Bacterial DNA Sifted from the Trichoplax adhaerens (Animalia: Placozoa) Genome Project Reveals a Putative Rickettsial Endosymbiont
Identifieur interne : 000395 ( Ncbi/Curation ); précédent : 000394; suivant : 000396Bacterial DNA Sifted from the Trichoplax adhaerens (Animalia: Placozoa) Genome Project Reveals a Putative Rickettsial Endosymbiont
Auteurs : Timothy Driscoll ; Joseph J. Gillespie ; Eric K. Nordberg ; Abdu F. Azad ; Bruno W. Sobral [Suisse]Source :
- Genome Biology and Evolution [ 1759-6653 ] ; 2013.
Abstract
Eukaryotic genome sequencing projects often yield bacterial DNA sequences, data typically considered as microbial contamination. However, these sequences may also indicate either symbiont genes or lateral gene transfer (LGT) to host genomes. These bacterial sequences can provide clues about eukaryote–microbe interactions. Here, we used the genome of the primitive animal
Url:
DOI: 10.1093/gbe/evt036
PubMed: 23475938
PubMed Central: 3641634
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Joseph J. Gillespie<affiliation><nlm:aff id="evt036-AFF2">Department of Microbiology and Immunology, University of Maryland School of Medicine</nlm:aff>
<wicri:noCountry code="subfield">University of Maryland School of Medicine</wicri:noCountry>
</affiliation>
<affiliation><nlm:aff id="evt036-AFF2">Department of Microbiology and Immunology, University of Maryland School of Medicine</nlm:aff>
<wicri:noCountry code="subfield">University of Maryland School of Medicine</wicri:noCountry>
</affiliation>
Le document en format XML
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(Animalia: Placozoa) Genome Project Reveals a Putative Rickettsial Endosymbiont</title>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Bacterial DNA Sifted from the <italic>Trichoplax adhaerens</italic>
(Animalia: Placozoa) Genome Project Reveals a Putative Rickettsial Endosymbiont</title>
<author><name sortKey="Driscoll, Timothy" sort="Driscoll, Timothy" uniqKey="Driscoll T" first="Timothy" last="Driscoll">Timothy Driscoll</name>
<affiliation><nlm:aff id="evt036-AFF1">Virginia Bioinformatics Institute at Virginia Polytechnic Institute and State University</nlm:aff>
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<author><name sortKey="Gillespie, Joseph J" sort="Gillespie, Joseph J" uniqKey="Gillespie J" first="Joseph J." last="Gillespie">Joseph J. Gillespie</name>
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<affiliation><nlm:aff id="evt036-AFF2">Department of Microbiology and Immunology, University of Maryland School of Medicine</nlm:aff>
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<author><name sortKey="Nordberg, Eric K" sort="Nordberg, Eric K" uniqKey="Nordberg E" first="Eric K." last="Nordberg">Eric K. Nordberg</name>
<affiliation><nlm:aff id="evt036-AFF1">Virginia Bioinformatics Institute at Virginia Polytechnic Institute and State University</nlm:aff>
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<author><name sortKey="Azad, Abdu F" sort="Azad, Abdu F" uniqKey="Azad A" first="Abdu F." last="Azad">Abdu F. Azad</name>
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<author><name sortKey="Sobral, Bruno W" sort="Sobral, Bruno W" uniqKey="Sobral B" first="Bruno W." last="Sobral">Bruno W. Sobral</name>
<affiliation><nlm:aff id="evt036-AFF1">Virginia Bioinformatics Institute at Virginia Polytechnic Institute and State University</nlm:aff>
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<series><title level="j">Genome Biology and Evolution</title>
<idno type="eISSN">1759-6653</idno>
<imprint><date when="2013">2013</date>
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<front><div type="abstract" xml:lang="en"><p>Eukaryotic genome sequencing projects often yield bacterial DNA sequences, data typically considered as microbial contamination. However, these sequences may also indicate either symbiont genes or lateral gene transfer (LGT) to host genomes. These bacterial sequences can provide clues about eukaryote–microbe interactions. Here, we used the genome of the primitive animal <italic>Trichoplax adhaerens</italic>
(Metazoa: Placozoa), which is known to harbor an uncharacterized Gram-negative endosymbiont, to search for the presence of bacterial DNA sequences. Bioinformatic and phylogenomic analyses of extracted data from the genome assembly (181 bacterial coding sequences [CDS]) and trace read archive (16S rDNA) revealed a dominant proteobacterial profile strongly skewed to Rickettsiales (<italic>Alphaproteobacteria</italic>
) genomes. By way of phylogenetic analysis of 16S rDNA and 113 proteins conserved across proteobacterial genomes, as well as identification of 27 rickettsial signature genes, we propose a Rickettsiales endosymbiont of <italic>T. adhaerens</italic>
(RETA). The majority (93%) of the identified bacterial CDS belongs to small scaffolds containing prokaryotic-like genes; however, 12 CDS were identified on large scaffolds comprised of eukaryotic-like genes, suggesting that <italic>T</italic>
. <italic>adhaerens</italic>
might have recently acquired bacterial genes. These putative LGTs may coincide with the placozoan’s aquatic niche and symbiosis with RETA. This work underscores the rich, and relatively untapped, resource of eukaryotic genome projects for harboring data pertinent to host–microbial interactions. The nature of unknown (or poorly characterized) bacterial species may only emerge via analysis of host genome sequencing projects, particularly if these species are resistant to cell culturing, as are many obligate intracellular microbes. Our work provides methodological insight for such an approach.</p>
</div>
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