Gene Network Visualization and Quantitative Synteny Analysis of more than 300 Marine T4-Like Phage Scaffolds from the GOS Metagenome
Identifieur interne : 000126 ( Ncbi/Merge ); précédent : 000125; suivant : 000127Gene Network Visualization and Quantitative Synteny Analysis of more than 300 Marine T4-Like Phage Scaffolds from the GOS Metagenome
Auteurs : André M. Comeau [France] ; Christine Arbiol [France] ; H. M. Krisch [France]Source :
- Molecular Biology and Evolution [ 0737-4038 ] ; 2010.
Abstract
Bacteriophages (phages) are the most abundant biological entities in the biosphere and are the dominant “organisms” in marine environments, exerting an enormous influence on marine microbial populations. Metagenomic projects, such as the Global Ocean Sampling expedition (GOS), have demonstrated the predominance of tailed phages (Caudovirales), particularly T4 superfamily cyanophages (Cyano-T4s), in the marine milieu. Whereas previous metagenomic analyses were limited to gene content information, here we present a comparative analysis of over 300 phage scaffolds assembled from the viral fraction of the GOS data. This assembly permits the examination of synteny (organization) of the genes on the scaffolds and their comparison with the genome sequences from cultured Cyano-T4s. We employ comparative genomics and a novel usage of network visualization software to show that the scaffold phylogenies are similar to those of the traditional marker genes they contain. Importantly, these uncultured metagenomic scaffolds quite closely match the organization of the “core genome” of the known Cyano-T4s. This indicates that the current view of genome architecture in the Cyano-T4s is not seriously biased by being based on a small number of cultured phages, and we can be confident that they accurately reflect the diverse population of such viruses in marine surface waters.
Url:
DOI: 10.1093/molbev/msq076
PubMed: 20231334
PubMed Central: 2908710
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<front><journal-meta><journal-id journal-id-type="nlm-ta">Mol Biol Evol</journal-id><journal-id journal-id-type="hwp">molbiolevol</journal-id><journal-id journal-id-type="publisher-id">molbev</journal-id><journal-title-group><journal-title>Molecular Biology and Evolution</journal-title></journal-title-group><issn pub-type="ppub">0737-4038</issn><issn pub-type="epub">1537-1719</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">20231334</article-id><article-id pub-id-type="pmc">2908710</article-id><article-id pub-id-type="doi">10.1093/molbev/msq076</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Articles</subject></subj-group></article-categories><title-group><article-title>Gene Network Visualization and Quantitative Synteny Analysis of more than 300 Marine T4-Like Phage Scaffolds from the GOS Metagenome</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Comeau</surname><given-names>André M.</given-names></name><xref ref-type="author-notes" rid="fn1">†</xref><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="aff" rid="aff2">2</xref></contrib><contrib contrib-type="author"><name><surname>Arbiol</surname><given-names>Christine</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="aff" rid="aff2">2</xref><xref ref-type="aff" rid="aff3">3</xref></contrib><contrib contrib-type="author"><name><surname>Krisch</surname><given-names>H.M.</given-names></name><xref ref-type="corresp" rid="cor1">*</xref><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="aff" rid="aff2">2</xref></contrib></contrib-group><aff id="aff1"><label>1</label>Centre National de la Recherche Scientifique, UMR5100, Toulouse, France</aff><aff id="aff2"><label>2</label>Laboratoire de Microbiologie et Génétique Moléculaires, Université de Toulouse, Université Paul Sabatier, Toulouse, France</aff><aff id="aff3"><label>3</label>Institut d'Exploration Fonctionnelle des Génomes, Centre National de la Recherche Scientifique, IFR109, Toulouse, France</aff><author-notes><fn id="fn1"><label>†</label><p>Present address: Institut de Biologie Intégrative et des Systémes/Québec-Océan, Department of Biology, Université Laval, Québec, Canada.</p></fn><corresp id="cor1"><label>*</label><bold>Corresponding author:</bold> E-mail: <email>krisch@ibcg.biotoul.fr</email>.</corresp><fn><p><bold>Associate editor:</bold> Hervé Philippe</p></fn></author-notes><pub-date pub-type="ppub"><month>8</month><year>2010</year></pub-date><pub-date pub-type="epub"><day>15</day><month>3</month><year>2010</year></pub-date><pub-date pub-type="pmc-release"><day>15</day><month>3</month><year>2010</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>27</volume><issue>8</issue><fpage>1935</fpage><lpage>1944</lpage><permissions><copyright-statement>© The Author(s) 2010. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.</copyright-statement><copyright-year>2010</copyright-year><license license-type="open-access"><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/2.5">http://creativecommons.org/licenses/by-nc/2.5</ext-link>), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><abstract><p>Bacteriophages (phages) are the most abundant biological entities in the biosphere and are the dominant “organisms” in marine environments, exerting an enormous influence on marine microbial populations. Metagenomic projects, such as the Global Ocean Sampling expedition (GOS), have demonstrated the predominance of tailed phages (Caudovirales), particularly T4 superfamily cyanophages (Cyano-T4s), in the marine milieu. Whereas previous metagenomic analyses were limited to gene content information, here we present a comparative analysis of over 300 phage scaffolds assembled from the viral fraction of the GOS data. This assembly permits the examination of synteny (organization) of the genes on the scaffolds and their comparison with the genome sequences from cultured Cyano-T4s. We employ comparative genomics and a novel usage of network visualization software to show that the scaffold phylogenies are similar to those of the traditional marker genes they contain. Importantly, these uncultured metagenomic scaffolds quite closely match the organization of the “core genome” of the known Cyano-T4s. This indicates that the current view of genome architecture in the Cyano-T4s is not seriously biased by being based on a small number of cultured phages, and we can be confident that they accurately reflect the diverse population of such viruses in marine surface waters.</p></abstract><kwd-group><kwd>T4-like phage</kwd><kwd>cyanophage</kwd><kwd>metagenome</kwd><kwd>synteny</kwd></kwd-group></article-meta></front></pmc><affiliations><list><country><li>France</li></country><settlement><li>Toulouse</li></settlement></list><tree><country name="France"><noRegion><name sortKey="Comeau, Andre M" sort="Comeau, Andre M" uniqKey="Comeau A" first="André M." last="Comeau">André M. Comeau</name></noRegion><name sortKey="Arbiol, Christine" sort="Arbiol, Christine" uniqKey="Arbiol C" first="Christine" last="Arbiol">Christine Arbiol</name><name sortKey="Arbiol, Christine" sort="Arbiol, Christine" uniqKey="Arbiol C" first="Christine" last="Arbiol">Christine Arbiol</name><name sortKey="Arbiol, Christine" sort="Arbiol, Christine" uniqKey="Arbiol C" first="Christine" last="Arbiol">Christine Arbiol</name><name sortKey="Comeau, Andre M" sort="Comeau, Andre M" uniqKey="Comeau A" first="André M." last="Comeau">André M. Comeau</name><name sortKey="Krisch, H M" sort="Krisch, H M" uniqKey="Krisch H" first="H. M." last="Krisch">H. M. Krisch</name><name sortKey="Krisch, H M" sort="Krisch, H M" uniqKey="Krisch H" first="H. M." last="Krisch">H. M. Krisch</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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