Analysis of synonymous codon usage and evolution of begomoviruses
Identifieur interne : 001671 ( Istex/Corpus ); précédent : 001670; suivant : 001672Analysis of synonymous codon usage and evolution of begomoviruses
Auteurs : Xiao-Zhong Xu ; Qing-Po Liu ; Long-Jiang Fan ; Xiao-Feng Cui ; Xue-Ping ZhouSource :
- Journal of Zhejiang University SCIENCE B [ 1673-1581 ] ; 2008-09-01.
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Abstract
Abstract: Begomoviruses are single-stranded DNA viruses and cause severe diseases in major crop plants worldwide. Based on current genome sequence analyses, we found that synonymous codon usage variations in the protein-coding genes of begomoviruses are mainly influenced by mutation bias. Base composition analysis suggested that the codon usage bias of AV1 and BV1 genes is significant and their expressions are high. Fourteen codons were determined as translational optimal ones according to the comparison of codon usage patterns between highly and lowly expressed genes. Interestingly the codon usages between begomoviruses from the Old and the New Worlds are apparently different, which supports the idea that the bipartite begomoviruses of the New World might originate from bipartite ones of the Old World, whereas the latter evolve from the Old World monopartite begomoviruses.
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DOI: 10.1631/jzus.B0820005
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Based on current genome sequence analyses, we found that synonymous codon usage variations in the protein-coding genes of begomoviruses are mainly influenced by mutation bias. Base composition analysis suggested that the codon usage bias of AV1 and BV1 genes is significant and their expressions are high. Fourteen codons were determined as translational optimal ones according to the comparison of codon usage patterns between highly and lowly expressed genes. Interestingly the codon usages between begomoviruses from the Old and the New Worlds are apparently different, which supports the idea that the bipartite begomoviruses of the New World might originate from bipartite ones of the Old World, whereas the latter evolve from the Old World monopartite begomoviruses.</div></front></TEI><istex><corpusName>springer-journals</corpusName><author><json:item><name>Xiao-zhong Xu</name><affiliations><json:string>College of Agriculture and Biotechnology, Zhejiang University, 310029, Hangzhou, China</json:string></affiliations></json:item><json:item><name>Qing-po Liu</name><affiliations><json:string>School of Agriculture and Food Science, Zhejiang Forestry University, 311300, Lin’an, China</json:string></affiliations></json:item><json:item><name>Long-jiang Fan</name><affiliations><json:string>College of Agriculture and Biotechnology, Zhejiang University, 310029, Hangzhou, China</json:string></affiliations></json:item><json:item><name>Xiao-feng Cui</name><affiliations><json:string>College of Agriculture and Biotechnology, Zhejiang University, 310029, Hangzhou, China</json:string></affiliations></json:item><json:item><name>Xue-ping Zhou</name><affiliations><json:string>College of Agriculture and Biotechnology, Zhejiang University, 310029, Hangzhou, China</json:string><json:string>E-mail: zzhou@zju.edu.cn</json:string></affiliations></json:item></author><subject><json:item><lang><json:string>eng</json:string></lang><value>Begomovirus</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>Synonymous codon usage</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>Evolution</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>Bioinformatics</value></json:item></subject><articleId><json:string>2236</json:string><json:string>jzus.B0820005</json:string></articleId><arkIstex>ark:/67375/VQC-F7ND7FG3-2</arkIstex><language><json:string>eng</json:string></language><originalGenre><json:string>OriginalPaper</json:string></originalGenre><abstract>Abstract: Begomoviruses are single-stranded DNA viruses and cause severe diseases in major crop plants worldwide. 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Interestingly the codon usages between begomoviruses from the Old and the New Worlds are apparently different, which supports the idea that the bipartite begomoviruses of the New World might originate from bipartite ones of the Old World, whereas the latter evolve from the Old World monopartite begomoviruses.</p></abstract><textClass xml:lang="en"><keywords scheme="keyword"><list><head>Key words</head><item><term>Begomovirus</term></item><item><term>Synonymous codon usage</term></item><item><term>Evolution</term></item><item><term>Bioinformatics</term></item></list></keywords></textClass><textClass><classCode scheme="CLC number">Q939.46</classCode><classCode scheme="CLC number">S432.1</classCode></textClass><textClass><keywords scheme="Journal Subject"><list><head>Biomedicine</head><item><term>Biomedicine general</term></item></list></keywords></textClass></profileDesc><revisionDesc><change when="2008-01-06">Created</change><change when="2008-09-01">Published</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><extension>txt</extension><original>false</original><mimetype>text/plain</mimetype><uri>https://api.istex.fr/ark:/67375/VQC-F7ND7FG3-2/fulltext.txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="corpus springer-journals not found" wicri:toSee="no header"><istex:xmlDeclaration>version="1.0" encoding="UTF-8"</istex:xmlDeclaration><istex:docType PUBLIC="-//Springer-Verlag//DTD A++ V2.4//EN" URI="http://devel.springer.de/A++/V2.4/DTD/A++V2.4.dtd" name="istex:docType"></istex:docType><istex:document><Publisher><PublisherInfo><PublisherName>SP Zhejiang University Press</PublisherName><PublisherLocation>Heidelberg</PublisherLocation></PublisherInfo><Journal OutputMedium="All"><JournalInfo JournalProductType="ArchiveJournal" NumberingStyle="Unnumbered"><JournalID>11585</JournalID><JournalPrintISSN>1673-1581</JournalPrintISSN><JournalElectronicISSN>1862-1783</JournalElectronicISSN><JournalTitle>Journal of Zhejiang University SCIENCE B</JournalTitle><JournalSubTitle>An international biomedicine & biotechnology journal</JournalSubTitle><JournalAbbreviatedTitle>J. 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Based on current genome sequence analyses, we found that synonymous codon usage variations in the protein-coding genes of begomoviruses are mainly influenced by mutation bias. Base composition analysis suggested that the codon usage bias of <Emphasis Type="Italic">AV1</Emphasis> and <Emphasis Type="Italic">BV1</Emphasis> genes is significant and their expressions are high. Fourteen codons were determined as translational optimal ones according to the comparison of codon usage patterns between highly and lowly expressed genes. Interestingly the codon usages between begomoviruses from the Old and the New Worlds are apparently different, which supports the idea that the bipartite begomoviruses of the New World might originate from bipartite ones of the Old World, whereas the latter evolve from the Old World monopartite begomoviruses.</Para></Abstract><KeywordGroup Language="En"><Heading>Key words</Heading><Keyword>Begomovirus</Keyword><Keyword>Synonymous codon usage</Keyword><Keyword>Evolution</Keyword><Keyword>Bioinformatics</Keyword></KeywordGroup><KeywordGroup Language="--"><Heading>CLC number</Heading><Keyword>Q939.46</Keyword><Keyword>S432.1</Keyword></KeywordGroup><ArticleNote Type="Misc"><SimplePara>Project supported by the National Basic Research and Development Program (973) of China (No. 2006CB101903) and the National Excellent Doctoral Dissertation of China (No. 200768)</SimplePara></ArticleNote></ArticleHeader><NoBody></NoBody></Article></Issue></Volume></Journal></Publisher></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Analysis of synonymous codon usage and evolution of begomoviruses</title></titleInfo><titleInfo type="alternative" contentType="CDATA"><title>Analysis of synonymous codon usage and evolution of begomoviruses</title></titleInfo><name type="personal"><namePart type="given">Xiao-zhong</namePart><namePart type="family">Xu</namePart><affiliation>College of Agriculture and Biotechnology, Zhejiang University, 310029, Hangzhou, China</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Qing-po</namePart><namePart type="family">Liu</namePart><affiliation>School of Agriculture and Food Science, Zhejiang Forestry University, 311300, Lin’an, China</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Long-jiang</namePart><namePart type="family">Fan</namePart><affiliation>College of Agriculture and Biotechnology, Zhejiang University, 310029, Hangzhou, China</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Xiao-feng</namePart><namePart type="family">Cui</namePart><affiliation>College of Agriculture and Biotechnology, Zhejiang University, 310029, Hangzhou, China</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal" displayLabel="corresp"><namePart type="given">Xue-ping</namePart><namePart type="family">Zhou</namePart><affiliation>College of Agriculture and Biotechnology, Zhejiang University, 310029, Hangzhou, China</affiliation><affiliation>E-mail: zzhou@zju.edu.cn</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="research-article" displayLabel="OriginalPaper" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-1JC4F85T-7">research-article</genre><originInfo><publisher>SP Zhejiang University Press</publisher><place><placeTerm type="text">Heidelberg</placeTerm></place><dateCreated encoding="w3cdtf">2008-01-06</dateCreated><dateIssued encoding="w3cdtf">2008-09-01</dateIssued><copyrightDate encoding="w3cdtf">2008</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><abstract lang="en">Abstract: Begomoviruses are single-stranded DNA viruses and cause severe diseases in major crop plants worldwide. Based on current genome sequence analyses, we found that synonymous codon usage variations in the protein-coding genes of begomoviruses are mainly influenced by mutation bias. Base composition analysis suggested that the codon usage bias of AV1 and BV1 genes is significant and their expressions are high. Fourteen codons were determined as translational optimal ones according to the comparison of codon usage patterns between highly and lowly expressed genes. Interestingly the codon usages between begomoviruses from the Old and the New Worlds are apparently different, which supports the idea that the bipartite begomoviruses of the New World might originate from bipartite ones of the Old World, whereas the latter evolve from the Old World monopartite begomoviruses.</abstract><subject lang="en"><genre>Key words</genre><topic>Begomovirus</topic><topic>Synonymous codon usage</topic><topic>Evolution</topic><topic>Bioinformatics</topic></subject><classification displayLabel="CLC number">Q939.46</classification><classification displayLabel="CLC number">S432.1</classification><relatedItem type="host"><titleInfo><title>Journal of Zhejiang University SCIENCE B</title><subTitle>An international biomedicine & biotechnology journal</subTitle></titleInfo><titleInfo type="abbreviated"><title>J. Zhejiang Univ. Sci. B</title></titleInfo><genre type="journal" authority="ISTEX" authorityURI="https://publication-type.data.istex.fr" valueURI="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</genre><originInfo><publisher>Springer</publisher><dateIssued encoding="w3cdtf">2008-08-29</dateIssued><copyrightDate encoding="w3cdtf">2008</copyrightDate></originInfo><subject><genre>Biomedicine</genre><topic>Biomedicine general</topic></subject><identifier type="ISSN">1673-1581</identifier><identifier type="eISSN">1862-1783</identifier><identifier type="JournalID">11585</identifier><identifier type="IssueArticleCount">11</identifier><identifier type="VolumeIssueCount">12</identifier><part><date>2008</date><detail type="volume"><number>9</number><caption>vol.</caption></detail><detail type="issue"><number>9</number><caption>no.</caption></detail><extent unit="pages"><start>667</start><end>674</end></extent></part><recordInfo><recordOrigin>Zhejiang University and Springer-Verlag GmbH, 2008</recordOrigin></recordInfo></relatedItem><identifier type="istex">4CDFC1A8C4B94938FBC48807943F99188BFC8FBE</identifier><identifier type="ark">ark:/67375/VQC-F7ND7FG3-2</identifier><identifier type="DOI">10.1631/jzus.B0820005</identifier><identifier type="ArticleID">2236</identifier><identifier type="ArticleID">jzus.B0820005</identifier><accessCondition type="use and reproduction" contentType="copyright">Zhejiang University and Springer-Verlag GmbH, 2008</accessCondition><recordInfo><recordContentSource authority="ISTEX" authorityURI="https://loaded-corpus.data.istex.fr" valueURI="https://loaded-corpus.data.istex.fr/ark:/67375/XBH-3XSW68JL-F">springer</recordContentSource><recordOrigin>Zhejiang University and Springer-Verlag GmbH, 2008</recordOrigin></recordInfo></mods><json:item><extension>json</extension><original>false</original><mimetype>application/json</mimetype><uri>https://api.istex.fr/ark:/67375/VQC-F7ND7FG3-2/record.json</uri></json:item></metadata><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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