Comparative in silico analysis of EST-SSRs in angiosperm and gymnosperm tree genera
Identifieur interne : 000B64 ( Main/Exploration ); précédent : 000B63; suivant : 000B65Comparative in silico analysis of EST-SSRs in angiosperm and gymnosperm tree genera
Auteurs : Sonali Sachin Ranade [Suède] ; Yao-Cheng Lin [Belgique] ; Andrea Zuccolo [Italie] ; Yves Van De Peer [Belgique, Afrique du Sud] ; María Del Rosario García-Gil [Suède]Source :
- BMC Plant Biology [ 1471-2229 ] ; 2014.
Abstract
Simple Sequence Repeats (SSRs) derived from Expressed Sequence Tags (ESTs) belong to the expressed fraction of the genome and are important for gene regulation, recombination, DNA replication, cell cycle and mismatch repair. Here, we present a comparative analysis of the SSR motif distribution in the 5′UTR, ORF and 3′UTR fractions of ESTs across selected genera of woody trees representing gymnosperms (17 species from seven genera) and angiosperms (40 species from eight genera).
Our analysis supports a modest contribution of EST-SSR length to genome size in gymnosperms, while EST-SSR density was not associated with genome size in neither angiosperms nor gymnosperms. Multiple factors seem to have contributed to the lower abundance of EST-SSRs in gymnosperms that has resulted in a non-linear relationship with genome size diversity. The AG/CT motif was found to be the most abundant in SSRs of both angiosperms and gymnosperms, with a relative increase in AT/AT in the latter. Our data also reveals a higher abundance of hexamers across the gymnosperm genera.
Our analysis provides the foundation for future comparative studies at the species level to unravel the evolutionary processes that control the SSR genesis and divergence between angiosperm and gymnosperm tree species.
The online version of this article (doi:10.1186/s12870-014-0220-8) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12870-014-0220-8
PubMed: 25143005
PubMed Central: 4160553
Affiliations:
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Linussio 51, 33100 Udine, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Istituto di Genomica Applicata, Via J. Linussio 51, 33100 Udine</wicri:regionArea><wicri:noRegion>33100 Udine</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff4">Institute of Life Sciences, Scuola Superiore Sant’Anna, 56127 Pisa, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Institute of Life Sciences, Scuola Superiore Sant’Anna, 56127 Pisa</wicri:regionArea><placeName><settlement type="city">Pise</settlement><region nuts="2">Toscane</region></placeName></affiliation></author><author><name sortKey="Van De Peer, Yves" sort="Van De Peer, Yves" uniqKey="Van De Peer Y" first="Yves" last="Van De Peer">Yves Van De Peer</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent</wicri:regionArea><wicri:noRegion>9052 Ghent</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff5">Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria, 0028 South Africa</nlm:aff><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea>Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria</wicri:regionArea><wicri:noRegion>Pretoria</wicri:noRegion></affiliation></author><author><name sortKey="Garcia Gil, Maria Del Rosario" sort="Garcia Gil, Maria Del Rosario" uniqKey="Garcia Gil M" first="María Del Rosario" last="García-Gil">María Del Rosario García-Gil</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901-83 Umeå, Sweden</nlm:aff><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901-83 Umeå</wicri:regionArea><wicri:noRegion>SE-901-83 Umeå</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Plant Biology</title><idno type="eISSN">1471-2229</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Simple Sequence Repeats (SSRs) derived from Expressed Sequence Tags (ESTs) belong to the expressed fraction of the genome and are important for gene regulation, recombination, DNA replication, cell cycle and mismatch repair. Here, we present a comparative analysis of the SSR motif distribution in the 5′UTR, ORF and 3′UTR fractions of ESTs across selected genera of woody trees representing gymnosperms (17 species from seven genera) and angiosperms (40 species from eight genera).</p></sec><sec><title>Results</title><p>Our analysis supports a modest contribution of EST-SSR length to genome size in gymnosperms, while EST-SSR density was not associated with genome size in neither angiosperms nor gymnosperms. Multiple factors seem to have contributed to the lower abundance of EST-SSRs in gymnosperms that has resulted in a non-linear relationship with genome size diversity. The AG/CT motif was found to be the most abundant in SSRs of both angiosperms and gymnosperms, with a relative increase in AT/AT in the latter. Our data also reveals a higher abundance of hexamers across the gymnosperm genera.</p></sec><sec><title>Conclusions</title><p>Our analysis provides the foundation for future comparative studies at the species level to unravel the evolutionary processes that control the SSR genesis and divergence between angiosperm and gymnosperm tree species.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12870-014-0220-8) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Tautz, D" uniqKey="Tautz D">D Tautz</name></author><author><name sortKey="Renz, M" uniqKey="Renz M">M Renz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zane, L" uniqKey="Zane L">L Zane</name></author><author><name sortKey="Bargelloni, L" uniqKey="Bargelloni L">L 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Salin</name></author><author><name sortKey="Petit, Rj" uniqKey="Petit R">RJ Petit</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kim, Ts" uniqKey="Kim T">TS Kim</name></author><author><name sortKey="Booth, Jg" uniqKey="Booth J">JG Booth</name></author><author><name sortKey="Gauch, Hg" uniqKey="Gauch H">HG Gauch</name></author><author><name sortKey="Sun, Q" uniqKey="Sun Q">Q Sun</name></author><author><name sortKey="Park, J" uniqKey="Park J">J Park</name></author><author><name sortKey="Lee, Yh" uniqKey="Lee Y">YH Lee</name></author><author><name sortKey="Lee, K" uniqKey="Lee K">K Lee</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sun, Jx" uniqKey="Sun J">JX Sun</name></author><author><name sortKey="Mullikin, Jc" uniqKey="Mullikin J">JC Mullikin</name></author><author><name sortKey="Patterson, N" uniqKey="Patterson N">N Patterson</name></author><author><name sortKey="Reich, De" uniqKey="Reich D">DE Reich</name></author></analytic></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Afrique du Sud</li><li>Belgique</li><li>Italie</li><li>Suède</li></country><region><li>Toscane</li></region><settlement><li>Pise</li></settlement></list><tree><country name="Suède"><noRegion><name sortKey="Ranade, Sonali Sachin" sort="Ranade, Sonali Sachin" uniqKey="Ranade S" first="Sonali Sachin" last="Ranade">Sonali Sachin Ranade</name></noRegion><name sortKey="Garcia Gil, Maria Del Rosario" sort="Garcia Gil, Maria Del Rosario" uniqKey="Garcia Gil M" first="María Del Rosario" last="García-Gil">María Del Rosario García-Gil</name></country><country name="Belgique"><noRegion><name sortKey="Lin, Yao Cheng" sort="Lin, Yao Cheng" uniqKey="Lin Y" first="Yao-Cheng" last="Lin">Yao-Cheng Lin</name></noRegion><name sortKey="Van De Peer, Yves" sort="Van De Peer, Yves" uniqKey="Van De Peer Y" first="Yves" last="Van De Peer">Yves Van De Peer</name></country><country name="Italie"><noRegion><name sortKey="Zuccolo, Andrea" sort="Zuccolo, Andrea" uniqKey="Zuccolo A" first="Andrea" last="Zuccolo">Andrea Zuccolo</name></noRegion><name sortKey="Zuccolo, Andrea" sort="Zuccolo, Andrea" uniqKey="Zuccolo A" first="Andrea" last="Zuccolo">Andrea Zuccolo</name></country><country name="Afrique du Sud"><noRegion><name sortKey="Van De Peer, Yves" sort="Van De Peer, Yves" uniqKey="Van De Peer Y" first="Yves" last="Van De Peer">Yves Van De Peer</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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