Differentiation of Indian, East Timorese, Papuan and Floridian ‘Candidatus Liberibacter asiaticus’ isolates on the basis of simple sequence repeat and single nucleotide polymorphism profiles at 25 loci
Identifieur interne : 001607 ( Istex/Corpus ); précédent : 001606; suivant : 001608Differentiation of Indian, East Timorese, Papuan and Floridian ‘Candidatus Liberibacter asiaticus’ isolates on the basis of simple sequence repeat and single nucleotide polymorphism profiles at 25 loci
Auteurs : H. Katoh ; R. Davis ; M. W. Smith ; M. Weinert ; T. IwanamiSource :
- Annals of Applied Biology [ 0003-4746 ] ; 2012-05.
Abstract
Japanese isolates of ‘Candidatus Liberibacter asiaticus’ have been shown to be clearly differentiated by simple sequence repeat (SSR) profiles at four loci. In this study, 25 SSR loci, including these four loci, were selected from the whole‐genome sequence and were used to differentiate non‐Japanese samples of ‘Ca. Liberibacter asiaticus’ (13 Indian, 3 East Timorese, 1 Papuan and 8 Floridian samples). Out of the 25 SSR loci, 13 were polymorphic. Dendrogram analysis using SSR loci showed that the clusters were mostly consistent with the geographical origins of the isolates. When single nucleotide polymorphisms (SNPs) were searched around these 25 loci, only the upstream region of locus 091 exhibited polymorphism. Phylogenetic tree analysis of the SNPs in the upstream region of locus 091 showed that Floridian samples were clustered into one group as shown by dendrogram analysis using SSR loci. The differences in nucleotide sequences were not associated with differences in the citrus hosts (lime, mandarin, lemon and sour orange) from which the isolates were originally derived.
Url:
DOI: 10.1111/j.1744-7348.2012.00541.x
Links to Exploration step
ISTEX:A9E8051058DB2D517FD96EB1B2540A06A5E3994ALe document en format XML
<record><TEI wicri:istexFullTextTei="biblStruct"><teiHeader><fileDesc><titleStmt><title xml:lang="en">Differentiation of Indian, East Timorese, Papuan and Floridian ‘Candidatus Liberibacter asiaticus’ isolates on the basis of simple sequence repeat and single nucleotide polymorphism profiles at 25 loci</title><author><name sortKey="Katoh, H" sort="Katoh, H" uniqKey="Katoh H" first="H." last="Katoh">H. Katoh</name><affiliation><mods:affiliation>National Institute of Fruit Tree Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2‐1, Tsukuba, Ibaraki, Japan</mods:affiliation></affiliation></author><author><name sortKey="Davis, R" sort="Davis, R" uniqKey="Davis R" first="R." last="Davis">R. Davis</name><affiliation><mods:affiliation>Northern Australia Quarantine Strategy, Australian Quarantine and Inspection Service, Cairns International Airport, QLD, Cairns, Australia</mods:affiliation></affiliation></author><author><name sortKey="Smith, M W" sort="Smith, M W" uniqKey="Smith M" first="M. W." last="Smith">M. W. Smith</name><affiliation><mods:affiliation>Bundaberg Research Station, Department of Employment, Economic Development and Innovation, QLD, Bundaberg, Australia</mods:affiliation></affiliation></author><author><name sortKey="Weinert, M" sort="Weinert, M" uniqKey="Weinert M" first="M." last="Weinert">M. Weinert</name><affiliation><mods:affiliation>Centre for Tropical Agriculture, Department of Employment, Economic Development and Innovation, QLD, Mareeba, Australia</mods:affiliation></affiliation></author><author><name sortKey="Iwanami, T" sort="Iwanami, T" uniqKey="Iwanami T" first="T." last="Iwanami">T. Iwanami</name><affiliation><mods:affiliation>National Institute of Fruit Tree Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2‐1, Tsukuba, Ibaraki, Japan</mods:affiliation></affiliation><affiliation><mods:affiliation>T. Iwanami, National Institute of Fruit TreeScience, National Agriculture and FoodResearch Organization (NARO), Fujimoto 2‐1,Tsukuba, Ibaraki305‐8605, Japan.Email:</mods:affiliation></affiliation><affiliation><mods:affiliation>E-mail: tiwsw37@affrc.go.jp</mods:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno type="RBID">ISTEX:A9E8051058DB2D517FD96EB1B2540A06A5E3994A</idno><date when="2012" year="2012">2012</date><idno type="doi">10.1111/j.1744-7348.2012.00541.x</idno><idno type="url">https://api.istex.fr/document/A9E8051058DB2D517FD96EB1B2540A06A5E3994A/fulltext/pdf</idno><idno type="wicri:Area/Istex/Corpus">001607</idno></publicationStmt><sourceDesc><biblStruct><analytic><title level="a" type="main" xml:lang="en">Differentiation of Indian, East Timorese, Papuan and Floridian ‘Candidatus Liberibacter asiaticus’ isolates on the basis of simple sequence repeat and single nucleotide polymorphism profiles at 25 loci</title><author><name sortKey="Katoh, H" sort="Katoh, H" uniqKey="Katoh H" first="H." last="Katoh">H. Katoh</name><affiliation><mods:affiliation>National Institute of Fruit Tree Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2‐1, Tsukuba, Ibaraki, Japan</mods:affiliation></affiliation></author><author><name sortKey="Davis, R" sort="Davis, R" uniqKey="Davis R" first="R." last="Davis">R. Davis</name><affiliation><mods:affiliation>Northern Australia Quarantine Strategy, Australian Quarantine and Inspection Service, Cairns International Airport, QLD, Cairns, Australia</mods:affiliation></affiliation></author><author><name sortKey="Smith, M W" sort="Smith, M W" uniqKey="Smith M" first="M. W." last="Smith">M. W. Smith</name><affiliation><mods:affiliation>Bundaberg Research Station, Department of Employment, Economic Development and Innovation, QLD, Bundaberg, Australia</mods:affiliation></affiliation></author><author><name sortKey="Weinert, M" sort="Weinert, M" uniqKey="Weinert M" first="M." last="Weinert">M. Weinert</name><affiliation><mods:affiliation>Centre for Tropical Agriculture, Department of Employment, Economic Development and Innovation, QLD, Mareeba, Australia</mods:affiliation></affiliation></author><author><name sortKey="Iwanami, T" sort="Iwanami, T" uniqKey="Iwanami T" first="T." last="Iwanami">T. Iwanami</name><affiliation><mods:affiliation>National Institute of Fruit Tree Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2‐1, Tsukuba, Ibaraki, Japan</mods:affiliation></affiliation><affiliation><mods:affiliation>T. Iwanami, National Institute of Fruit TreeScience, National Agriculture and FoodResearch Organization (NARO), Fujimoto 2‐1,Tsukuba, Ibaraki305‐8605, Japan.Email:</mods:affiliation></affiliation><affiliation><mods:affiliation>E-mail: tiwsw37@affrc.go.jp</mods:affiliation></affiliation></author></analytic><monogr></monogr><series><title level="j">Annals of Applied Biology</title><title level="j" type="abbrev">Ann Appl Biol</title><idno type="ISSN">0003-4746</idno><idno type="eISSN">1744-7348</idno><imprint><publisher>Blackwell Publishing Ltd</publisher><pubPlace>Oxford, UK</pubPlace><date type="published" when="2012-05">2012-05</date><biblScope unit="volume">160</biblScope><biblScope unit="issue">3</biblScope><biblScope unit="page" from="291">291</biblScope><biblScope unit="page" to="297">297</biblScope></imprint><idno type="ISSN">0003-4746</idno></series><idno type="istex">A9E8051058DB2D517FD96EB1B2540A06A5E3994A</idno><idno type="DOI">10.1111/j.1744-7348.2012.00541.x</idno><idno type="ArticleID">AAB541</idno></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0003-4746</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract">Japanese isolates of ‘Candidatus Liberibacter asiaticus’ have been shown to be clearly differentiated by simple sequence repeat (SSR) profiles at four loci. In this study, 25 SSR loci, including these four loci, were selected from the whole‐genome sequence and were used to differentiate non‐Japanese samples of ‘Ca. Liberibacter asiaticus’ (13 Indian, 3 East Timorese, 1 Papuan and 8 Floridian samples). Out of the 25 SSR loci, 13 were polymorphic. Dendrogram analysis using SSR loci showed that the clusters were mostly consistent with the geographical origins of the isolates. When single nucleotide polymorphisms (SNPs) were searched around these 25 loci, only the upstream region of locus 091 exhibited polymorphism. Phylogenetic tree analysis of the SNPs in the upstream region of locus 091 showed that Floridian samples were clustered into one group as shown by dendrogram analysis using SSR loci. The differences in nucleotide sequences were not associated with differences in the citrus hosts (lime, mandarin, lemon and sour orange) from which the isolates were originally derived.</div></front></TEI><istex><corpusName>wiley</corpusName><author><json:item><name>H. Katoh</name><affiliations><json:string>National Institute of Fruit Tree Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2‐1, Tsukuba, Ibaraki, Japan</json:string></affiliations></json:item><json:item><name>R. Davis</name><affiliations><json:string>Northern Australia Quarantine Strategy, Australian Quarantine and Inspection Service, Cairns International Airport, QLD, Cairns, Australia</json:string></affiliations></json:item><json:item><name>M.W. Smith</name><affiliations><json:string>Bundaberg Research Station, Department of Employment, Economic Development and Innovation, QLD, Bundaberg, Australia</json:string></affiliations></json:item><json:item><name>M. Weinert</name><affiliations><json:string>Centre for Tropical Agriculture, Department of Employment, Economic Development and Innovation, QLD, Mareeba, Australia</json:string></affiliations></json:item><json:item><name>T. Iwanami</name><affiliations><json:string>National Institute of Fruit Tree Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2‐1, Tsukuba, Ibaraki, Japan</json:string><json:string>T. Iwanami, National Institute of Fruit TreeScience, National Agriculture and FoodResearch Organization (NARO), Fujimoto 2‐1,Tsukuba, Ibaraki305‐8605, Japan.Email:</json:string><json:string>E-mail: tiwsw37@affrc.go.jp</json:string></affiliations></json:item></author><subject><json:item><lang><json:string>eng</json:string></lang><value>‘Candidatus Liberibacter asiaticus’</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>citrus</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>genetic diversity</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>simple sequence repeats</value></json:item></subject><articleId><json:string>AAB541</json:string></articleId><language><json:string>eng</json:string></language><originalGenre><json:string>article</json:string></originalGenre><abstract>Japanese isolates of ‘Candidatus Liberibacter asiaticus’ have been shown to be clearly differentiated by simple sequence repeat (SSR) profiles at four loci. In this study, 25 SSR loci, including these four loci, were selected from the whole‐genome sequence and were used to differentiate non‐Japanese samples of ‘Ca. Liberibacter asiaticus’ (13 Indian, 3 East Timorese, 1 Papuan and 8 Floridian samples). Out of the 25 SSR loci, 13 were polymorphic. Dendrogram analysis using SSR loci showed that the clusters were mostly consistent with the geographical origins of the isolates. When single nucleotide polymorphisms (SNPs) were searched around these 25 loci, only the upstream region of locus 091 exhibited polymorphism. Phylogenetic tree analysis of the SNPs in the upstream region of locus 091 showed that Floridian samples were clustered into one group as shown by dendrogram analysis using SSR loci. The differences in nucleotide sequences were not associated with differences in the citrus hosts (lime, mandarin, lemon and sour orange) from which the isolates were originally derived.</abstract><qualityIndicators><score>5.111</score><pdfVersion>1.3</pdfVersion><pdfPageSize>595.276 x 841.89 pts (A4)</pdfPageSize><refBibsNative>true</refBibsNative><keywordCount>4</keywordCount><abstractCharCount>1090</abstractCharCount><pdfWordCount>3131</pdfWordCount><pdfCharCount>23426</pdfCharCount><pdfPageCount>7</pdfPageCount><abstractWordCount>165</abstractWordCount></qualityIndicators><title>Differentiation of Indian, East Timorese, Papuan and Floridian ‘Candidatus Liberibacter asiaticus’ isolates on the basis of simple sequence repeat and single nucleotide polymorphism profiles at 25 loci</title><genre><json:string>article</json:string></genre><host><volume>160</volume><publisherId><json:string>AAB</json:string></publisherId><pages><total>7</total><last>297</last><first>291</first></pages><issn><json:string>0003-4746</json:string></issn><issue>3</issue><subject><json:item><value>RESEARCH ARTICLE</value></json:item></subject><genre><json:string>journal</json:string></genre><language><json:string>unknown</json:string></language><eissn><json:string>1744-7348</json:string></eissn><title>Annals of Applied Biology</title><doi><json:string>10.1111/(ISSN)1744-7348</json:string></doi></host><publicationDate>2012</publicationDate><copyrightDate>2012</copyrightDate><doi><json:string>10.1111/j.1744-7348.2012.00541.x</json:string></doi><id>A9E8051058DB2D517FD96EB1B2540A06A5E3994A</id><score>0.16342375</score><fulltext><json:item><original>true</original><mimetype>application/pdf</mimetype><extension>pdf</extension><uri>https://api.istex.fr/document/A9E8051058DB2D517FD96EB1B2540A06A5E3994A/fulltext/pdf</uri></json:item><json:item><original>false</original><mimetype>application/zip</mimetype><extension>zip</extension><uri>https://api.istex.fr/document/A9E8051058DB2D517FD96EB1B2540A06A5E3994A/fulltext/zip</uri></json:item><istex:fulltextTEI uri="https://api.istex.fr/document/A9E8051058DB2D517FD96EB1B2540A06A5E3994A/fulltext/tei"><teiHeader><fileDesc><titleStmt><title level="a" type="main" xml:lang="en">Differentiation of Indian, East Timorese, Papuan and Floridian ‘Candidatus Liberibacter asiaticus’ isolates on the basis of simple sequence repeat and single nucleotide polymorphism profiles at 25 loci</title></titleStmt><publicationStmt><authority>ISTEX</authority><publisher>Blackwell Publishing Ltd</publisher><pubPlace>Oxford, UK</pubPlace><availability><p>Annals of Applied Biology © 2012 Association of Applied Biologists© 2012 The Authors. Annals of Applied Biology © 2012 Association of Applied Biologists</p></availability><date>2012-03-05</date></publicationStmt><sourceDesc><biblStruct type="inbook"><analytic><title level="a" type="main" xml:lang="en">Differentiation of Indian, East Timorese, Papuan and Floridian ‘Candidatus Liberibacter asiaticus’ isolates on the basis of simple sequence repeat and single nucleotide polymorphism profiles at 25 loci</title><author xml:id="author-1"><persName><forename type="first">H.</forename><surname>Katoh</surname></persName><affiliation>National Institute of Fruit Tree Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2‐1, Tsukuba, Ibaraki, Japan</affiliation></author><author xml:id="author-2"><persName><forename type="first">R.</forename><surname>Davis</surname></persName><affiliation>Northern Australia Quarantine Strategy, Australian Quarantine and Inspection Service, Cairns International Airport, QLD, Cairns, Australia</affiliation></author><author xml:id="author-3"><persName><forename type="first">M.W.</forename><surname>Smith</surname></persName><affiliation>Bundaberg Research Station, Department of Employment, Economic Development and Innovation, QLD, Bundaberg, Australia</affiliation></author><author xml:id="author-4"><persName><forename type="first">M.</forename><surname>Weinert</surname></persName><affiliation>Centre for Tropical Agriculture, Department of Employment, Economic Development and Innovation, QLD, Mareeba, Australia</affiliation></author><author xml:id="author-5"><persName><forename type="first">T.</forename><surname>Iwanami</surname></persName><email>tiwsw37@affrc.go.jp</email><affiliation>National Institute of Fruit Tree Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2‐1, Tsukuba, Ibaraki, Japan</affiliation><affiliation>T. Iwanami, National Institute of Fruit TreeScience, National Agriculture and FoodResearch Organization (NARO), Fujimoto 2‐1,Tsukuba, Ibaraki305‐8605, Japan.Email:</affiliation></author></analytic><monogr><title level="j">Annals of Applied Biology</title><title level="j" type="abbrev">Ann Appl Biol</title><idno type="pISSN">0003-4746</idno><idno type="eISSN">1744-7348</idno><idno type="DOI">10.1111/(ISSN)1744-7348</idno><imprint><publisher>Blackwell Publishing Ltd</publisher><pubPlace>Oxford, UK</pubPlace><date type="published" when="2012-05"></date><biblScope unit="volume">160</biblScope><biblScope unit="issue">3</biblScope><biblScope unit="page" from="291">291</biblScope><biblScope unit="page" to="297">297</biblScope></imprint></monogr><idno type="istex">A9E8051058DB2D517FD96EB1B2540A06A5E3994A</idno><idno type="DOI">10.1111/j.1744-7348.2012.00541.x</idno><idno type="ArticleID">AAB541</idno></biblStruct></sourceDesc></fileDesc><profileDesc><creation><date>2012-03-05</date></creation><langUsage><language ident="en">en</language></langUsage><abstract><p>Japanese isolates of ‘Candidatus Liberibacter asiaticus’ have been shown to be clearly differentiated by simple sequence repeat (SSR) profiles at four loci. In this study, 25 SSR loci, including these four loci, were selected from the whole‐genome sequence and were used to differentiate non‐Japanese samples of ‘Ca. Liberibacter asiaticus’ (13 Indian, 3 East Timorese, 1 Papuan and 8 Floridian samples). Out of the 25 SSR loci, 13 were polymorphic. Dendrogram analysis using SSR loci showed that the clusters were mostly consistent with the geographical origins of the isolates. When single nucleotide polymorphisms (SNPs) were searched around these 25 loci, only the upstream region of locus 091 exhibited polymorphism. Phylogenetic tree analysis of the SNPs in the upstream region of locus 091 showed that Floridian samples were clustered into one group as shown by dendrogram analysis using SSR loci. The differences in nucleotide sequences were not associated with differences in the citrus hosts (lime, mandarin, lemon and sour orange) from which the isolates were originally derived.</p></abstract><textClass><keywords scheme="keyword"><list><head>keywords</head><item><term>‘Candidatus Liberibacter asiaticus’</term></item><item><term>citrus</term></item><item><term>genetic diversity</term></item><item><term>simple sequence repeats</term></item></list></keywords></textClass><textClass><keywords scheme="Journal Subject"><list><head>article-category</head><item><term>RESEARCH ARTICLE</term></item></list></keywords></textClass></profileDesc><revisionDesc><change when="2011-09-27">Received</change><change when="2012-02-04">Registration</change><change when="2012-03-05">Created</change><change when="2012-05">Published</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><original>false</original><mimetype>text/plain</mimetype><extension>txt</extension><uri>https://api.istex.fr/document/A9E8051058DB2D517FD96EB1B2540A06A5E3994A/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" xml:id="aab541"><header><publicationMeta level="product"><publisherInfo><publisherName>Blackwell Publishing Ltd</publisherName><publisherLoc>Oxford, UK</publisherLoc></publisherInfo><doi origin="wiley" registered="yes">10.1111/(ISSN)1744-7348</doi><issn type="print">0003-4746</issn><issn type="electronic">1744-7348</issn><idGroup><id type="product" value="AAB"></id></idGroup><titleGroup><title type="main" sort="ANNALS OF APPLIED BIOLOGY">Annals of Applied Biology</title><title type="short">Ann Appl Biol</title></titleGroup></publicationMeta><publicationMeta level="part" position="05103"><doi origin="wiley">10.1111/aab.2012.160.issue-3</doi><copyright ownership="publisher">Annals of Applied Biology © 2012 Association of Applied Biologists</copyright><numberingGroup><numbering type="journalVolume" number="160">160</numbering><numbering type="journalIssue">3</numbering></numberingGroup><coverDate startDate="2012-05">May 2012</coverDate></publicationMeta><publicationMeta level="unit" position="90" type="article" status="forIssue"><doi>10.1111/j.1744-7348.2012.00541.x</doi><idGroup><id type="unit" value="AAB541"></id></idGroup><countGroup><count type="pageTotal" number="7"></count></countGroup><titleGroup><title type="articleCategory">RESEARCH ARTICLE</title><title type="tocHeading1">RESEARCH ARTICLES</title></titleGroup><copyright ownership="publisher">© 2012 The Authors. Annals of Applied Biology © 2012 Association of Applied Biologists</copyright><eventGroup><event type="manuscriptReceived" date="2011-09-27"></event><event type="manuscriptRevised" date="2011-12-07"></event><event type="manuscriptAccepted" date="2012-02-04"></event><event type="xmlCreated" agent="Laserwords Private Ltd." date="2012-03-05"></event><event type="publishedOnlineEarlyUnpaginated" date="2012-03-26"></event><event type="firstOnline" date="2012-03-26"></event><event type="publishedOnlineFinalForm" date="2012-04-09"></event><event type="xmlConverted" agent="Converter:WILEY_ML3G_TO_WILEY_ML3GV2 version:4.0.1" date="2014-03-14"></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">291</numbering><numbering type="pageLast">297</numbering></numberingGroup><correspondenceTo><lineatedText><line><b>Correspondence</b></line><line>T. Iwanami, National Institute of Fruit Tree</line><line>Science, National Agriculture and Food</line><line>Research Organization (NARO), Fujimoto 2‐1,</line><line>Tsukuba, Ibaraki</line><line>305‐8605, Japan.</line><line>Email: <email>tiwsw37@affrc.go.jp</email></line></lineatedText></correspondenceTo><linkGroup><link type="toTypesetVersion" href="file:AAB.AAB541.pdf"></link></linkGroup></publicationMeta><contentMeta><titleGroup><title type="main">Differentiation of <fc>I</fc>ndian, <fc>E</fc>ast <fc>T</fc>imorese, <fc>P</fc>apuan and <fc>F</fc>loridian ‘<fi>Candidatus</fi> <fc>L</fc>iberibacter asiaticus’ isolates on the basis of simple sequence repeat and single nucleotide polymorphism profiles at 25 loci</title><title type="shortAuthors"><fc>H</fc>. <fc>K</fc>atoh <i>et al.</i></title><title type="short"><fc>SSRs</fc> and <fc>SNPs</fc> in ‘<fi>Candidatus</fi> <fc>L</fc>iberibacter asiaticus’</title></titleGroup><creators><creator creatorRole="author" xml:id="aab541-cr-0001" affiliationRef="#aab541-aff-0001"><personName><givenNames>H.</givenNames><familyName>Katoh</familyName></personName></creator><creator creatorRole="author" xml:id="aab541-cr-0002" affiliationRef="#aab541-aff-0002"><personName><givenNames>R.</givenNames><familyName>Davis</familyName></personName></creator><creator creatorRole="author" xml:id="aab541-cr-0003" affiliationRef="#aab541-aff-0003"><personName><givenNames>M.W.</givenNames><familyName>Smith</familyName></personName></creator><creator creatorRole="author" xml:id="aab541-cr-0004" affiliationRef="#aab541-aff-0004"><personName><givenNames>M.</givenNames><familyName>Weinert</familyName></personName></creator><creator creatorRole="author" xml:id="aab541-cr-0005" affiliationRef="#aab541-aff-0001" corresponding="yes"><personName><givenNames>T.</givenNames><familyName>Iwanami</familyName></personName></creator></creators><affiliationGroup><affiliation countryCode="JP" type="organization" xml:id="aab541-aff-0001"><orgDiv>National Institute of Fruit Tree Science</orgDiv><orgName>National Agriculture and Food Research Organization (NARO)</orgName><address><street>Fujimoto 2‐1</street><countryPart>Tsukuba</countryPart><city>Ibaraki</city><country>Japan</country></address></affiliation><affiliation countryCode="AU" type="organization" xml:id="aab541-aff-0002"><orgDiv>Northern Australia Quarantine Strategy</orgDiv><orgDiv>Australian Quarantine and Inspection Service</orgDiv><orgName>Cairns International Airport</orgName><address><city>Cairns</city><countryPart>QLD</countryPart><country>Australia</country></address></affiliation><affiliation countryCode="AU" type="organization" xml:id="aab541-aff-0003"><orgDiv>Bundaberg Research Station</orgDiv><orgDiv>Department of Employment</orgDiv><orgName>Economic Development and Innovation</orgName><address><city>Bundaberg</city><countryPart>QLD</countryPart><country>Australia</country></address></affiliation><affiliation countryCode="AU" type="organization" xml:id="aab541-aff-0004"><orgDiv>Centre for Tropical Agriculture</orgDiv><orgDiv>Department of Employment</orgDiv><orgName>Economic Development and Innovation</orgName><address><city>Mareeba</city><countryPart>QLD</countryPart><country>Australia</country></address></affiliation></affiliationGroup><keywordGroup type="author"><keyword xml:id="aab541-kwd-0001">‘<fi>Candidatus</fi> Liberibacter asiaticus’</keyword><keyword xml:id="aab541-kwd-0002">citrus</keyword><keyword xml:id="aab541-kwd-0003">genetic diversity</keyword><keyword xml:id="aab541-kwd-0004">simple sequence repeats</keyword></keywordGroup><abstractGroup><abstract type="main"><title type="main">Abstract</title><p>Japanese isolates of ‘<fi>Candidatus</fi> Liberibacter asiaticus’ have been shown to be clearly differentiated by simple sequence repeat (<fc>SSR</fc>) profiles at four loci. In this study, 25 <fc>SSR</fc> loci, including these four loci, were selected from the whole‐genome sequence and were used to differentiate non‐Japanese samples of ‘<fi>Ca</fi>. Liberibacter asiaticus’ (13 Indian, 3 East Timorese, 1 Papuan and 8 Floridian samples). Out of the 25 <fc>SSR</fc> loci, 13 were polymorphic. Dendrogram analysis using <fc>SSR</fc> loci showed that the clusters were mostly consistent with the geographical origins of the isolates. When single nucleotide polymorphisms (<fc>SNPs</fc>) were searched around these 25 loci, only the upstream region of locus 091 exhibited polymorphism. Phylogenetic tree analysis of the <fc>SNPs</fc> in the upstream region of locus 091 showed that Floridian samples were clustered into one group as shown by dendrogram analysis using <fc>SSR</fc> loci. The differences in nucleotide sequences were not associated with differences in the citrus hosts (lime, mandarin, lemon and sour orange) from which the isolates were originally derived.</p></abstract></abstractGroup></contentMeta></header></component></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Differentiation of Indian, East Timorese, Papuan and Floridian ‘Candidatus Liberibacter asiaticus’ isolates on the basis of simple sequence repeat and single nucleotide polymorphism profiles at 25 loci</title></titleInfo><titleInfo type="abbreviated" lang="en"><title>SSRs and SNPs in ‘Candidatus Liberibacter asiaticus’</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>Differentiation of Indian, East Timorese, Papuan and Floridian ‘Candidatus Liberibacter asiaticus’ isolates on the basis of simple sequence repeat and single nucleotide polymorphism profiles at 25 loci</title></titleInfo><name type="personal"><namePart type="given">H.</namePart><namePart type="family">Katoh</namePart><affiliation>National Institute of Fruit Tree Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2‐1, Tsukuba, Ibaraki, Japan</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">R.</namePart><namePart type="family">Davis</namePart><affiliation>Northern Australia Quarantine Strategy, Australian Quarantine and Inspection Service, Cairns International Airport, QLD, Cairns, Australia</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">M.W.</namePart><namePart type="family">Smith</namePart><affiliation>Bundaberg Research Station, Department of Employment, Economic Development and Innovation, QLD, Bundaberg, Australia</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">M.</namePart><namePart type="family">Weinert</namePart><affiliation>Centre for Tropical Agriculture, Department of Employment, Economic Development and Innovation, QLD, Mareeba, Australia</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">T.</namePart><namePart type="family">Iwanami</namePart><affiliation>National Institute of Fruit Tree Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2‐1, Tsukuba, Ibaraki, Japan</affiliation><affiliation>T. Iwanami, National Institute of Fruit TreeScience, National Agriculture and FoodResearch Organization (NARO), Fujimoto 2‐1,Tsukuba, Ibaraki305‐8605, Japan.Email:</affiliation><affiliation>E-mail: tiwsw37@affrc.go.jp</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">2012-05</dateIssued><dateCreated encoding="w3cdtf">2012-03-05</dateCreated><dateCaptured encoding="w3cdtf">2011-09-27</dateCaptured><dateValid encoding="w3cdtf">2012-02-04</dateValid><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></physicalDescription><abstract>Japanese isolates of ‘Candidatus Liberibacter asiaticus’ have been shown to be clearly differentiated by simple sequence repeat (SSR) profiles at four loci. In this study, 25 SSR loci, including these four loci, were selected from the whole‐genome sequence and were used to differentiate non‐Japanese samples of ‘Ca. Liberibacter asiaticus’ (13 Indian, 3 East Timorese, 1 Papuan and 8 Floridian samples). Out of the 25 SSR loci, 13 were polymorphic. Dendrogram analysis using SSR loci showed that the clusters were mostly consistent with the geographical origins of the isolates. When single nucleotide polymorphisms (SNPs) were searched around these 25 loci, only the upstream region of locus 091 exhibited polymorphism. Phylogenetic tree analysis of the SNPs in the upstream region of locus 091 showed that Floridian samples were clustered into one group as shown by dendrogram analysis using SSR loci. The differences in nucleotide sequences were not associated with differences in the citrus hosts (lime, mandarin, lemon and sour orange) from which the isolates were originally derived.</abstract><subject><genre>keywords</genre><topic>‘Candidatus Liberibacter asiaticus’</topic><topic>citrus</topic><topic>genetic diversity</topic><topic>simple sequence repeats</topic></subject><relatedItem type="host"><titleInfo><title>Annals of Applied Biology</title></titleInfo><titleInfo type="abbreviated"><title>Ann Appl Biol</title></titleInfo><genre type="journal">journal</genre><subject><genre>article-category</genre><topic>RESEARCH ARTICLE</topic></subject><identifier type="ISSN">0003-4746</identifier><identifier type="eISSN">1744-7348</identifier><identifier type="DOI">10.1111/(ISSN)1744-7348</identifier><identifier type="PublisherID">AAB</identifier><part><date>2012</date><detail type="volume"><caption>vol.</caption><number>160</number></detail><detail type="issue"><caption>no.</caption><number>3</number></detail><extent unit="pages"><start>291</start><end>297</end><total>7</total></extent></part></relatedItem><identifier type="istex">A9E8051058DB2D517FD96EB1B2540A06A5E3994A</identifier><identifier type="DOI">10.1111/j.1744-7348.2012.00541.x</identifier><identifier type="ArticleID">AAB541</identifier><accessCondition type="use and reproduction" contentType="copyright">Annals of Applied Biology © 2012 Association of Applied Biologists© 2012 The Authors. Annals of Applied Biology © 2012 Association of Applied Biologists</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/A9E8051058DB2D517FD96EB1B2540A06A5E3994A/enrichments/multicat</uri></json:item></enrichments><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Bois/explor/OrangerV1/Data/Istex/Corpus
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001607 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Istex/Corpus/biblio.hfd -nk 001607 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Wicri/Bois
|area= OrangerV1
|flux= Istex
|étape= Corpus
|type= RBID
|clé= ISTEX:A9E8051058DB2D517FD96EB1B2540A06A5E3994A
|texte= Differentiation of Indian, East Timorese, Papuan and Floridian ‘Candidatus Liberibacter asiaticus’ isolates on the basis of simple sequence repeat and single nucleotide polymorphism profiles at 25 loci
}}
| This area was generated with Dilib version V0.6.25. |  |