Genomic and functional analysis of Vibrio phage SIO‐2 reveals novel insights into ecology and evolution of marine siphoviruses
Identifieur interne : 000763 ( Istex/Corpus ); précédent : 000762; suivant : 000764Genomic and functional analysis of Vibrio phage SIO‐2 reveals novel insights into ecology and evolution of marine siphoviruses
Auteurs : A. Baudoux ; R. W. Hendrix ; G. C. Lander ; X. Bailly ; S. Podell ; C. Paillard ; J. E. Johnson ; C. S. Potter ; B. Carragher ; F. AzamSource :
- Environmental Microbiology [ 1462-2912 ] ; 2012-08.
Abstract
We report on a genomic and functional analysis of a novel marine siphovirus, the Vibrio phage SIO‐2. This phage is lytic for related Vibrio species of great ecological interest including the broadly antagonistic bacterium Vibrio sp. SWAT3 as well as notable members of the Harveyi clade (V. harveyi ATTC BAA‐1116 and V. campbellii ATCC 25920). Vibrio phage SIO‐2 has a circularly permuted genome of 80 598 bp, which displays unusual features. This genome is larger than that of most known siphoviruses and only 38 of the 116 predicted proteins had homologues in databases. Another divergence is manifest by the origin of core genes, most of which share robust similarities with unrelated viruses and bacteria spanning a wide range of phyla. These core genes are arranged in the same order as in most bacteriophages but they are unusually interspaced at two places with insertions of DNA comprising a high density of uncharacterized genes. The acquisition of these DNA inserts is associated with morphological variation of SIO‐2 capsid, which assembles as a large (80 nm) shell with a novel T = 12 symmetry. These atypical structural features confer on SIO‐2 a remarkable stability to a variety of physical, chemical and environmental factors. Given this high level of functional and genomic novelty, SIO‐2 emerges as a model of considerable interest in ecological and evolutionary studies.
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DOI: 10.1111/j.1462-2920.2011.02685.x
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This phage is lytic for related Vibrio species of great ecological interest including the broadly antagonistic bacterium Vibrio sp. SWAT3 as well as notable members of the Harveyi clade (V. harveyi ATTC BAA‐1116 and V. campbellii ATCC 25920). Vibrio phage SIO‐2 has a circularly permuted genome of 80 598 bp, which displays unusual features. This genome is larger than that of most known siphoviruses and only 38 of the 116 predicted proteins had homologues in databases. Another divergence is manifest by the origin of core genes, most of which share robust similarities with unrelated viruses and bacteria spanning a wide range of phyla. These core genes are arranged in the same order as in most bacteriophages but they are unusually interspaced at two places with insertions of DNA comprising a high density of uncharacterized genes. The acquisition of these DNA inserts is associated with morphological variation of SIO‐2 capsid, which assembles as a large (80 nm) shell with a novel T = 12 symmetry. These atypical structural features confer on SIO‐2 a remarkable stability to a variety of physical, chemical and environmental factors. Given this high level of functional and genomic novelty, SIO‐2 emerges as a model of considerable interest in ecological and evolutionary studies.</div></front></TEI><istex><corpusName>wiley</corpusName><author><json:item><name>A.‐C. Baudoux</name><affiliations><json:string>Scripps Institution of Oceanography, Marine Biology Research Division, University of California San Diego, La Jolla, CA 92093, USA</json:string></affiliations></json:item><json:item><name>R. W. Hendrix</name><affiliations><json:string>Pittsburgh Bacteriophage Institute, Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA</json:string></affiliations></json:item><json:item><name>G. C. 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Another divergence is manifest by the origin of core genes, most of which share robust similarities with unrelated viruses and bacteria spanning a wide range of phyla. These core genes are arranged in the same order as in most bacteriophages but they are unusually interspaced at two places with insertions of DNA comprising a high density of uncharacterized genes. The acquisition of these DNA inserts is associated with morphological variation of SIO‐2 capsid, which assembles as a large (80 nm) shell with a novel T = 12 symmetry. These atypical structural features confer on SIO‐2 a remarkable stability to a variety of physical, chemical and environmental factors. 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Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29682 Roscoff, France;</note><affiliation>Present addresses: CNRS/UPMC Univ. Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29682 Roscoff, France;</affiliation><note type="correspondence"><p>Correspondence: E‐mail ; Tel. (+33) 298 292 323; Fax (+33) 298 292 324.</p></note><affiliation>Scripps Institution of Oceanography, Marine Biology Research Division, University of California San Diego, La Jolla, CA 92093, USA</affiliation></author><author xml:id="author-2"><persName><forename type="first">R. W.</forename><surname>Hendrix</surname></persName><affiliation>Pittsburgh Bacteriophage Institute, Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA</affiliation></author><author xml:id="author-3"><persName><forename type="first">G. C.</forename><surname>Lander</surname></persName><note type="biography">Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.</note><affiliation>Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.</affiliation><affiliation>National Resource for Automated Molecular Microscopy, The Scripps Research Institute, La Jolla, CA 92037, USA</affiliation><affiliation>Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA</affiliation></author><author xml:id="author-4"><persName><forename type="first">X.</forename><surname>Bailly</surname></persName><affiliation>CNRS/UPMC Univ. 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This phage is lytic for related Vibrio species of great ecological interest including the broadly antagonistic bacterium Vibrio sp. SWAT3 as well as notable members of the Harveyi clade (V. harveyi ATTC BAA‐1116 and V. campbellii ATCC 25920). Vibrio phage SIO‐2 has a circularly permuted genome of 80 598 bp, which displays unusual features. This genome is larger than that of most known siphoviruses and only 38 of the 116 predicted proteins had homologues in databases. Another divergence is manifest by the origin of core genes, most of which share robust similarities with unrelated viruses and bacteria spanning a wide range of phyla. These core genes are arranged in the same order as in most bacteriophages but they are unusually interspaced at two places with insertions of DNA comprising a high density of uncharacterized genes. The acquisition of these DNA inserts is associated with morphological variation of SIO‐2 capsid, which assembles as a large (80 nm) shell with a novel T = 12 symmetry. These atypical structural features confer on SIO‐2 a remarkable stability to a variety of physical, chemical and environmental factors. Given this high level of functional and genomic novelty, SIO‐2 emerges as a model of considerable interest in ecological and evolutionary studies.</p></abstract></profileDesc><revisionDesc><change when="2012-08">Published</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><original>false</original><mimetype>text/plain</mimetype><extension>txt</extension><uri>https://api.istex.fr/document/9D25744D4A309D6FD5B67F2FDCB83A6EB6EED0D1/fulltext/txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="Wiley, elements deleted: body"><istex:xmlDeclaration>version="1.0" encoding="UTF-8" standalone="yes"</istex:xmlDeclaration><istex:document><component version="2.0" type="serialArticle" xml:lang="en"><header><publicationMeta level="product"><publisherInfo><publisherName>Blackwell Publishing Ltd</publisherName><publisherLoc>Oxford, UK</publisherLoc></publisherInfo><doi origin="wiley" registered="yes">10.1111/(ISSN)1462-2920</doi><issn type="print">1462-2912</issn><issn type="electronic">1462-2920</issn><idGroup><id type="product" value="EMI"></id><id type="publisherDivision" value="ST"></id></idGroup><titleGroup><title type="main" sort="ENVIRONMENTAL MICROBIOLOGY">Environmental Microbiology</title></titleGroup></publicationMeta><publicationMeta level="part" position="08108"><doi origin="wiley">10.1111/emi.2012.14.issue-8</doi><titleGroup><title type="specialIssueTitle">Ecology, Evolution and Population Genetics of Pathogenic Microbes</title></titleGroup><numberingGroup><numbering type="journalVolume" number="14">14</numbering><numbering type="journalIssue">8</numbering></numberingGroup><coverDate startDate="2012-08">August 2012</coverDate></publicationMeta><publicationMeta level="unit" type="article" position="21" status="forIssue"><doi origin="wiley">10.1111/j.1462-2920.2011.02685.x</doi><idGroup><id type="unit" value="EMI2685"></id></idGroup><countGroup><count type="pageTotal" number="16"></count></countGroup><titleGroup><title type="tocHeading1">Research articles</title></titleGroup><copyright>© 2012 Society for Applied Microbiology and Blackwell Publishing Ltd</copyright><eventGroup><event type="xmlConverted" agent="Converter:BPG_TO_WML3G version:3.1.6 mode:FullText" date="2012-08-21"></event><event type="publishedOnlineEarlyUnpaginated" date="2012-01-09"></event><event type="publishedOnlineFinalForm" date="2012-07-26"></event><event type="firstOnline" date="2012-01-09"></event><event type="xmlConverted" agent="Converter:WILEY_ML3G_TO_WILEY_ML3GV2 version:3.8.8" date="2014-01-24"></event><event type="xmlConverted" agent="Converter:WML3G_To_WML3G version:4.3.4 mode:FullText" date="2015-02-25"></event></eventGroup><numberingGroup><numbering type="pageFirst" number="2071">2071</numbering><numbering type="pageLast" number="2086">2086</numbering></numberingGroup><correspondenceTo> E‐mail <email normalForm="acbaudoux@sb-roscoff.fr">acbaudoux@sb‐roscoff.fr</email>; Tel. (+33) 298 292 323; Fax (+33) 298 292 324.</correspondenceTo><linkGroup><link type="toTypesetVersion" href="file:EMI.EMI2685.pdf"></link></linkGroup></publicationMeta><contentMeta><unparsedEditorialHistory>Received 29 June, 2011; revised 15 November, 2011; accepted 27 November, 2011.</unparsedEditorialHistory><countGroup><count type="figureTotal" number="5"></count><count type="tableTotal" number="3"></count><count type="formulaTotal" number="0"></count><count type="referenceTotal" number="80"></count><count type="wordTotal" number="11718"></count><count type="linksPubMed" number="0"></count><count type="linksCrossRef" number="0"></count></countGroup><titleGroup><title type="main">Genomic and functional analysis of <i>Vibrio</i> phage SIO‐2 reveals novel insights into ecology and evolution of marine siphoviruses</title><title type="shortAuthors">A.‐C. Baudoux <i>et al.</i></title><title type="short">Characterization of the novel marine siphovirus SIO‐2</title></titleGroup><creators><creator creatorRole="author" xml:id="cr1" affiliationRef="#a1" noteRef="#fn1" corresponding="yes"><personName><givenNames>A.‐C.</givenNames><familyName>Baudoux</familyName></personName></creator><creator creatorRole="author" xml:id="cr2" affiliationRef="#a2"><personName><givenNames>R. W.</givenNames><familyName>Hendrix</familyName></personName></creator><creator creatorRole="author" xml:id="cr3" affiliationRef="#a3 #a4" noteRef="#fn2"><personName><givenNames>G. C.</givenNames><familyName>Lander</familyName></personName></creator><creator creatorRole="author" xml:id="cr4" affiliationRef="#a5"><personName><givenNames>X.</givenNames><familyName>Bailly</familyName></personName></creator><creator creatorRole="author" xml:id="cr5" affiliationRef="#a1"><personName><givenNames>S.</givenNames><familyName>Podell</familyName></personName></creator><creator creatorRole="author" xml:id="cr6" affiliationRef="#a6"><personName><givenNames>C.</givenNames><familyName>Paillard</familyName></personName></creator><creator creatorRole="author" xml:id="cr7" affiliationRef="#a4"><personName><givenNames>J. E.</givenNames><familyName>Johnson</familyName></personName></creator><creator creatorRole="author" xml:id="cr8" affiliationRef="#a3"><personName><givenNames>C. S.</givenNames><familyName>Potter</familyName></personName></creator><creator creatorRole="author" xml:id="cr9" affiliationRef="#a3"><personName><givenNames>B.</givenNames><familyName>Carragher</familyName></personName></creator><creator creatorRole="author" xml:id="cr10" affiliationRef="#a1"><personName><givenNames>F.</givenNames><familyName>Azam</familyName></personName></creator></creators><affiliationGroup><affiliation xml:id="a1" countryCode="US"><unparsedAffiliation>Scripps Institution of Oceanography, Marine Biology Research Division, University of California San Diego, La Jolla, CA 92093, USA</unparsedAffiliation></affiliation><affiliation xml:id="a2" countryCode="US"><unparsedAffiliation>Pittsburgh Bacteriophage Institute, Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA</unparsedAffiliation></affiliation><affiliation xml:id="a3" countryCode="US"><unparsedAffiliation>National Resource for Automated Molecular Microscopy, The Scripps Research Institute, La Jolla, CA 92037, USA</unparsedAffiliation></affiliation><affiliation xml:id="a4" countryCode="US"><unparsedAffiliation>Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA</unparsedAffiliation></affiliation><affiliation xml:id="a5" countryCode="FR"><unparsedAffiliation>CNRS/UPMC Univ. Paris 06, FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29682 Roscoff, France</unparsedAffiliation></affiliation><affiliation xml:id="a6" countryCode="FR"><unparsedAffiliation>Institut Universitaire Européen de la Mer, Laboratoire des Sciences de l’Environnement Marin, 29280 Plouzané, France</unparsedAffiliation></affiliation></affiliationGroup><supportingInformation><p><b>Fig. S1.</b> Isolation of <i>Vibrio</i> phage SIO‐2 from plaque assay.</p><p><b>Fig. S2.</b> Vibrioid cell tagged with fluorescently labelled SIO‐2 observed by epifluorescence microscopy.</p><p><b>Fig. S3.</b> Genome size of SIO‐2 isolate as determined by PFGE. Lane M: Lambda concatamers ladder, Lane 1: SIO‐2 genome incubated with DNase RQ1 for 24 h, Lane 2: untreated SIO‐2 genome.</p><p><b>Fig. S4.</b> Intergenic repeats observed in SIO‐2 genome. The termination codons of the upstream genes are shown in red, and the initiation codons of the downstream genes are shown in green. The five different repeated sequences are shown in five different colours. Putative transcription and translation signals indicated with labels and underlines include −35 and −10 regions of promoters (with the predicted + 1 nucleotide of the transcript indicated in bold), transcription terminators and Shine–Dalgarno ribosome‐binding sequences.</p><p><b>Fig. S5.</b> Codon usage in the genome of <i>Vibrio</i> sp. SWAT3 (H1) and <i>Vibrio harveyi</i> ATCC BAA‐1116 (H2) and <i>Vibrio</i> phage SIO‐2 (P).</p><p><b>Table S1.</b> Bacterial cultures tested for the determination of SIO‐2 host specificity. Efficiency of plating (EOP) was determined by the ratio of SIO‐2 plaque titre obtained with the heterologous host to that obtained with <i>Vibrio</i> sp. SWAT3.</p><p><b>Table S2.</b> Phage polymerase gene sequences (family A, PF00476.13) used for phylogenetic analysis.</p><p><b>Table S3.</b> Metagenomic analysis.</p><p><b>Appendix S1.</b> Material and methods.</p><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:14622912:media:emi2685:EMI_2685_sm_FigS1-5-TabS1-3-AppS1"></mediaResource><caption>Supporting info item</caption></supportingInfoItem><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:14622912:media:emi2685:EMI_2685_sm_SIO2-Genome-sequence"></mediaResource><caption>Supporting info item</caption></supportingInfoItem></supportingInformation><abstractGroup><abstract type="main" xml:lang="en"><title type="main">Summary</title><p>We report on a genomic and functional analysis of a novel marine siphovirus, the <i>Vibrio</i> phage SIO‐2. This phage is lytic for related <i>Vibrio</i> species of great ecological interest including the broadly antagonistic bacterium <i>Vibrio</i> sp. SWAT3 as well as notable members of the Harveyi clade (<i>V. harveyi</i> ATTC BAA‐1116 and <i>V. campbellii</i> ATCC 25920). <i>Vibrio</i> phage SIO‐2 has a circularly permuted genome of 80 598 bp, which displays unusual features. This genome is larger than that of most known siphoviruses and only 38 of the 116 predicted proteins had homologues in databases. Another divergence is manifest by the origin of core genes, most of which share robust similarities with unrelated viruses and bacteria spanning a wide range of phyla. These core genes are arranged in the same order as in most bacteriophages but they are unusually interspaced at two places with insertions of DNA comprising a high density of uncharacterized genes. The acquisition of these DNA inserts is associated with morphological variation of SIO‐2 capsid, which assembles as a large (80 nm) shell with a novel T = 12 symmetry. These atypical structural features confer on SIO‐2 a remarkable stability to a variety of physical, chemical and environmental factors. Given this high level of functional and genomic novelty, SIO‐2 emerges as a model of considerable interest in ecological and evolutionary studies.</p></abstract></abstractGroup></contentMeta><noteGroup><note xml:id="fn1"><p>Present addresses: CNRS/UPMC Univ. Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29682 Roscoff, France; </p></note><note xml:id="fn2"><p> Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.</p></note></noteGroup></header></component></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Genomic and functional analysis of Vibrio phage SIO‐2 reveals novel insights into ecology and evolution of marine siphoviruses</title></titleInfo><titleInfo type="abbreviated" lang="en"><title>Characterization of the novel marine siphovirus SIO‐2</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>Genomic and functional analysis of Vibrio phage SIO‐2 reveals novel insights into ecology and evolution of marine siphoviruses</title></titleInfo><name type="personal"><namePart type="given">A.‐C.</namePart><namePart type="family">Baudoux</namePart><affiliation>Scripps Institution of Oceanography, Marine Biology Research Division, University of California San Diego, La Jolla, CA 92093, USA</affiliation><description>Present addresses: CNRS/UPMC Univ. Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29682 Roscoff, France;</description><description>Correspondence: E‐mail ; Tel. (+33) 298 292 323; Fax (+33) 298 292 324.</description><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">R. W.</namePart><namePart type="family">Hendrix</namePart><affiliation>Pittsburgh Bacteriophage Institute, Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">G. C.</namePart><namePart type="family">Lander</namePart><affiliation>National Resource for Automated Molecular Microscopy, The Scripps Research Institute, La Jolla, CA 92037, USA</affiliation><affiliation>Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA</affiliation><description>Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.</description><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">X.</namePart><namePart type="family">Bailly</namePart><affiliation>CNRS/UPMC Univ. Paris 06, FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29682 Roscoff, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">S.</namePart><namePart type="family">Podell</namePart><affiliation>Scripps Institution of Oceanography, Marine Biology Research Division, University of California San Diego, La Jolla, CA 92093, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">C.</namePart><namePart type="family">Paillard</namePart><affiliation>Institut Universitaire Européen de la Mer, Laboratoire des Sciences de l’Environnement Marin, 29280 Plouzané, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">J. E.</namePart><namePart type="family">Johnson</namePart><affiliation>Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">C. S.</namePart><namePart type="family">Potter</namePart><affiliation>National Resource for Automated Molecular Microscopy, The Scripps Research Institute, La Jolla, CA 92037, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">B.</namePart><namePart type="family">Carragher</namePart><affiliation>National Resource for Automated Molecular Microscopy, The Scripps Research Institute, La Jolla, CA 92037, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">F.</namePart><namePart type="family">Azam</namePart><affiliation>Scripps Institution of Oceanography, Marine Biology Research Division, University of California San Diego, La Jolla, CA 92093, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="article" displayLabel="article"></genre><originInfo><publisher>Blackwell Publishing Ltd</publisher><place><placeTerm type="text">Oxford, UK</placeTerm></place><dateIssued encoding="w3cdtf">2012-08</dateIssued><edition>Received 29 June, 2011; revised 15 November, 2011; accepted 27 November, 2011.</edition><copyrightDate encoding="w3cdtf">2012</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><physicalDescription><internetMediaType>text/html</internetMediaType><extent unit="figures">5</extent><extent unit="tables">3</extent><extent unit="references">80</extent><extent unit="words">11718</extent></physicalDescription><abstract lang="en">We report on a genomic and functional analysis of a novel marine siphovirus, the Vibrio phage SIO‐2. This phage is lytic for related Vibrio species of great ecological interest including the broadly antagonistic bacterium Vibrio sp. SWAT3 as well as notable members of the Harveyi clade (V. harveyi ATTC BAA‐1116 and V. campbellii ATCC 25920). Vibrio phage SIO‐2 has a circularly permuted genome of 80 598 bp, which displays unusual features. This genome is larger than that of most known siphoviruses and only 38 of the 116 predicted proteins had homologues in databases. Another divergence is manifest by the origin of core genes, most of which share robust similarities with unrelated viruses and bacteria spanning a wide range of phyla. These core genes are arranged in the same order as in most bacteriophages but they are unusually interspaced at two places with insertions of DNA comprising a high density of uncharacterized genes. The acquisition of these DNA inserts is associated with morphological variation of SIO‐2 capsid, which assembles as a large (80 nm) shell with a novel T = 12 symmetry. These atypical structural features confer on SIO‐2 a remarkable stability to a variety of physical, chemical and environmental factors. Given this high level of functional and genomic novelty, SIO‐2 emerges as a model of considerable interest in ecological and evolutionary studies.</abstract><relatedItem type="host"><titleInfo><title>Environmental Microbiology</title></titleInfo><genre type="journal">journal</genre><note type="content"> Fig. S1. Isolation of Vibrio phage SIO‐2 from plaque assay. Fig. S2. Vibrioid cell tagged with fluorescently labelled SIO‐2 observed by epifluorescence microscopy. Fig. S3. Genome size of SIO‐2 isolate as determined by PFGE. Lane M: Lambda concatamers ladder, Lane 1: SIO‐2 genome incubated with DNase RQ1 for 24 h, Lane 2: untreated SIO‐2 genome. Fig. S4. Intergenic repeats observed in SIO‐2 genome. The termination codons of the upstream genes are shown in red, and the initiation codons of the downstream genes are shown in green. The five different repeated sequences are shown in five different colours. Putative transcription and translation signals indicated with labels and underlines include −35 and −10 regions of promoters (with the predicted + 1 nucleotide of the transcript indicated in bold), transcription terminators and Shine–Dalgarno ribosome‐binding sequences. Fig. S5. Codon usage in the genome of Vibrio sp. SWAT3 (H1) and Vibrio harveyi ATCC BAA‐1116 (H2) and Vibrio phage SIO‐2 (P). Table S1. Bacterial cultures tested for the determination of SIO‐2 host specificity. Efficiency of plating (EOP) was determined by the ratio of SIO‐2 plaque titre obtained with the heterologous host to that obtained with Vibrio sp. SWAT3. Table S2. Phage polymerase gene sequences (family A, PF00476.13) used for phylogenetic analysis. Table S3. Metagenomic analysis. Appendix S1. Material and methods. Fig. S1. Isolation of Vibrio phage SIO‐2 from plaque assay. Fig. S2. Vibrioid cell tagged with fluorescently labelled SIO‐2 observed by epifluorescence microscopy. Fig. S3. Genome size of SIO‐2 isolate as determined by PFGE. Lane M: Lambda concatamers ladder, Lane 1: SIO‐2 genome incubated with DNase RQ1 for 24 h, Lane 2: untreated SIO‐2 genome. Fig. S4. Intergenic repeats observed in SIO‐2 genome. The termination codons of the upstream genes are shown in red, and the initiation codons of the downstream genes are shown in green. The five different repeated sequences are shown in five different colours. Putative transcription and translation signals indicated with labels and underlines include −35 and −10 regions of promoters (with the predicted + 1 nucleotide of the transcript indicated in bold), transcription terminators and Shine–Dalgarno ribosome‐binding sequences. Fig. S5. Codon usage in the genome of Vibrio sp. SWAT3 (H1) and Vibrio harveyi ATCC BAA‐1116 (H2) and Vibrio phage SIO‐2 (P). Table S1. Bacterial cultures tested for the determination of SIO‐2 host specificity. Efficiency of plating (EOP) was determined by the ratio of SIO‐2 plaque titre obtained with the heterologous host to that obtained with Vibrio sp. SWAT3. Table S2. Phage polymerase gene sequences (family A, PF00476.13) used for phylogenetic analysis. Table S3. Metagenomic analysis. Appendix S1. Material and methods. Fig. S1. Isolation of Vibrio phage SIO‐2 from plaque assay. Fig. S2. Vibrioid cell tagged with fluorescently labelled SIO‐2 observed by epifluorescence microscopy. Fig. S3. Genome size of SIO‐2 isolate as determined by PFGE. Lane M: Lambda concatamers ladder, Lane 1: SIO‐2 genome incubated with DNase RQ1 for 24 h, Lane 2: untreated SIO‐2 genome. Fig. S4. Intergenic repeats observed in SIO‐2 genome. The termination codons of the upstream genes are shown in red, and the initiation codons of the downstream genes are shown in green. The five different repeated sequences are shown in five different colours. Putative transcription and translation signals indicated with labels and underlines include −35 and −10 regions of promoters (with the predicted + 1 nucleotide of the transcript indicated in bold), transcription terminators and Shine–Dalgarno ribosome‐binding sequences. Fig. S5. Codon usage in the genome of Vibrio sp. SWAT3 (H1) and Vibrio harveyi ATCC BAA‐1116 (H2) and Vibrio phage SIO‐2 (P). Table S1. Bacterial cultures tested for the determination of SIO‐2 host specificity. Efficiency of plating (EOP) was determined by the ratio of SIO‐2 plaque titre obtained with the heterologous host to that obtained with Vibrio sp. SWAT3. Table S2. Phage polymerase gene sequences (family A, PF00476.13) used for phylogenetic analysis. Table S3. Metagenomic analysis. Appendix S1. Material and methods. Fig. S1. Isolation of Vibrio phage SIO‐2 from plaque assay. Fig. S2. Vibrioid cell tagged with fluorescently labelled SIO‐2 observed by epifluorescence microscopy. Fig. S3. Genome size of SIO‐2 isolate as determined by PFGE. Lane M: Lambda concatamers ladder, Lane 1: SIO‐2 genome incubated with DNase RQ1 for 24 h, Lane 2: untreated SIO‐2 genome. Fig. S4. Intergenic repeats observed in SIO‐2 genome. The termination codons of the upstream genes are shown in red, and the initiation codons of the downstream genes are shown in green. The five different repeated sequences are shown in five different colours. Putative transcription and translation signals indicated with labels and underlines include −35 and −10 regions of promoters (with the predicted + 1 nucleotide of the transcript indicated in bold), transcription terminators and Shine–Dalgarno ribosome‐binding sequences. Fig. S5. Codon usage in the genome of Vibrio sp. SWAT3 (H1) and Vibrio harveyi ATCC BAA‐1116 (H2) and Vibrio phage SIO‐2 (P). Table S1. Bacterial cultures tested for the determination of SIO‐2 host specificity. Efficiency of plating (EOP) was determined by the ratio of SIO‐2 plaque titre obtained with the heterologous host to that obtained with Vibrio sp. SWAT3. Table S2. Phage polymerase gene sequences (family A, PF00476.13) used for phylogenetic analysis. Table S3. Metagenomic analysis. Appendix S1. Material and methods. Fig. S1. Isolation of Vibrio phage SIO‐2 from plaque assay. Fig. S2. Vibrioid cell tagged with fluorescently labelled SIO‐2 observed by epifluorescence microscopy. Fig. S3. Genome size of SIO‐2 isolate as determined by PFGE. Lane M: Lambda concatamers ladder, Lane 1: SIO‐2 genome incubated with DNase RQ1 for 24 h, Lane 2: untreated SIO‐2 genome. Fig. S4. Intergenic repeats observed in SIO‐2 genome. The termination codons of the upstream genes are shown in red, and the initiation codons of the downstream genes are shown in green. The five different repeated sequences are shown in five different colours. Putative transcription and translation signals indicated with labels and underlines include −35 and −10 regions of promoters (with the predicted + 1 nucleotide of the transcript indicated in bold), transcription terminators and Shine–Dalgarno ribosome‐binding sequences. Fig. S5. Codon usage in the genome of Vibrio sp. SWAT3 (H1) and Vibrio harveyi ATCC BAA‐1116 (H2) and Vibrio phage SIO‐2 (P). Table S1. Bacterial cultures tested for the determination of SIO‐2 host specificity. Efficiency of plating (EOP) was determined by the ratio of SIO‐2 plaque titre obtained with the heterologous host to that obtained with Vibrio sp. SWAT3. Table S2. Phage polymerase gene sequences (family A, PF00476.13) used for phylogenetic analysis. Table S3. Metagenomic analysis. Appendix S1. Material and methods. Fig. S1. Isolation of Vibrio phage SIO‐2 from plaque assay. Fig. S2. Vibrioid cell tagged with fluorescently labelled SIO‐2 observed by epifluorescence microscopy. Fig. S3. Genome size of SIO‐2 isolate as determined by PFGE. Lane M: Lambda concatamers ladder, Lane 1: SIO‐2 genome incubated with DNase RQ1 for 24 h, Lane 2: untreated SIO‐2 genome. Fig. S4. Intergenic repeats observed in SIO‐2 genome. The termination codons of the upstream genes are shown in red, and the initiation codons of the downstream genes are shown in green. The five different repeated sequences are shown in five different colours. Putative transcription and translation signals indicated with labels and underlines include −35 and −10 regions of promoters (with the predicted + 1 nucleotide of the transcript indicated in bold), transcription terminators and Shine–Dalgarno ribosome‐binding sequences. Fig. S5. Codon usage in the genome of Vibrio sp. SWAT3 (H1) and Vibrio harveyi ATCC BAA‐1116 (H2) and Vibrio phage SIO‐2 (P). Table S1. Bacterial cultures tested for the determination of SIO‐2 host specificity. Efficiency of plating (EOP) was determined by the ratio of SIO‐2 plaque titre obtained with the heterologous host to that obtained with Vibrio sp. SWAT3. Table S2. Phage polymerase gene sequences (family A, PF00476.13) used for phylogenetic analysis. Table S3. Metagenomic analysis. Appendix S1. Material and methods. Fig. S1. Isolation of Vibrio phage SIO‐2 from plaque assay. Fig. S2. Vibrioid cell tagged with fluorescently labelled SIO‐2 observed by epifluorescence microscopy. Fig. S3. Genome size of SIO‐2 isolate as determined by PFGE. Lane M: Lambda concatamers ladder, Lane 1: SIO‐2 genome incubated with DNase RQ1 for 24 h, Lane 2: untreated SIO‐2 genome. Fig. S4. Intergenic repeats observed in SIO‐2 genome. The termination codons of the upstream genes are shown in red, and the initiation codons of the downstream genes are shown in green. The five different repeated sequences are shown in five different colours. Putative transcription and translation signals indicated with labels and underlines include −35 and −10 regions of promoters (with the predicted + 1 nucleotide of the transcript indicated in bold), transcription terminators and Shine–Dalgarno ribosome‐binding sequences. Fig. S5. Codon usage in the genome of Vibrio sp. SWAT3 (H1) and Vibrio harveyi ATCC BAA‐1116 (H2) and Vibrio phage SIO‐2 (P). Table S1. Bacterial cultures tested for the determination of SIO‐2 host specificity. Efficiency of plating (EOP) was determined by the ratio of SIO‐2 plaque titre obtained with the heterologous host to that obtained with Vibrio sp. SWAT3. Table S2. Phage polymerase gene sequences (family A, PF00476.13) used for phylogenetic analysis. Table S3. Metagenomic analysis. Appendix S1. Material and methods. Fig. S1. Isolation of Vibrio phage SIO‐2 from plaque assay. Fig. S2. Vibrioid cell tagged with fluorescently labelled SIO‐2 observed by epifluorescence microscopy. Fig. S3. Genome size of SIO‐2 isolate as determined by PFGE. Lane M: Lambda concatamers ladder, Lane 1: SIO‐2 genome incubated with DNase RQ1 for 24 h, Lane 2: untreated SIO‐2 genome. Fig. S4. Intergenic repeats observed in SIO‐2 genome. The termination codons of the upstream genes are shown in red, and the initiation codons of the downstream genes are shown in green. The five different repeated sequences are shown in five different colours. Putative transcription and translation signals indicated with labels and underlines include −35 and −10 regions of promoters (with the predicted + 1 nucleotide of the transcript indicated in bold), transcription terminators and Shine–Dalgarno ribosome‐binding sequences. Fig. S5. Codon usage in the genome of Vibrio sp. SWAT3 (H1) and Vibrio harveyi ATCC BAA‐1116 (H2) and Vibrio phage SIO‐2 (P). Table S1. Bacterial cultures tested for the determination of SIO‐2 host specificity. Efficiency of plating (EOP) was determined by the ratio of SIO‐2 plaque titre obtained with the heterologous host to that obtained with Vibrio sp. SWAT3. Table S2. Phage polymerase gene sequences (family A, PF00476.13) used for phylogenetic analysis. Table S3. Metagenomic analysis. Appendix S1. Material and methods. Fig. S1. Isolation of Vibrio phage SIO‐2 from plaque assay. Fig. S2. Vibrioid cell tagged with fluorescently labelled SIO‐2 observed by epifluorescence microscopy. Fig. S3. Genome size of SIO‐2 isolate as determined by PFGE. Lane M: Lambda concatamers ladder, Lane 1: SIO‐2 genome incubated with DNase RQ1 for 24 h, Lane 2: untreated SIO‐2 genome. Fig. S4. Intergenic repeats observed in SIO‐2 genome. The termination codons of the upstream genes are shown in red, and the initiation codons of the downstream genes are shown in green. The five different repeated sequences are shown in five different colours. Putative transcription and translation signals indicated with labels and underlines include −35 and −10 regions of promoters (with the predicted + 1 nucleotide of the transcript indicated in bold), transcription terminators and Shine–Dalgarno ribosome‐binding sequences. Fig. S5. Codon usage in the genome of Vibrio sp. SWAT3 (H1) and Vibrio harveyi ATCC BAA‐1116 (H2) and Vibrio phage SIO‐2 (P). Table S1. Bacterial cultures tested for the determination of SIO‐2 host specificity. Efficiency of plating (EOP) was determined by the ratio of SIO‐2 plaque titre obtained with the heterologous host to that obtained with Vibrio sp. SWAT3. Table S2. Phage polymerase gene sequences (family A, PF00476.13) used for phylogenetic analysis. Table S3. Metagenomic analysis. Appendix S1. Material and methods.Supporting Info Item: Supporting info item - Supporting info item - </note><identifier type="ISSN">1462-2912</identifier><identifier type="eISSN">1462-2920</identifier><identifier type="DOI">10.1111/(ISSN)1462-2920</identifier><identifier type="PublisherID">EMI</identifier><part><date>2012</date><detail type="title"><title>Ecology, Evolution and Population Genetics of Pathogenic Microbes</title></detail><detail type="volume"><caption>vol.</caption><number>14</number></detail><detail type="issue"><caption>no.</caption><number>8</number></detail><extent unit="pages"><start>2071</start><end>2086</end><total>16</total></extent></part></relatedItem><identifier type="istex">9D25744D4A309D6FD5B67F2FDCB83A6EB6EED0D1</identifier><identifier type="DOI">10.1111/j.1462-2920.2011.02685.x</identifier><identifier type="ArticleID">EMI2685</identifier><accessCondition type="use and reproduction" contentType="copyright">© 2012 Society for Applied Microbiology and Blackwell Publishing Ltd</accessCondition><recordInfo><recordContentSource>WILEY</recordContentSource><recordOrigin>Blackwell Publishing Ltd</recordOrigin></recordInfo></mods></metadata><enrichments><json:item><type>multicat</type><uri>https://api.istex.fr/document/9D25744D4A309D6FD5B67F2FDCB83A6EB6EED0D1/enrichments/multicat</uri></json:item></enrichments><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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