Gene Network Visualization and Quantitative Synteny Analysis of more than 300 Marine T4-Like Phage Scaffolds from the GOS Metagenome
Identifieur interne : 000040 ( France/Analysis ); précédent : 000039; suivant : 000041Gene 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
Affiliations:
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PMC:2908710Le document en format XML
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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></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Ackermann, Hw" uniqKey="Ackermann H">HW Ackermann</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Angly, Fe" uniqKey="Angly F">FE Angly</name></author><author><name sortKey="Felts, B" uniqKey="Felts B">B Felts</name></author><author><name sortKey="Breitbart, M" uniqKey="Breitbart M">M Breitbart</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Besemer, J" uniqKey="Besemer J">J Besemer</name></author><author><name sortKey="Borodovsky, M" uniqKey="Borodovsky M">M Borodovsky</name></author></analytic></biblStruct><biblStruct><analytic><author><name 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uniqKey="Wishart D">DS Wishart</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sullivan, Mb" uniqKey="Sullivan M">MB Sullivan</name></author><author><name sortKey="Coleman, Ml" uniqKey="Coleman M">ML Coleman</name></author><author><name sortKey="Weigele, P" uniqKey="Weigele P">P Weigele</name></author><author><name sortKey="Rohwer, F" uniqKey="Rohwer F">F Rohwer</name></author><author><name sortKey="Chisholm, Sw" uniqKey="Chisholm S">SW Chisholm</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Suttle, Ca" uniqKey="Suttle C">CA Suttle</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Thompson, Jd" uniqKey="Thompson J">JD Thompson</name></author><author><name sortKey="Higgins, Dg" uniqKey="Higgins D">DG Higgins</name></author><author><name sortKey="Gibson, Tj" uniqKey="Gibson T">TJ Gibson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Weigele, Pr" uniqKey="Weigele P">PR Weigele</name></author><author><name sortKey="Pope, Wh" uniqKey="Pope W">WH Pope</name></author><author><name sortKey="Pedulla, Ml" uniqKey="Pedulla M">ML Pedulla</name></author><author><name sortKey="Houtz, Jm" uniqKey="Houtz J">JM Houtz</name></author><author><name sortKey="Smith, Al" uniqKey="Smith A">AL Smith</name></author><author><name sortKey="Conway, Jf" uniqKey="Conway J">JF Conway</name></author><author><name sortKey="King, J" uniqKey="King J">J King</name></author><author><name sortKey="Hatfull, Gf" uniqKey="Hatfull G">GF Hatfull</name></author><author><name sortKey="Lawrence, Jg" uniqKey="Lawrence J">JG Lawrence</name></author><author><name sortKey="Hendrix, Rw" uniqKey="Hendrix R">RW Hendrix</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Williamson, Sj" uniqKey="Williamson S">SJ Williamson</name></author><author><name sortKey="Rusch, Db" uniqKey="Rusch D">DB Rusch</name></author><author><name sortKey="Yooseph, S" uniqKey="Yooseph S">S Yooseph</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zeidner, G" uniqKey="Zeidner G">G Zeidner</name></author><author><name sortKey="Bielawski, Jp" uniqKey="Bielawski J">JP Bielawski</name></author><author><name sortKey="Shmoish, M" uniqKey="Shmoish M">M Shmoish</name></author><author><name sortKey="Scanlan, Dj" uniqKey="Scanlan D">DJ Scanlan</name></author><author><name sortKey="Sabehi, G" uniqKey="Sabehi G">G Sabehi</name></author><author><name sortKey="Beja, O" uniqKey="Beja O">O Béjà</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhong, Y" uniqKey="Zhong Y">Y Zhong</name></author><author><name sortKey="Chen, F" uniqKey="Chen F">F Chen</name></author><author><name sortKey="Wilhelm, Sw" uniqKey="Wilhelm S">SW Wilhelm</name></author><author><name sortKey="Poorvin, L" uniqKey="Poorvin L">L Poorvin</name></author><author><name sortKey="Hodson, Re" uniqKey="Hodson R">RE Hodson</name></author></analytic></biblStruct></listBibl></div1></back></TEI><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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