Analysis of synonymous codon usage in foot-and-mouth disease virus
Identifieur interne : 001510 ( Istex/Corpus ); précédent : 001509; suivant : 001511Analysis of synonymous codon usage in foot-and-mouth disease virus
Auteurs : Jian-Hua Zhou ; Jie Zhang ; Hao-Tai Chen ; Li-Na Ma ; Yong-Sheng LiuSource :
- Veterinary Research Communications [ 0165-7380 ] ; 2010-04-01.
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Abstract
Abstract: In this study, we calculate the relative synonymous codon usage (RSCU) values and codon usage bias (CUB) values to carry out a comparative analysis of codon usage pattern for open reading frames (ORFs) among 85 samples which belong to all seven serotypes of foot-and-mouth disease virus (FMDV). Although the degree of CUB for ORFs is a relatively slight, there is a significant variation for CUB among different serotypes, which is mainly determined by codon usage pattern depending on RSCU. By comparison with RSCU values for all samples, although RSCU values fail to show the relationship of specific-lineage serotype, there are two main genetic populations existing in FMDV, namely (i) serotypes Asia 1, A, C &O; (ii) serotypes SAT 1, 2 & 3. This interesting characteristic may be formed by the mechanism of RNA virus recombination. The analysis of quantitative & qualitative evaluation based on CUB indicates interesting characteristic of codon usage, which suggests that more FMDV genome diversity may exist in specific-lineage serotypes rather than exist randomly. Furthermore, the relationship between amino acids and codon usage pattern indicates that mutation pressure rather than translational selection in nature is the important determinant of the codon usage bias observed. Our work might give some sight into some characteristics of FMDV ORF and some evolutionary information of this virus.
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DOI: 10.1007/s11259-010-9359-4
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China</mods:affiliation></affiliation></author><author><name sortKey="Chen, Hao Tai" sort="Chen, Hao Tai" uniqKey="Chen H" first="Hao-Tai" last="Chen">Hao-Tai Chen</name><affiliation><mods:affiliation>Key Laboratory of Animal Virology of Ministry of Agriculture, State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 730046, Lanzhou, China</mods:affiliation></affiliation></author><author><name sortKey="Ma, Li Na" sort="Ma, Li Na" uniqKey="Ma L" first="Li-Na" last="Ma">Li-Na Ma</name><affiliation><mods:affiliation>Key Laboratory of Animal Virology of Ministry of Agriculture, State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 730046, Lanzhou, China</mods:affiliation></affiliation></author><author><name sortKey="Liu, Yong Sheng" sort="Liu, Yong Sheng" uniqKey="Liu Y" first="Yong-Sheng" last="Liu">Yong-Sheng Liu</name><affiliation><mods:affiliation>Key Laboratory of Animal Virology of Ministry of Agriculture, State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 730046, Lanzhou, China</mods:affiliation></affiliation><affiliation><mods:affiliation>E-mail: liuyongshengvip@sina.com.cn</mods:affiliation></affiliation></author></analytic><monogr></monogr><series><title level="j">Veterinary Research Communications</title><title level="j" type="sub">An International Journal Publishing Topical Reviews and Research Articles on all Aspects of the Veterinary Sciences</title><title level="j" type="abbrev">Vet Res Commun</title><idno type="ISSN">0165-7380</idno><idno type="eISSN">1573-7446</idno><imprint><publisher>Springer Netherlands</publisher><pubPlace>Dordrecht</pubPlace><date type="published" when="2010-04-01">2010-04-01</date><biblScope unit="volume">34</biblScope><biblScope unit="issue">4</biblScope><biblScope unit="page" from="393">393</biblScope><biblScope unit="page" to="404">404</biblScope></imprint><idno type="ISSN">0165-7380</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0165-7380</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Codon usage bias</term><term>Codon usage pattern</term><term>Foot-and-mouth disease virus</term><term>Genetic population</term><term>Relative synonymous codon usage</term></keywords></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Abstract: In this study, we calculate the relative synonymous codon usage (RSCU) values and codon usage bias (CUB) values to carry out a comparative analysis of codon usage pattern for open reading frames (ORFs) among 85 samples which belong to all seven serotypes of foot-and-mouth disease virus (FMDV). Although the degree of CUB for ORFs is a relatively slight, there is a significant variation for CUB among different serotypes, which is mainly determined by codon usage pattern depending on RSCU. By comparison with RSCU values for all samples, although RSCU values fail to show the relationship of specific-lineage serotype, there are two main genetic populations existing in FMDV, namely (i) serotypes Asia 1, A, C &O; (ii) serotypes SAT 1, 2 & 3. This interesting characteristic may be formed by the mechanism of RNA virus recombination. The analysis of quantitative & qualitative evaluation based on CUB indicates interesting characteristic of codon usage, which suggests that more FMDV genome diversity may exist in specific-lineage serotypes rather than exist randomly. Furthermore, the relationship between amino acids and codon usage pattern indicates that mutation pressure rather than translational selection in nature is the important determinant of the codon usage bias observed. Our work might give some sight into some characteristics of FMDV ORF and some evolutionary information of this virus.</div></front></TEI><istex><corpusName>springer-journals</corpusName><author><json:item><name>Jian-Hua Zhou</name><affiliations><json:string>Key Laboratory of Animal Virology of Ministry of Agriculture, State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 730046, Lanzhou, China</json:string><json:string>E-mail: zhoujianhuazjh@163.com</json:string></affiliations></json:item><json:item><name>Jie Zhang</name><affiliations><json:string>Key Laboratory of Animal Virology of Ministry of Agriculture, State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 730046, Lanzhou, China</json:string></affiliations></json:item><json:item><name>Hao-Tai Chen</name><affiliations><json:string>Key Laboratory of Animal Virology of Ministry of Agriculture, State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 730046, Lanzhou, China</json:string></affiliations></json:item><json:item><name>Li-Na Ma</name><affiliations><json:string>Key Laboratory of Animal Virology of Ministry of Agriculture, State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 730046, Lanzhou, China</json:string></affiliations></json:item><json:item><name>Yong-Sheng Liu</name><affiliations><json:string>Key Laboratory of Animal Virology of Ministry of Agriculture, State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 730046, Lanzhou, China</json:string><json:string>E-mail: liuyongshengvip@sina.com.cn</json:string></affiliations></json:item></author><subject><json:item><lang><json:string>eng</json:string></lang><value>Foot-and-mouth disease virus</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>Relative synonymous codon usage</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>Codon usage bias</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>Codon usage pattern</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>Genetic population</value></json:item></subject><articleId><json:string>9359</json:string><json:string>s11259-010-9359-4</json:string></articleId><arkIstex>ark:/67375/VQC-F8DVQNFT-2</arkIstex><language><json:string>eng</json:string></language><originalGenre><json:string>BriefCommunication</json:string></originalGenre><abstract>Abstract: In this study, we calculate the relative synonymous codon usage (RSCU) values and codon usage bias (CUB) values to carry out a comparative analysis of codon usage pattern for open reading frames (ORFs) among 85 samples which belong to all seven serotypes of foot-and-mouth disease virus (FMDV). Although the degree of CUB for ORFs is a relatively slight, there is a significant variation for CUB among different serotypes, which is mainly determined by codon usage pattern depending on RSCU. By comparison with RSCU values for all samples, although RSCU values fail to show the relationship of specific-lineage serotype, there are two main genetic populations existing in FMDV, namely (i) serotypes Asia 1, A, C &O; (ii) serotypes SAT 1, 2 & 3. This interesting characteristic may be formed by the mechanism of RNA virus recombination. The analysis of quantitative & qualitative evaluation based on CUB indicates interesting characteristic of codon usage, which suggests that more FMDV genome diversity may exist in specific-lineage serotypes rather than exist randomly. Furthermore, the relationship between amino acids and codon usage pattern indicates that mutation pressure rather than translational selection in nature is the important determinant of the codon usage bias observed. 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Although the degree of CUB for ORFs is a relatively slight, there is a significant variation for CUB among different serotypes, which is mainly determined by codon usage pattern depending on RSCU. By comparison with RSCU values for all samples, although RSCU values fail to show the relationship of specific-lineage serotype, there are two main genetic populations existing in FMDV, namely (i) serotypes Asia 1, A, C &O; (ii) serotypes SAT 1, 2 & 3. This interesting characteristic may be formed by the mechanism of RNA virus recombination. The analysis of quantitative & qualitative evaluation based on CUB indicates interesting characteristic of codon usage, which suggests that more FMDV genome diversity may exist in specific-lineage serotypes rather than exist randomly. Furthermore, the relationship between amino acids and codon usage pattern indicates that mutation pressure rather than translational selection in nature is the important determinant of the codon usage bias observed. 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Communication</ArticleCategory><ArticleFirstPage>393</ArticleFirstPage><ArticleLastPage>404</ArticleLastPage><ArticleHistory><RegistrationDate><Year>2010</Year><Month>3</Month><Day>30</Day></RegistrationDate><Accepted><Year>2010</Year><Month>3</Month><Day>29</Day></Accepted><OnlineDate><Year>2010</Year><Month>4</Month><Day>28</Day></OnlineDate></ArticleHistory><ArticleCopyright><CopyrightHolderName>Springer Science+Business Media B.V.</CopyrightHolderName><CopyrightYear>2010</CopyrightYear></ArticleCopyright><ArticleGrants Type="Regular"><MetadataGrant Grant="OpenAccess"></MetadataGrant><AbstractGrant Grant="OpenAccess"></AbstractGrant><BodyPDFGrant Grant="Restricted"></BodyPDFGrant><BodyHTMLGrant Grant="Restricted"></BodyHTMLGrant><BibliographyGrant Grant="Restricted"></BibliographyGrant><ESMGrant Grant="Restricted"></ESMGrant></ArticleGrants></ArticleInfo><ArticleHeader><AuthorGroup><Author AffiliationIDS="Aff1"><AuthorName DisplayOrder="Western"><GivenName>Jian-Hua</GivenName><FamilyName>Zhou</FamilyName></AuthorName><Contact><Email>zhoujianhuazjh@163.com</Email></Contact></Author><Author AffiliationIDS="Aff1"><AuthorName DisplayOrder="Western"><GivenName>Jie</GivenName><FamilyName>Zhang</FamilyName></AuthorName></Author><Author AffiliationIDS="Aff1"><AuthorName DisplayOrder="Western"><GivenName>Hao-Tai</GivenName><FamilyName>Chen</FamilyName></AuthorName></Author><Author AffiliationIDS="Aff1"><AuthorName DisplayOrder="Western"><GivenName>Li-Na</GivenName><FamilyName>Ma</FamilyName></AuthorName></Author><Author AffiliationIDS="Aff1" CorrespondingAffiliationID="Aff1"><AuthorName DisplayOrder="Western"><GivenName>Yong-Sheng</GivenName><FamilyName>Liu</FamilyName></AuthorName><Contact><Phone>+86-931-8342166</Phone><Fax>+86-931-8340977</Fax><Email>liuyongshengvip@sina.com.cn</Email></Contact></Author><Affiliation ID="Aff1"><OrgDivision>Key Laboratory of Animal Virology of Ministry of Agriculture, State Key Laboratory of Veterinary Etiological Biology</OrgDivision><OrgName>Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences</OrgName><OrgAddress><City>Lanzhou</City><Postcode>730046</Postcode><Country Code="CN">China</Country></OrgAddress></Affiliation></AuthorGroup><Abstract ID="Abs1" Language="En" OutputMedium="All"><Heading>Abstract</Heading><Para>In this study, we calculate the relative synonymous codon usage (RSCU) values and codon usage bias (CUB) values to carry out a comparative analysis of codon usage pattern for open reading frames (ORFs) among 85 samples which belong to all seven serotypes of foot-and-mouth disease virus (FMDV). Although the degree of CUB for ORFs is a relatively slight, there is a significant variation for CUB among different serotypes, which is mainly determined by codon usage pattern depending on RSCU. By comparison with RSCU values for all samples, although RSCU values fail to show the relationship of specific-lineage serotype, there are two main genetic populations existing in FMDV, namely (i) serotypes Asia 1, A, C &O; (ii) serotypes SAT 1, 2 & 3. This interesting characteristic may be formed by the mechanism of RNA virus recombination. The analysis of quantitative & qualitative evaluation based on CUB indicates interesting characteristic of codon usage, which suggests that more FMDV genome diversity may exist in specific-lineage serotypes rather than exist randomly. Furthermore, the relationship between amino acids and codon usage pattern indicates that mutation pressure rather than translational selection in nature is the important determinant of the codon usage bias observed. Our work might give some sight into some characteristics of FMDV ORF and some evolutionary information of this virus.</Para></Abstract><KeywordGroup Language="En" OutputMedium="All"><Heading>Keywords</Heading><Keyword>Foot-and-mouth disease virus</Keyword><Keyword>Relative synonymous codon usage</Keyword><Keyword>Codon usage bias</Keyword><Keyword>Codon usage pattern</Keyword><Keyword>Genetic population</Keyword></KeywordGroup></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 in foot-and-mouth disease virus</title></titleInfo><titleInfo type="alternative" contentType="CDATA"><title>Analysis of synonymous codon usage in foot-and-mouth disease virus</title></titleInfo><name type="personal"><namePart type="given">Jian-Hua</namePart><namePart type="family">Zhou</namePart><affiliation>Key Laboratory of Animal Virology of Ministry of Agriculture, State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 730046, Lanzhou, China</affiliation><affiliation>E-mail: zhoujianhuazjh@163.com</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Jie</namePart><namePart type="family">Zhang</namePart><affiliation>Key Laboratory of Animal Virology of Ministry of Agriculture, State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 730046, Lanzhou, China</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Hao-Tai</namePart><namePart type="family">Chen</namePart><affiliation>Key Laboratory of Animal Virology of Ministry of Agriculture, State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 730046, Lanzhou, China</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Li-Na</namePart><namePart type="family">Ma</namePart><affiliation>Key Laboratory of Animal Virology of Ministry of Agriculture, State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 730046, Lanzhou, China</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal" displayLabel="corresp"><namePart type="given">Yong-Sheng</namePart><namePart type="family">Liu</namePart><affiliation>Key Laboratory of Animal Virology of Ministry of Agriculture, State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 730046, Lanzhou, China</affiliation><affiliation>E-mail: liuyongshengvip@sina.com.cn</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="brief-communication" displayLabel="BriefCommunication" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-S9SX2MFS-0">brief-communication</genre><originInfo><publisher>Springer Netherlands</publisher><place><placeTerm type="text">Dordrecht</placeTerm></place><dateIssued encoding="w3cdtf">2010-04-01</dateIssued><copyrightDate encoding="w3cdtf">2010</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><abstract lang="en">Abstract: In this study, we calculate the relative synonymous codon usage (RSCU) values and codon usage bias (CUB) values to carry out a comparative analysis of codon usage pattern for open reading frames (ORFs) among 85 samples which belong to all seven serotypes of foot-and-mouth disease virus (FMDV). Although the degree of CUB for ORFs is a relatively slight, there is a significant variation for CUB among different serotypes, which is mainly determined by codon usage pattern depending on RSCU. By comparison with RSCU values for all samples, although RSCU values fail to show the relationship of specific-lineage serotype, there are two main genetic populations existing in FMDV, namely (i) serotypes Asia 1, A, C &O; (ii) serotypes SAT 1, 2 & 3. This interesting characteristic may be formed by the mechanism of RNA virus recombination. The analysis of quantitative & qualitative evaluation based on CUB indicates interesting characteristic of codon usage, which suggests that more FMDV genome diversity may exist in specific-lineage serotypes rather than exist randomly. Furthermore, the relationship between amino acids and codon usage pattern indicates that mutation pressure rather than translational selection in nature is the important determinant of the codon usage bias observed. Our work might give some sight into some characteristics of FMDV ORF and some evolutionary information of this virus.</abstract><note>Short Communication</note><subject lang="en"><genre>Keywords</genre><topic>Foot-and-mouth disease virus</topic><topic>Relative synonymous codon usage</topic><topic>Codon usage bias</topic><topic>Codon usage pattern</topic><topic>Genetic population</topic></subject><relatedItem type="host"><titleInfo><title>Veterinary Research Communications</title><subTitle>An International Journal Publishing Topical Reviews and Research Articles on all Aspects of the Veterinary Sciences</subTitle></titleInfo><titleInfo type="abbreviated"><title>Vet Res Commun</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">2010-05-09</dateIssued><copyrightDate encoding="w3cdtf">2010</copyrightDate></originInfo><subject><genre>Life Sciences</genre><topic>Veterinary Medicine</topic><topic>Zoology</topic></subject><identifier type="ISSN">0165-7380</identifier><identifier type="eISSN">1573-7446</identifier><identifier type="JournalID">11259</identifier><identifier type="IssueArticleCount">10</identifier><identifier type="VolumeIssueCount">8</identifier><part><date>2010</date><detail type="volume"><number>34</number><caption>vol.</caption></detail><detail type="issue"><number>4</number><caption>no.</caption></detail><extent unit="pages"><start>393</start><end>404</end></extent></part><recordInfo><recordOrigin>Springer Science+Business Media B.V., 2010</recordOrigin></recordInfo></relatedItem><identifier type="istex">F90798B5A76E9B3509D2D57315DFF5F0E881A798</identifier><identifier type="ark">ark:/67375/VQC-F8DVQNFT-2</identifier><identifier type="DOI">10.1007/s11259-010-9359-4</identifier><identifier type="ArticleID">9359</identifier><identifier type="ArticleID">s11259-010-9359-4</identifier><accessCondition type="use and reproduction" contentType="copyright">Springer Science+Business Media B.V., 2010</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>Springer Science+Business Media B.V., 2010</recordOrigin></recordInfo></mods><json:item><extension>json</extension><original>false</original><mimetype>application/json</mimetype><uri>https://api.istex.fr/ark:/67375/VQC-F8DVQNFT-2/record.json</uri></json:item></metadata><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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