and reveals the key to invertebrate colonization of these challenging environments. they exist in environments such as hydrothermal vents and cold seeps and have a reduced gut and feeding groove, indicating a large dependence on their endosymbionts for nutrition. these four symbionts were chosen to include a broad phylogenetic sampling of the vesicomyid symbionts and represent distinct chemosynthetic environments: cold seeps and hydrothermal vents. recently, two vesicomyid symbiont genomes were sequenced, illuminating the possible nutritional contributions of the symbiont to the host and making genome-wide evolutionary analyses possible. the results of this comparative genomics analysis emphasize the importance of the symbionts' chemoautotrophic metabolism within their hosts.
 the vesicomyidae are a family of clams that form symbioses with chemosynthetic gamma-proteobacteria. they exist in environments such as hydrothermal vents and cold seeps and have a reduced gut and feeding groove, indicating a large dependence on their endosymbionts for nutrition. recently, two vesicomyid symbiont genomes were sequenced, illuminating the possible nutritional contributions of the symbiont to the host and making genome-wide evolutionary analyses possible.  to examine the genomic evolution of the vesicomyid symbionts, a comparative genomics framework, including the existing genomic data combined with heterologous microarray hybridization results, was used to analyze conserved gene content in four vesicomyid symbiont genomes. these four symbionts were chosen to include a broad phylogenetic sampling of the vesicomyid symbionts and represent distinct chemosynthetic environments: cold seeps and hydrothermal vents.  the results of this comparative genomics analysis emphasize the importance of the symbionts' chemoautotrophic metabolism within their hosts. the fact that these symbionts appear to be metabolically capable autotrophs underscores the extent to which the host depends on them for nutrition and reveals the key to invertebrate colonization of these challenging environments. 