Analysis of synonymous codon usage and evolution of begomoviruses
Identifieur interne : 003528 ( Main/Merge ); précédent : 003527; suivant : 003529Analysis of synonymous codon usage and evolution of begomoviruses
Auteurs : Xiao-Zhong Xu [République populaire de Chine] ; Qing-Po Liu [République populaire de Chine] ; Long-Jiang Fan [République populaire de Chine] ; Xiao-Feng Cui [République populaire de Chine] ; Xue-Ping Zhou [République populaire de Chine]Source :
- Journal of Zhejiang University SCIENCE B [ 1673-1581 ] ; 2008-09-01.
English descriptors
- KwdEn :
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.
Url:
DOI: 10.1631/jzus.B0820005
Links toward previous steps (curation, corpus...)
- to stream Istex, to step Corpus: 001671
- to stream Istex, to step Curation: 001671
- to stream Istex, to step Checkpoint: 001100
Links to Exploration step
ISTEX:4CDFC1A8C4B94938FBC48807943F99188BFC8FBELe document en format XML
<record><TEI wicri:istexFullTextTei="biblStruct"><teiHeader><fileDesc><titleStmt><title xml:lang="en">Analysis of synonymous codon usage and evolution of begomoviruses</title>
<author><name sortKey="Xu, Xiao Zhong" sort="Xu, Xiao Zhong" uniqKey="Xu X" first="Xiao-Zhong" last="Xu">Xiao-Zhong Xu</name>
</author>
<author><name sortKey="Liu, Qing Po" sort="Liu, Qing Po" uniqKey="Liu Q" first="Qing-Po" last="Liu">Qing-Po Liu</name>
</author>
<author><name sortKey="Fan, Long Jiang" sort="Fan, Long Jiang" uniqKey="Fan L" first="Long-Jiang" last="Fan">Long-Jiang Fan</name>
</author>
<author><name sortKey="Cui, Xiao Feng" sort="Cui, Xiao Feng" uniqKey="Cui X" first="Xiao-Feng" last="Cui">Xiao-Feng Cui</name>
</author>
<author><name sortKey="Zhou, Xue Ping" sort="Zhou, Xue Ping" uniqKey="Zhou X" first="Xue-Ping" last="Zhou">Xue-Ping Zhou</name>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">ISTEX</idno>
<idno type="RBID">ISTEX:4CDFC1A8C4B94938FBC48807943F99188BFC8FBE</idno>
<date when="2008" year="2008">2008</date>
<idno type="doi">10.1631/jzus.B0820005</idno>
<idno type="url">https://api.istex.fr/ark:/67375/VQC-F7ND7FG3-2/fulltext.pdf</idno>
<idno type="wicri:Area/Istex/Corpus">001671</idno>
<idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Corpus" wicri:corpus="ISTEX">001671</idno>
<idno type="wicri:Area/Istex/Curation">001671</idno>
<idno type="wicri:Area/Istex/Checkpoint">001100</idno>
<idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Checkpoint">001100</idno>
<idno type="wicri:doubleKey">1673-1581:2008:Xu X:analysis:of:synonymous</idno>
<idno type="wicri:Area/Main/Merge">003528</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title level="a" type="main" xml:lang="en">Analysis of synonymous codon usage and evolution of begomoviruses</title>
<author><name sortKey="Xu, Xiao Zhong" sort="Xu, Xiao Zhong" uniqKey="Xu X" first="Xiao-Zhong" last="Xu">Xiao-Zhong Xu</name>
<affiliation wicri:level="4"><country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>College of Agriculture and Biotechnology, Zhejiang University, 310029, Hangzhou</wicri:regionArea>
<placeName><settlement type="city">Hangzhou</settlement>
<region type="province">Zhejiang</region>
</placeName>
<orgName type="university">Université de Zhejiang</orgName>
</affiliation>
</author>
<author><name sortKey="Liu, Qing Po" sort="Liu, Qing Po" uniqKey="Liu Q" first="Qing-Po" last="Liu">Qing-Po Liu</name>
<affiliation wicri:level="1"><country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>School of Agriculture and Food Science, Zhejiang Forestry University, 311300, Lin’an</wicri:regionArea>
<wicri:noRegion>Lin’an</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Fan, Long Jiang" sort="Fan, Long Jiang" uniqKey="Fan L" first="Long-Jiang" last="Fan">Long-Jiang Fan</name>
<affiliation wicri:level="4"><country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>College of Agriculture and Biotechnology, Zhejiang University, 310029, Hangzhou</wicri:regionArea>
<placeName><settlement type="city">Hangzhou</settlement>
<region type="province">Zhejiang</region>
</placeName>
<orgName type="university">Université de Zhejiang</orgName>
</affiliation>
</author>
<author><name sortKey="Cui, Xiao Feng" sort="Cui, Xiao Feng" uniqKey="Cui X" first="Xiao-Feng" last="Cui">Xiao-Feng Cui</name>
<affiliation wicri:level="4"><country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>College of Agriculture and Biotechnology, Zhejiang University, 310029, Hangzhou</wicri:regionArea>
<placeName><settlement type="city">Hangzhou</settlement>
<region type="province">Zhejiang</region>
</placeName>
<orgName type="university">Université de Zhejiang</orgName>
</affiliation>
</author>
<author><name sortKey="Zhou, Xue Ping" sort="Zhou, Xue Ping" uniqKey="Zhou X" first="Xue-Ping" last="Zhou">Xue-Ping Zhou</name>
<affiliation wicri:level="4"><country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>College of Agriculture and Biotechnology, Zhejiang University, 310029, Hangzhou</wicri:regionArea>
<placeName><settlement type="city">Hangzhou</settlement>
<region type="province">Zhejiang</region>
</placeName>
<orgName type="university">Université de Zhejiang</orgName>
</affiliation>
<affiliation wicri:level="1"><country wicri:rule="url">République populaire de Chine</country>
</affiliation>
</author>
</analytic>
<monogr></monogr>
<series><title level="j">Journal of Zhejiang University SCIENCE B</title>
<title level="j" type="sub">An international biomedicine & biotechnology journal</title>
<title level="j" type="abbrev">J. Zhejiang Univ. Sci. B</title>
<idno type="ISSN">1673-1581</idno>
<idno type="eISSN">1862-1783</idno>
<imprint><publisher>SP Zhejiang University Press</publisher>
<pubPlace>Heidelberg</pubPlace>
<date type="published" when="2008-09-01">2008-09-01</date>
<biblScope unit="volume">9</biblScope>
<biblScope unit="issue">9</biblScope>
<biblScope unit="page" from="667">667</biblScope>
<biblScope unit="page" to="674">674</biblScope>
</imprint>
<idno type="ISSN">1673-1581</idno>
</series>
</biblStruct>
</sourceDesc>
<seriesStmt><idno type="ISSN">1673-1581</idno>
</seriesStmt>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Begomovirus</term>
<term>Bioinformatics</term>
<term>Evolution</term>
<term>Synonymous codon usage</term>
</keywords>
</textClass>
<langUsage><language ident="en">en</language>
</langUsage>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml: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.</div>
</front>
</TEI>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/SrasV1/Data/Main/Merge
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 003528 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Merge/biblio.hfd -nk 003528 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Sante |area= SrasV1 |flux= Main |étape= Merge |type= RBID |clé= ISTEX:4CDFC1A8C4B94938FBC48807943F99188BFC8FBE |texte= Analysis of synonymous codon usage and evolution of begomoviruses }}
This area was generated with Dilib version V0.6.33. |