Evaluation of Codon Biology in Citrus and Poncirus trifoliata Based on Genomic Features and Frame Corrected Expressed Sequence Tags
Identifieur interne : 000E58 ( Main/Exploration ); précédent : 000E57; suivant : 000E59Evaluation of Codon Biology in Citrus and Poncirus trifoliata Based on Genomic Features and Frame Corrected Expressed Sequence Tags
Auteurs : Touqeer Ahmad [République populaire de Chine] ; Gaurav Sablok [Italie] ; Tatiana V. Tatarinova [Royaume-Uni] ; Qiang Xu [République populaire de Chine] ; Xiu-Xin Deng [République populaire de Chine] ; Wen-Wu Guo [République populaire de Chine]Source :
- DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes [ 1340-2838 ] ; 2013.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Codon.
- genetics : Citrus, Poncirus.
- Conserved Sequence, Expressed Sequence Tags, Gene Expression Regulation, Plant, Genetic Variation, Genome, Plant, Genomics.
Abstract
Url:
DOI: 10.1093/dnares/dss039
PubMed: 23315666
PubMed Central: 3628444
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Evaluation of Codon Biology in <italic>Citrus</italic> and <italic>Poncirus trifoliata</italic> Based on Genomic Features and Frame Corrected Expressed Sequence Tags</title><author><name sortKey="Ahmad, Touqeer" sort="Ahmad, Touqeer" uniqKey="Ahmad T" first="Touqeer" last="Ahmad">Touqeer Ahmad</name><affiliation wicri:level="1"><nlm:aff id="af1"><addr-line>Key Laboratory of Horticultural Plant Biology (MOE)</addr-line>,<institution>Huazhong Agricultural University</institution>,<addr-line>Wuhan 430070</addr-line>,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Sablok, Gaurav" sort="Sablok, Gaurav" uniqKey="Sablok G" first="Gaurav" last="Sablok">Gaurav Sablok</name><affiliation wicri:level="1"><nlm:aff id="af2"><institution>Research and Innovation Center, Fondazione Edmund Mach (FEM), Istituto Agrario San Michele (IASMA)</institution>,<addr-line>Via Mach 1., San Michele all'Adige, Trentino 38010</addr-line>,<country>Italy</country></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Tatarinova, Tatiana V" sort="Tatarinova, Tatiana V" uniqKey="Tatarinova T" first="Tatiana V." last="Tatarinova">Tatiana V. Tatarinova</name><affiliation wicri:level="1"><nlm:aff id="af3"><addr-line>Glamorgan Computational Biology Group, University of Glamorgan, Pontypridd CF37 1DL</addr-line>,<country>UK</country></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Xu, Qiang" sort="Xu, Qiang" uniqKey="Xu Q" first="Qiang" last="Xu">Qiang Xu</name><affiliation wicri:level="1"><nlm:aff id="af1"><addr-line>Key Laboratory of Horticultural Plant Biology (MOE)</addr-line>,<institution>Huazhong Agricultural University</institution>,<addr-line>Wuhan 430070</addr-line>,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Deng, Xiu Xin" sort="Deng, Xiu Xin" uniqKey="Deng X" first="Xiu-Xin" last="Deng">Xiu-Xin Deng</name><affiliation wicri:level="1"><nlm:aff id="af1"><addr-line>Key Laboratory of Horticultural Plant Biology (MOE)</addr-line>,<institution>Huazhong Agricultural University</institution>,<addr-line>Wuhan 430070</addr-line>,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Guo, Wen Wu" sort="Guo, Wen Wu" uniqKey="Guo W" first="Wen-Wu" last="Guo">Wen-Wu Guo</name><affiliation wicri:level="1"><nlm:aff id="af1"><addr-line>Key Laboratory of Horticultural Plant Biology (MOE)</addr-line>,<institution>Huazhong Agricultural University</institution>,<addr-line>Wuhan 430070</addr-line>,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">23315666</idno><idno type="pmc">3628444</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3628444</idno><idno type="RBID">PMC:3628444</idno><idno type="doi">10.1093/dnares/dss039</idno><date when="2013">2013</date><idno type="wicri:Area/Pmc/Corpus">000E72</idno><idno type="wicri:Area/Pmc/Curation">000E71</idno><idno type="wicri:Area/Pmc/Checkpoint">000A81</idno><idno type="wicri:source">PubMed</idno><idno type="wicri:Area/PubMed/Corpus">000477</idno><idno type="wicri:Area/PubMed/Curation">000477</idno><idno type="wicri:Area/PubMed/Checkpoint">000477</idno><idno type="wicri:Area/Ncbi/Merge">001193</idno><idno type="wicri:Area/Ncbi/Curation">001193</idno><idno type="wicri:Area/Ncbi/Checkpoint">001193</idno><idno type="wicri:doubleKey">1340-2838:2013:Ahmad T:evaluation:of:codon</idno><idno type="wicri:Area/Main/Merge">000E62</idno><idno type="wicri:Area/Main/Curation">000E58</idno><idno type="wicri:Area/Main/Exploration">000E58</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Evaluation of Codon Biology in <italic>Citrus</italic> and <italic>Poncirus trifoliata</italic> Based on Genomic Features and Frame Corrected Expressed Sequence Tags</title><author><name sortKey="Ahmad, Touqeer" sort="Ahmad, Touqeer" uniqKey="Ahmad T" first="Touqeer" last="Ahmad">Touqeer Ahmad</name><affiliation wicri:level="1"><nlm:aff id="af1"><addr-line>Key Laboratory of Horticultural Plant Biology (MOE)</addr-line>,<institution>Huazhong Agricultural University</institution>,<addr-line>Wuhan 430070</addr-line>,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Sablok, Gaurav" sort="Sablok, Gaurav" uniqKey="Sablok G" first="Gaurav" last="Sablok">Gaurav Sablok</name><affiliation wicri:level="1"><nlm:aff id="af2"><institution>Research and Innovation Center, Fondazione Edmund Mach (FEM), Istituto Agrario San Michele (IASMA)</institution>,<addr-line>Via Mach 1., San Michele all'Adige, Trentino 38010</addr-line>,<country>Italy</country></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Tatarinova, Tatiana V" sort="Tatarinova, Tatiana V" uniqKey="Tatarinova T" first="Tatiana V." last="Tatarinova">Tatiana V. Tatarinova</name><affiliation wicri:level="1"><nlm:aff id="af3"><addr-line>Glamorgan Computational Biology Group, University of Glamorgan, Pontypridd CF37 1DL</addr-line>,<country>UK</country></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Xu, Qiang" sort="Xu, Qiang" uniqKey="Xu Q" first="Qiang" last="Xu">Qiang Xu</name><affiliation wicri:level="1"><nlm:aff id="af1"><addr-line>Key Laboratory of Horticultural Plant Biology (MOE)</addr-line>,<institution>Huazhong Agricultural University</institution>,<addr-line>Wuhan 430070</addr-line>,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Deng, Xiu Xin" sort="Deng, Xiu Xin" uniqKey="Deng X" first="Xiu-Xin" last="Deng">Xiu-Xin Deng</name><affiliation wicri:level="1"><nlm:aff id="af1"><addr-line>Key Laboratory of Horticultural Plant Biology (MOE)</addr-line>,<institution>Huazhong Agricultural University</institution>,<addr-line>Wuhan 430070</addr-line>,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Guo, Wen Wu" sort="Guo, Wen Wu" uniqKey="Guo W" first="Wen-Wu" last="Guo">Wen-Wu Guo</name><affiliation wicri:level="1"><nlm:aff id="af1"><addr-line>Key Laboratory of Horticultural Plant Biology (MOE)</addr-line>,<institution>Huazhong Agricultural University</institution>,<addr-line>Wuhan 430070</addr-line>,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><series><title level="j">DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes</title><idno type="ISSN">1340-2838</idno><idno type="eISSN">1756-1663</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Citrus (genetics)</term><term>Codon (genetics)</term><term>Conserved Sequence</term><term>Expressed Sequence Tags</term><term>Gene Expression Regulation, Plant</term><term>Genetic Variation</term><term>Genome, Plant</term><term>Genomics</term><term>Poncirus (genetics)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Codon</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Citrus</term><term>Poncirus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Conserved Sequence</term><term>Expressed Sequence Tags</term><term>Gene Expression Regulation, Plant</term><term>Genetic Variation</term><term>Genome, Plant</term><term>Genomics</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><italic>Citrus</italic>, as one of the globally important fruit trees, has been an object of interest for understanding genetics and evolutionary process in fruit crops. Meta-analyses of 19 <italic>Citrus</italic> species, including 4 globally and economically important <italic>Citrus sinensis</italic>, <italic>Citrus clementina</italic>, <italic>Citrus reticulata</italic>, and 1 <italic>Citrus</italic> relative <italic>Poncirus trifoliata</italic>, were performed. We observed that codons ending with A- or T- at the wobble position were preferred in contrast to C- or G- ending codons, indicating a close association with AT richness of <italic>Citrus</italic> species and <italic>P. trifoliata</italic>. The present study postulates a large repertoire of a set of optimal codons for the <italic>Citrus</italic> genus and <italic>P. trifoliata</italic> and demonstrates that GCT and GGT are evolutionary conserved optimal codons. Our observation suggested that mutational bias is the dominating force in shaping the codon usage bias (CUB) in <italic>Citrus</italic> and <italic>P. trifoliata</italic>. Correspondence analysis (COA) revealed that the principal axis [axis 1; COA/relative synonymous codon usage (RSCU)] contributes only a minor portion (∼10.96%) of the recorded variance. In all analysed species, except <italic>P. trifoliata</italic>, Gravy and aromaticity played minor roles in resolving CUB. Compositional constraints were found to be strongly associated with the amino acid signatures in <italic>Citrus</italic> species and <italic>P. trifoliata</italic>. Our present analysis postulates compositional constraints in <italic>Citrus</italic> species and <italic>P. trifoliata</italic> and plausible role of the stress with GC<sub>3</sub> and coevolution pattern of amino acid.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Serres Giardi, L" uniqKey="Serres Giardi L">L. Serres-Giardi</name></author><author><name sortKey="Belkhir, K" uniqKey="Belkhir K">K. 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Sankararamakrishnan</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Italie</li><li>Royaume-Uni</li><li>République populaire de Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Ahmad, Touqeer" sort="Ahmad, Touqeer" uniqKey="Ahmad T" first="Touqeer" last="Ahmad">Touqeer Ahmad</name></noRegion><name sortKey="Deng, Xiu Xin" sort="Deng, Xiu Xin" uniqKey="Deng X" first="Xiu-Xin" last="Deng">Xiu-Xin Deng</name><name sortKey="Guo, Wen Wu" sort="Guo, Wen Wu" uniqKey="Guo W" first="Wen-Wu" last="Guo">Wen-Wu Guo</name><name sortKey="Xu, Qiang" sort="Xu, Qiang" uniqKey="Xu Q" first="Qiang" last="Xu">Qiang Xu</name></country><country name="Italie"><noRegion><name sortKey="Sablok, Gaurav" sort="Sablok, Gaurav" uniqKey="Sablok G" first="Gaurav" last="Sablok">Gaurav Sablok</name></noRegion></country><country name="Royaume-Uni"><noRegion><name sortKey="Tatarinova, Tatiana V" sort="Tatarinova, Tatiana V" uniqKey="Tatarinova T" first="Tatiana V." last="Tatarinova">Tatiana V. 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