Genomic analysis of multiple Roseophage SIO1 strains
Identifieur interne : 000684 ( Istex/Corpus ); précédent : 000683; suivant : 000685Genomic analysis of multiple Roseophage SIO1 strains
Auteurs : Florent Angly ; Merry Youle ; Bahador Nosrat ; Shailaja Srinagesh ; Beltran Rodriguez-Brito ; Patrick Mcnairnie ; Gordafaried Deyanat-Yazdi ; Mya Breitbart ; Forest RohwerSource :
- Environmental Microbiology [ 1462-2912 ] ; 2009-11.
Abstract
Roseophage SIO1 is a lytic marine phage that infects Roseobacter SIO67, a member of the Roseobacter clade of near‐shore alphaproteobacteria. Roseophage SIO1 was first isolated in 1989 and sequenced in 2000. We have re‐sequenced and re‐annotated the original isolate. Our current annotation could only assign functions to seven additional open reading frames, indicating that, despite the advances in bioinformatics tools and increased genomic resources, we are still far from being able to translate phage genomic sequences into biological functions. In 2001, we isolated four new strains of Roseophage SIO1 from California near‐shore locations. The genomes of all four were sequenced and compared against the original Roseophage SIO1 isolated in 1989. A high degree of conservation was evident across all five genomes; comparisons at the nucleotide level yielded an average 97% identity. The observed differences were clustered in protein‐encoding regions and were mostly synonymous. The one strain that was found to possess an expanded host range also showed notable changes in putative tail protein‐coding regions. Despite the possibly rapid evolution of phage and the mostly uncharacterized diversity found in viral metagenomic data sets, these findings indicate that viral genomes such as the genome of SIO1‐like Roseophages can be stably maintained over ecologically significant time and distance (i.e. over a decade and ∼50 km).
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DOI: 10.1111/j.1462-2920.2009.02021.x
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Breitbart</name><affiliation><mods:affiliation>Department of Biology, San Diego State University, San Diego, CA, USA.</mods:affiliation></affiliation><affiliation><mods:affiliation>College of Marine Sciences, University of South Florida, St. Petersburg, FL, USA.</mods:affiliation></affiliation></author><author><name sortKey="Rohwer, Forest" sort="Rohwer, Forest" uniqKey="Rohwer F" first="Forest" last="Rohwer">Forest Rohwer</name><affiliation><mods:affiliation>Department of Biology, San Diego State University, San Diego, CA, USA.</mods:affiliation></affiliation><affiliation><mods:affiliation>Center for Microbial Sciences, San Diego State University, San Diego, CA, USA.</mods:affiliation></affiliation></author></analytic><monogr></monogr><series><title level="j">Environmental Microbiology</title><idno type="ISSN">1462-2912</idno><idno type="eISSN">1462-2920</idno><imprint><publisher>Blackwell Publishing Ltd</publisher><pubPlace>Oxford, UK</pubPlace><date type="published" 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Roseophage SIO1 was first isolated in 1989 and sequenced in 2000. We have re‐sequenced and re‐annotated the original isolate. Our current annotation could only assign functions to seven additional open reading frames, indicating that, despite the advances in bioinformatics tools and increased genomic resources, we are still far from being able to translate phage genomic sequences into biological functions. In 2001, we isolated four new strains of Roseophage SIO1 from California near‐shore locations. The genomes of all four were sequenced and compared against the original Roseophage SIO1 isolated in 1989. A high degree of conservation was evident across all five genomes; comparisons at the nucleotide level yielded an average 97% identity. The observed differences were clustered in protein‐encoding regions and were mostly synonymous. The one strain that was found to possess an expanded host range also showed notable changes in putative tail protein‐coding regions. Despite the possibly rapid evolution of phage and the mostly uncharacterized diversity found in viral metagenomic data sets, these findings indicate that viral genomes such as the genome of SIO1‐like Roseophages can be stably maintained over ecologically significant time and distance (i.e. over a decade and ∼50 km).</div></front></TEI><istex><corpusName>wiley</corpusName><author><json:item><name>Florent Angly</name><affiliations><json:string>Department of Biology, San Diego State University, San Diego, CA, USA.</json:string><json:string>Computational Science Research Center, San Diego State University, San Diego, CA, USA.</json:string></affiliations></json:item><json:item><name>Merry Youle</name><affiliations><json:string>Rainbow Rock, Ocean View, HI, USA.</json:string></affiliations></json:item><json:item><name>Bahador Nosrat</name><affiliations><json:string>Department of Biology, San Diego State University, San Diego, CA, USA.</json:string><json:string>Computational Science Research Center, San Diego State University, San Diego, CA, USA.</json:string></affiliations></json:item><json:item><name>Shailaja Srinagesh</name><affiliations><json:string>Department of Biology, San Diego State University, San Diego, CA, USA.</json:string></affiliations></json:item><json:item><name>Beltran Rodriguez‐Brito</name><affiliations><json:string>Department of Biology, San Diego State University, San Diego, CA, USA.</json:string><json:string>Computational Science Research Center, San Diego State University, San Diego, CA, USA.</json:string></affiliations></json:item><json:item><name>Patrick McNairnie</name><affiliations><json:string>Department of Biology, San Diego State University, San Diego, CA, USA.</json:string><json:string>Computational Science Research Center, San Diego State University, San Diego, CA, USA.</json:string></affiliations></json:item><json:item><name>Gordafaried Deyanat‐Yazdi</name><affiliations><json:string>Department of Biology, San Diego State University, San Diego, CA, USA.</json:string></affiliations></json:item><json:item><name>Mya Breitbart</name><affiliations><json:string>Department of Biology, San Diego State University, San Diego, CA, USA.</json:string><json:string>College of Marine Sciences, University of South Florida, St. Petersburg, FL, USA.</json:string></affiliations></json:item><json:item><name>Forest Rohwer</name><affiliations><json:string>Department of Biology, San Diego State University, San Diego, CA, USA.</json:string><json:string>Center for Microbial Sciences, San Diego State University, San Diego, CA, USA.</json:string></affiliations></json:item></author><articleId><json:string>EMI2021</json:string></articleId><language><json:string>eng</json:string></language><originalGenre><json:string>article</json:string></originalGenre><abstract>Roseophage SIO1 is a lytic marine phage that infects Roseobacter SIO67, a member of the Roseobacter clade of near‐shore alphaproteobacteria. Roseophage SIO1 was first isolated in 1989 and sequenced in 2000. We have re‐sequenced and re‐annotated the original isolate. Our current annotation could only assign functions to seven additional open reading frames, indicating that, despite the advances in bioinformatics tools and increased genomic resources, we are still far from being able to translate phage genomic sequences into biological functions. In 2001, we isolated four new strains of Roseophage SIO1 from California near‐shore locations. The genomes of all four were sequenced and compared against the original Roseophage SIO1 isolated in 1989. A high degree of conservation was evident across all five genomes; comparisons at the nucleotide level yielded an average 97% identity. The observed differences were clustered in protein‐encoding regions and were mostly synonymous. The one strain that was found to possess an expanded host range also showed notable changes in putative tail protein‐coding regions. Despite the possibly rapid evolution of phage and the mostly uncharacterized diversity found in viral metagenomic data sets, these findings indicate that viral genomes such as the genome of SIO1‐like Roseophages can be stably maintained over ecologically significant time and distance (i.e. over a decade and ∼50 km).</abstract><qualityIndicators><score>7.532</score><pdfVersion>1.3</pdfVersion><pdfPageSize>595.275 x 799.371 pts</pdfPageSize><refBibsNative>true</refBibsNative><keywordCount>0</keywordCount><abstractCharCount>1435</abstractCharCount><pdfWordCount>5704</pdfWordCount><pdfCharCount>37353</pdfCharCount><pdfPageCount>11</pdfPageCount><abstractWordCount>211</abstractWordCount></qualityIndicators><title>Genomic analysis of multiple Roseophage SIO1 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type="first">Bahador</forename><surname>Nosrat</surname></persName><affiliation>Department of Biology, San Diego State University, San Diego, CA, USA.</affiliation><affiliation>Computational Science Research Center, San Diego State University, San Diego, CA, USA.</affiliation></author><author xml:id="author-4"><persName><forename type="first">Shailaja</forename><surname>Srinagesh</surname></persName><affiliation>Department of Biology, San Diego State University, San Diego, CA, USA.</affiliation></author><author xml:id="author-5"><persName><forename type="first">Beltran</forename><surname>Rodriguez‐Brito</surname></persName><affiliation>Department of Biology, San Diego State University, San Diego, CA, USA.</affiliation><affiliation>Computational Science Research Center, San Diego State University, San Diego, CA, USA.</affiliation></author><author xml:id="author-6"><persName><forename type="first">Patrick</forename><surname>McNairnie</surname></persName><affiliation>Department of Biology, San Diego State University, San Diego, CA, USA.</affiliation><affiliation>Computational Science Research Center, San Diego State University, San Diego, CA, USA.</affiliation></author><author xml:id="author-7"><persName><forename type="first">Gordafaried</forename><surname>Deyanat‐Yazdi</surname></persName><affiliation>Department of Biology, San Diego State University, San Diego, CA, USA.</affiliation></author><author xml:id="author-8"><persName><forename type="first">Mya</forename><surname>Breitbart</surname></persName><affiliation>Department of Biology, San Diego State University, San Diego, CA, USA.</affiliation><affiliation>College of Marine Sciences, University of South Florida, St. Petersburg, FL, USA.</affiliation></author><author xml:id="author-9"><persName><forename type="first">Forest</forename><surname>Rohwer</surname></persName><note type="correspondence"><p>Correspondence: *E‐mail ; Tel. (+1) 619 594 1336; Fax (+1) 619 594 567.</p></note><affiliation>Department of Biology, San Diego State University, San Diego, CA, USA.</affiliation><affiliation>Center for Microbial Sciences, San Diego State University, San Diego, CA, USA.</affiliation></author></analytic><monogr><title level="j">Environmental Microbiology</title><idno type="pISSN">1462-2912</idno><idno type="eISSN">1462-2920</idno><idno type="DOI">10.1111/(ISSN)1462-2920</idno><imprint><publisher>Blackwell Publishing Ltd</publisher><pubPlace>Oxford, UK</pubPlace><date type="published" when="2009-11"></date><biblScope unit="volume">11</biblScope><biblScope unit="issue">11</biblScope><biblScope unit="page" from="2863">2863</biblScope><biblScope unit="page" to="2873">2873</biblScope></imprint></monogr><idno type="istex">FA593991B982ECBF93FE933CC35A5EAF0EA0634B</idno><idno type="DOI">10.1111/j.1462-2920.2009.02021.x</idno><idno type="ArticleID">EMI2021</idno></biblStruct></sourceDesc></fileDesc><profileDesc><creation><date>2009</date></creation><langUsage><language ident="en">en</language></langUsage><abstract xml:lang="en"><p>Roseophage SIO1 is a lytic marine phage that infects Roseobacter SIO67, a member of the Roseobacter clade of near‐shore alphaproteobacteria. Roseophage SIO1 was first isolated in 1989 and sequenced in 2000. We have re‐sequenced and re‐annotated the original isolate. Our current annotation could only assign functions to seven additional open reading frames, indicating that, despite the advances in bioinformatics tools and increased genomic resources, we are still far from being able to translate phage genomic sequences into biological functions. In 2001, we isolated four new strains of Roseophage SIO1 from California near‐shore locations. The genomes of all four were sequenced and compared against the original Roseophage SIO1 isolated in 1989. A high degree of conservation was evident across all five genomes; comparisons at the nucleotide level yielded an average 97% identity. The observed differences were clustered in protein‐encoding regions and were mostly synonymous. The one strain that was found to possess an expanded host range also showed notable changes in putative tail protein‐coding regions. Despite the possibly rapid evolution of phage and the mostly uncharacterized diversity found in viral metagenomic data sets, these findings indicate that viral genomes such as the genome of SIO1‐like Roseophages can be stably maintained over ecologically significant time and distance (i.e. over a decade and ∼50 km).</p></abstract></profileDesc><revisionDesc><change when="2009-11">Published</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><original>false</original><mimetype>text/plain</mimetype><extension>txt</extension><uri>https://api.istex.fr/document/FA593991B982ECBF93FE933CC35A5EAF0EA0634B/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="11011"><doi origin="wiley">10.1111/emi.2009.11.issue-11</doi><titleGroup><title type="specialIssueTitle">Environmental Viruses: Shaping the biosphere. Guest Editors: Forest Rohwer, David Prangishvili and Debbie Lindell</title></titleGroup><numberingGroup><numbering type="journalVolume" number="11">11</numbering><numbering type="journalIssue">11</numbering></numberingGroup><coverDate startDate="2009-11">November 2009</coverDate></publicationMeta><publicationMeta level="unit" type="article" position="9" status="forIssue"><doi origin="wiley">10.1111/j.1462-2920.2009.02021.x</doi><idGroup><id type="unit" value="EMI2021"></id></idGroup><countGroup><count type="pageTotal" number="11"></count></countGroup><titleGroup><title type="tocHeading1">Research articles</title></titleGroup><copyright>© 2009 Society for Applied Microbiology and Blackwell Publishing Ltd</copyright><eventGroup><event type="firstOnline" date="2009-07-31"></event><event type="publishedOnlineFinalForm" date="2009-10-27"></event><event type="xmlConverted" agent="Converter:BPG_TO_WML3G version:2.3.2 mode:FullText source:FullText result:FullText" date="2010-03-06"></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:4.1.7 mode:FullText,remove_FC" date="2014-10-16"></event></eventGroup><numberingGroup><numbering type="pageFirst" number="2863">2863</numbering><numbering type="pageLast" number="2873">2873</numbering></numberingGroup><correspondenceTo> *E‐mail <email>forest@sunstroke.sdsu.edu</email>; Tel. (+1) 619 594 1336; Fax (+1) 619 594 567.</correspondenceTo><linkGroup><link type="toTypesetVersion" href="file:EMI.EMI2021.pdf"></link></linkGroup></publicationMeta><contentMeta><unparsedEditorialHistory>Received 8 April, 2009; accepted 24 June, 2009.</unparsedEditorialHistory><countGroup><count type="figureTotal" number="6"></count><count type="tableTotal" number="2"></count><count type="formulaTotal" number="0"></count><count type="referenceTotal" number="52"></count><count type="wordTotal" number="6487"></count><count type="linksPubMed" number="0"></count><count type="linksCrossRef" number="0"></count></countGroup><titleGroup><title type="main">Genomic analysis of multiple Roseophage SIO1 strains</title><title type="shortAuthors">F. Angly <i>et al.</i></title><title type="short">Genomic analysis of multiple Roseophage SIO1 strains</title></titleGroup><creators><creator creatorRole="author" xml:id="cr1" affiliationRef="#a1 #a3"><personName><givenNames>Florent</givenNames><familyName>Angly</familyName></personName></creator><creator creatorRole="author" xml:id="cr2" affiliationRef="#a2"><personName><givenNames>Merry</givenNames><familyName>Youle</familyName></personName></creator><creator creatorRole="author" xml:id="cr3" affiliationRef="#a1 #a3"><personName><givenNames>Bahador</givenNames><familyName>Nosrat</familyName></personName></creator><creator creatorRole="author" xml:id="cr4" affiliationRef="#a1"><personName><givenNames>Shailaja</givenNames><familyName>Srinagesh</familyName></personName></creator><creator creatorRole="author" xml:id="cr5" affiliationRef="#a1 #a3"><personName><givenNames>Beltran</givenNames><familyName>Rodriguez‐Brito</familyName></personName></creator><creator creatorRole="author" xml:id="cr6" affiliationRef="#a1 #a3"><personName><givenNames>Patrick</givenNames><familyName>McNairnie</familyName></personName></creator><creator creatorRole="author" xml:id="cr7" affiliationRef="#a1"><personName><givenNames>Gordafaried</givenNames><familyName>Deyanat‐Yazdi</familyName></personName></creator><creator creatorRole="author" xml:id="cr8" affiliationRef="#a1 #a4"><personName><givenNames>Mya</givenNames><familyName>Breitbart</familyName></personName></creator><creator creatorRole="author" xml:id="cr9" affiliationRef="#a1 #a5" corresponding="yes"><personName><givenNames>Forest</givenNames><familyName>Rohwer</familyName></personName></creator></creators><affiliationGroup><affiliation xml:id="a1"><unparsedAffiliation>Department of Biology, San Diego State University, San Diego, CA, USA.</unparsedAffiliation></affiliation><affiliation xml:id="a2"><unparsedAffiliation>Rainbow Rock, Ocean View, HI, USA.</unparsedAffiliation></affiliation><affiliation xml:id="a3"><unparsedAffiliation>Computational Science Research Center, San Diego State University, San Diego, CA, USA.</unparsedAffiliation></affiliation><affiliation xml:id="a4" countryCode="US"><unparsedAffiliation>College of Marine Sciences, University of South Florida, St. Petersburg, FL, USA.</unparsedAffiliation></affiliation><affiliation xml:id="a5"><unparsedAffiliation>Center for Microbial Sciences, San Diego State University, San Diego, CA, USA.</unparsedAffiliation></affiliation></affiliationGroup><supportingInformation><p><b>Fig. S1.</b> Dotplot analysis comparing the Roseophage SBRSIO67‐2001 genome with the four other Roseophage genomes.</p><p><b>Fig. S2.</b> Roseophage plaques on a lawn of <i>Roseobacter</i> SIO67. Each circle represents a 5 μl spot of liquid lysate containing plaque forming units.</p><p><b>Table S1.</b> Sequences of the PCR primers designed to the archetypal Roseophage SIO1‐1989 genome.</p><p><b>Table S2.</b> Aquatic viral metagenomes used to map the global distribution of Roseophage‐like viruses (Fig. 4). Shown as the number of similarities (blastn, threshold <i>E</i>‐value of 1e‐4) to the Roseophage SIO‐1989 genome.</p><p>Please note: Blackwell Publishing are not responsible for the content or functionality of any supporting materials supplied by the authors. Any queries (other than missing material) should be directed to the corresponding author for the article.</p><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:14622912:media:emi2021:EMI_2021_sm_Figure_S1"></mediaResource><caption>Supporting info item</caption></supportingInfoItem><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:14622912:media:emi2021:EMI_2021_sm_Figure_S2"></mediaResource><caption>Supporting info item</caption></supportingInfoItem><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:14622912:media:emi2021:EMI_2021_sm_Table_S1-S2"></mediaResource><caption>Supporting info item</caption></supportingInfoItem></supportingInformation><abstractGroup><abstract type="main" xml:lang="en"><title type="main">Summary</title><p>Roseophage SIO1 is a lytic marine phage that infects <i>Roseobacter</i> SIO67, a member of the <i>Roseobacter</i> clade of near‐shore alphaproteobacteria. Roseophage SIO1 was first isolated in 1989 and sequenced in 2000. We have re‐sequenced and re‐annotated the original isolate. Our current annotation could only assign functions to seven additional open reading frames, indicating that, despite the advances in bioinformatics tools and increased genomic resources, we are still far from being able to translate phage genomic sequences into biological functions. In 2001, we isolated four new strains of Roseophage SIO1 from California near‐shore locations. The genomes of all four were sequenced and compared against the original Roseophage SIO1 isolated in 1989. A high degree of conservation was evident across all five genomes; comparisons at the nucleotide level yielded an average 97% identity. The observed differences were clustered in protein‐encoding regions and were mostly synonymous. The one strain that was found to possess an expanded host range also showed notable changes in putative tail protein‐coding regions. Despite the possibly rapid evolution of phage and the mostly uncharacterized diversity found in viral metagenomic data sets, these findings indicate that viral genomes such as the genome of SIO1‐like Roseophages can be stably maintained over ecologically significant time and distance (i.e. over a decade and ∼50 km).</p></abstract></abstractGroup></contentMeta></header></component></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Genomic analysis of multiple Roseophage SIO1 strains</title></titleInfo><titleInfo type="abbreviated" lang="en"><title>Genomic analysis of multiple Roseophage SIO1 strains</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>Genomic analysis of multiple Roseophage SIO1 strains</title></titleInfo><name type="personal"><namePart type="given">Florent</namePart><namePart type="family">Angly</namePart><affiliation>Department of Biology, San Diego State University, San Diego, CA, USA.</affiliation><affiliation>Computational Science Research Center, San Diego State University, San Diego, CA, USA.</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Merry</namePart><namePart type="family">Youle</namePart><affiliation>Rainbow Rock, Ocean View, HI, USA.</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Bahador</namePart><namePart type="family">Nosrat</namePart><affiliation>Department of Biology, San Diego State University, San Diego, CA, USA.</affiliation><affiliation>Computational Science Research Center, San Diego State University, San Diego, CA, USA.</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Shailaja</namePart><namePart type="family">Srinagesh</namePart><affiliation>Department of Biology, San Diego State University, San Diego, CA, USA.</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Beltran</namePart><namePart type="family">Rodriguez‐Brito</namePart><affiliation>Department of Biology, San Diego State University, San Diego, CA, USA.</affiliation><affiliation>Computational Science Research Center, San Diego State University, San Diego, CA, USA.</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Patrick</namePart><namePart type="family">McNairnie</namePart><affiliation>Department of Biology, San Diego State University, San Diego, CA, USA.</affiliation><affiliation>Computational Science Research Center, San Diego State University, San Diego, CA, USA.</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Gordafaried</namePart><namePart type="family">Deyanat‐Yazdi</namePart><affiliation>Department of Biology, San Diego State University, San Diego, CA, USA.</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Mya</namePart><namePart type="family">Breitbart</namePart><affiliation>Department of Biology, San Diego State University, San Diego, CA, USA.</affiliation><affiliation>College of Marine Sciences, University of South Florida, St. Petersburg, FL, USA.</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Forest</namePart><namePart type="family">Rohwer</namePart><affiliation>Department of Biology, San Diego State University, San Diego, CA, USA.</affiliation><affiliation>Center for Microbial Sciences, San Diego State University, San Diego, CA, USA.</affiliation><description>Correspondence: *E‐mail ; Tel. (+1) 619 594 1336; Fax (+1) 619 594 567.</description><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">2009-11</dateIssued><edition>Received 8 April, 2009; accepted 24 June, 2009.</edition><copyrightDate encoding="w3cdtf">2009</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">6</extent><extent unit="tables">2</extent><extent unit="references">52</extent><extent unit="words">6487</extent></physicalDescription><abstract lang="en">Roseophage SIO1 is a lytic marine phage that infects Roseobacter SIO67, a member of the Roseobacter clade of near‐shore alphaproteobacteria. Roseophage SIO1 was first isolated in 1989 and sequenced in 2000. We have re‐sequenced and re‐annotated the original isolate. Our current annotation could only assign functions to seven additional open reading frames, indicating that, despite the advances in bioinformatics tools and increased genomic resources, we are still far from being able to translate phage genomic sequences into biological functions. In 2001, we isolated four new strains of Roseophage SIO1 from California near‐shore locations. The genomes of all four were sequenced and compared against the original Roseophage SIO1 isolated in 1989. A high degree of conservation was evident across all five genomes; comparisons at the nucleotide level yielded an average 97% identity. The observed differences were clustered in protein‐encoding regions and were mostly synonymous. The one strain that was found to possess an expanded host range also showed notable changes in putative tail protein‐coding regions. Despite the possibly rapid evolution of phage and the mostly uncharacterized diversity found in viral metagenomic data sets, these findings indicate that viral genomes such as the genome of SIO1‐like Roseophages can be stably maintained over ecologically significant time and distance (i.e. over a decade and ∼50 km).</abstract><relatedItem type="host"><titleInfo><title>Environmental Microbiology</title></titleInfo><genre type="journal">journal</genre><note type="content"> Fig. S1. Dotplot analysis comparing the Roseophage SBRSIO67‐2001 genome with the four other Roseophage genomes. Fig. S2. Roseophage plaques on a lawn of Roseobacter SIO67. Each circle represents a 5 μl spot of liquid lysate containing plaque forming units. Table S1. Sequences of the PCR primers designed to the archetypal Roseophage SIO1‐1989 genome. Table S2. Aquatic viral metagenomes used to map the global distribution of Roseophage‐like viruses (Fig. 4). Shown as the number of similarities (blastn, threshold E‐value of 1e‐4) to the Roseophage SIO‐1989 genome. Please note: Blackwell Publishing are not responsible for the content or functionality of any supporting materials supplied by the authors. Any queries (other than missing material) should be directed to the corresponding author for the article. Fig. S1. Dotplot analysis comparing the Roseophage SBRSIO67‐2001 genome with the four other Roseophage genomes. Fig. S2. Roseophage plaques on a lawn of Roseobacter SIO67. Each circle represents a 5 μl spot of liquid lysate containing plaque forming units. Table S1. Sequences of the PCR primers designed to the archetypal Roseophage SIO1‐1989 genome. Table S2. Aquatic viral metagenomes used to map the global distribution of Roseophage‐like viruses (Fig. 4). Shown as the number of similarities (blastn, threshold E‐value of 1e‐4) to the Roseophage SIO‐1989 genome. Please note: Blackwell Publishing are not responsible for the content or functionality of any supporting materials supplied by the authors. Any queries (other than missing material) should be directed to the corresponding author for the article. Fig. S1. Dotplot analysis comparing the Roseophage SBRSIO67‐2001 genome with the four other Roseophage genomes. Fig. S2. Roseophage plaques on a lawn of Roseobacter SIO67. Each circle represents a 5 μl spot of liquid lysate containing plaque forming units. Table S1. Sequences of the PCR primers designed to the archetypal Roseophage SIO1‐1989 genome. Table S2. Aquatic viral metagenomes used to map the global distribution of Roseophage‐like viruses (Fig. 4). Shown as the number of similarities (blastn, threshold E‐value of 1e‐4) to the Roseophage SIO‐1989 genome. Please note: Blackwell Publishing are not responsible for the content or functionality of any supporting materials supplied by the authors. Any queries (other than missing material) should be directed to the corresponding author for the article. Fig. S1. Dotplot analysis comparing the Roseophage SBRSIO67‐2001 genome with the four other Roseophage genomes. Fig. S2. Roseophage plaques on a lawn of Roseobacter SIO67. Each circle represents a 5 μl spot of liquid lysate containing plaque forming units. Table S1. Sequences of the PCR primers designed to the archetypal Roseophage SIO1‐1989 genome. Table S2. Aquatic viral metagenomes used to map the global distribution of Roseophage‐like viruses (Fig. 4). Shown as the number of similarities (blastn, threshold E‐value of 1e‐4) to the Roseophage SIO‐1989 genome. Please note: Blackwell Publishing are not responsible for the content or functionality of any supporting materials supplied by the authors. Any queries (other than missing material) should be directed to the corresponding author for the article. Fig. S1. Dotplot analysis comparing the Roseophage SBRSIO67‐2001 genome with the four other Roseophage genomes. Fig. S2. Roseophage plaques on a lawn of Roseobacter SIO67. Each circle represents a 5 μl spot of liquid lysate containing plaque forming units. Table S1. Sequences of the PCR primers designed to the archetypal Roseophage SIO1‐1989 genome. Table S2. Aquatic viral metagenomes used to map the global distribution of Roseophage‐like viruses (Fig. 4). Shown as the number of similarities (blastn, threshold E‐value of 1e‐4) to the Roseophage SIO‐1989 genome. Please note: Blackwell Publishing are not responsible for the content or functionality of any supporting materials supplied by the authors. Any queries (other than missing material) should be directed to the corresponding author for the article.Supporting Info Item: 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>2009</date><detail type="title"><title>Environmental Viruses: Shaping the biosphere. Guest Editors: Forest Rohwer, David Prangishvili and Debbie Lindell</title></detail><detail type="volume"><caption>vol.</caption><number>11</number></detail><detail type="issue"><caption>no.</caption><number>11</number></detail><extent unit="pages"><start>2863</start><end>2873</end><total>11</total></extent></part></relatedItem><identifier type="istex">FA593991B982ECBF93FE933CC35A5EAF0EA0634B</identifier><identifier type="DOI">10.1111/j.1462-2920.2009.02021.x</identifier><identifier type="ArticleID">EMI2021</identifier><accessCondition type="use and reproduction" contentType="copyright">© 2009 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/FA593991B982ECBF93FE933CC35A5EAF0EA0634B/enrichments/multicat</uri></json:item></enrichments><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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