Annotation and re-sequencing of genes from de novo transcriptome assembly of Abies alba (Pinaceae)1
Identifieur interne : 000057 ( France/Analysis ); précédent : 000056; suivant : 000058Annotation and re-sequencing of genes from de novo transcriptome assembly of Abies alba (Pinaceae)1
Auteurs : Anna M. Roschanski [Allemagne] ; Bruno Fady [France] ; Birgit Ziegenhagen [Allemagne] ; Sascha Liepelt [Allemagne]Source :
- Applications in Plant Sciences [ 2168-0450 ] ; 2013.
Abstract
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Url:
DOI: 10.3732/apps.1200179
PubMed: 25202477
PubMed Central: 4105350
Affiliations:
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PMC:4105350Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Annotation and re-sequencing of genes from de novo transcriptome assembly of <italic>Abies alba</italic> (Pinaceae)<xref ref-type="author-notes" rid="fn1"><sup>1</sup></xref></title><author><name sortKey="Roschanski, Anna M" sort="Roschanski, Anna M" uniqKey="Roschanski A" first="Anna M." last="Roschanski">Anna M. Roschanski</name><affiliation wicri:level="3"><nlm:aff id="aff2">University of Marburg, Faculty of Biology, Conservation Biology, Karl-von-Frisch-Strasse 35032 Marburg, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>University of Marburg, Faculty of Biology, Conservation Biology, Karl-von-Frisch-Strasse 35032 Marburg</wicri:regionArea><placeName><region type="land" nuts="1">Hesse (Land)</region><region type="district" nuts="2">District de Giessen</region><settlement type="city">Marbourg</settlement></placeName></affiliation></author><author><name sortKey="Fady, Bruno" sort="Fady, Bruno" uniqKey="Fady B" first="Bruno" last="Fady">Bruno Fady</name><affiliation wicri:level="3"><nlm:aff id="aff3">INRA, UR629, Ecologie des Forêts Méditerranéennes (URFM), 84914 Avignon, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>INRA, UR629, Ecologie des Forêts Méditerranéennes (URFM), 84914 Avignon</wicri:regionArea><placeName><region type="region" nuts="2">Provence-Alpes-Côte d'Azur</region><settlement type="city">Avignon</settlement></placeName></affiliation></author><author><name sortKey="Ziegenhagen, Birgit" sort="Ziegenhagen, Birgit" uniqKey="Ziegenhagen B" first="Birgit" last="Ziegenhagen">Birgit Ziegenhagen</name><affiliation wicri:level="3"><nlm:aff id="aff2">University of Marburg, Faculty of Biology, Conservation Biology, Karl-von-Frisch-Strasse 35032 Marburg, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>University of Marburg, Faculty of Biology, Conservation Biology, Karl-von-Frisch-Strasse 35032 Marburg</wicri:regionArea><placeName><region type="land" nuts="1">Hesse (Land)</region><region type="district" nuts="2">District de Giessen</region><settlement type="city">Marbourg</settlement></placeName></affiliation></author><author><name sortKey="Liepelt, Sascha" sort="Liepelt, Sascha" uniqKey="Liepelt S" first="Sascha" last="Liepelt">Sascha Liepelt</name><affiliation wicri:level="3"><nlm:aff id="aff2">University of Marburg, Faculty of Biology, Conservation Biology, Karl-von-Frisch-Strasse 35032 Marburg, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>University of Marburg, Faculty of Biology, Conservation Biology, Karl-von-Frisch-Strasse 35032 Marburg</wicri:regionArea><placeName><region type="land" nuts="1">Hesse (Land)</region><region type="district" nuts="2">District de Giessen</region><settlement type="city">Marbourg</settlement></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25202477</idno><idno type="pmc">4105350</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4105350</idno><idno type="RBID">PMC:4105350</idno><idno type="doi">10.3732/apps.1200179</idno><date when="2013">2013</date><idno type="wicri:Area/Pmc/Corpus">000D91</idno><idno type="wicri:Area/Pmc/Curation">000D90</idno><idno type="wicri:Area/Pmc/Checkpoint">000B52</idno><idno type="wicri:Area/Ncbi/Merge">001829</idno><idno type="wicri:Area/Ncbi/Curation">001829</idno><idno type="wicri:Area/Ncbi/Checkpoint">001829</idno><idno type="wicri:Area/Main/Merge">000F62</idno><idno type="wicri:Area/Main/Curation">000F57</idno><idno type="wicri:Area/Main/Exploration">000F57</idno><idno type="wicri:Area/France/Extraction">000057</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Annotation and re-sequencing of genes from de novo transcriptome assembly of <italic>Abies alba</italic> (Pinaceae)<xref ref-type="author-notes" rid="fn1"><sup>1</sup></xref></title><author><name sortKey="Roschanski, Anna M" sort="Roschanski, Anna M" uniqKey="Roschanski A" first="Anna M." last="Roschanski">Anna M. Roschanski</name><affiliation wicri:level="3"><nlm:aff id="aff2">University of Marburg, Faculty of Biology, Conservation Biology, Karl-von-Frisch-Strasse 35032 Marburg, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>University of Marburg, Faculty of Biology, Conservation Biology, Karl-von-Frisch-Strasse 35032 Marburg</wicri:regionArea><placeName><region type="land" nuts="1">Hesse (Land)</region><region type="district" nuts="2">District de Giessen</region><settlement type="city">Marbourg</settlement></placeName></affiliation></author><author><name sortKey="Fady, Bruno" sort="Fady, Bruno" uniqKey="Fady B" first="Bruno" last="Fady">Bruno Fady</name><affiliation wicri:level="3"><nlm:aff id="aff3">INRA, UR629, Ecologie des Forêts Méditerranéennes (URFM), 84914 Avignon, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>INRA, UR629, Ecologie des Forêts Méditerranéennes (URFM), 84914 Avignon</wicri:regionArea><placeName><region type="region" nuts="2">Provence-Alpes-Côte d'Azur</region><settlement type="city">Avignon</settlement></placeName></affiliation></author><author><name sortKey="Ziegenhagen, Birgit" sort="Ziegenhagen, Birgit" uniqKey="Ziegenhagen B" first="Birgit" last="Ziegenhagen">Birgit Ziegenhagen</name><affiliation wicri:level="3"><nlm:aff id="aff2">University of Marburg, Faculty of Biology, Conservation Biology, Karl-von-Frisch-Strasse 35032 Marburg, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>University of Marburg, Faculty of Biology, Conservation Biology, Karl-von-Frisch-Strasse 35032 Marburg</wicri:regionArea><placeName><region type="land" nuts="1">Hesse (Land)</region><region type="district" nuts="2">District de Giessen</region><settlement type="city">Marbourg</settlement></placeName></affiliation></author><author><name sortKey="Liepelt, Sascha" sort="Liepelt, Sascha" uniqKey="Liepelt S" first="Sascha" last="Liepelt">Sascha Liepelt</name><affiliation wicri:level="3"><nlm:aff id="aff2">University of Marburg, Faculty of Biology, Conservation Biology, Karl-von-Frisch-Strasse 35032 Marburg, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>University of Marburg, Faculty of Biology, Conservation Biology, Karl-von-Frisch-Strasse 35032 Marburg</wicri:regionArea><placeName><region type="land" nuts="1">Hesse (Land)</region><region type="district" nuts="2">District de Giessen</region><settlement type="city">Marbourg</settlement></placeName></affiliation></author></analytic><series><title level="j">Applications in Plant Sciences</title><idno type="eISSN">2168-0450</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>• <italic>Premise of the study:</italic> We present a protocol for the annotation of transcriptome sequence data and the identification of candidate genes therein using the example of the nonmodel conifer <italic>Abies alba</italic>.</p><p>• <italic>Methods and Results:</italic> A normalized cDNA library was built from an <italic>A. alba</italic> seedling. The sequencing on a 454 platform yielded more than 1.5 million reads that were de novo assembled into 25149 contigs. Two complementary approaches were applied to annotate gene fragments that code for (1) well-known proteins and (2) proteins that are potentially adaptively relevant. Primer development and testing yielded 88 amplicons that could successfully be resequenced from genomic DNA.</p><p>• <italic>Conclusions:</italic> The annotation workflow offers an efficient way to identify potential adaptively relevant genes from the large quantity of transcriptome sequence data. The primer set presented should be prioritized for single-nucleotide polymorphism detection in adaptively relevant genes in <italic>A. alba</italic>.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Altschul, S F" uniqKey="Altschul S">S. F. Altschul</name></author><author><name sortKey="Gish, W" uniqKey="Gish W">W. 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Grahnen</name></author><author><name sortKey="Bankman, C W" uniqKey="Bankman C">C. W. Bankman</name></author><author><name sortKey="Buerkle, C A" uniqKey="Buerkle C">C. A. Buerkle</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Street, N R" uniqKey="Street N">N. R. Street</name></author><author><name sortKey="Skogstrom, O" uniqKey="Skogstrom O">O. Skogström</name></author><author><name sortKey="Sjodin, A" uniqKey="Sjodin A">A. Sjödin</name></author><author><name sortKey="Tucker, J" uniqKey="Tucker J">J. Tucker</name></author><author><name sortKey="Rodriguez Acosta, M" uniqKey="Rodriguez Acosta M">M. Rodríguez-Acosta</name></author><author><name sortKey="Nilsson, P" uniqKey="Nilsson P">P. Nilsson</name></author><author><name sortKey="Jansson, S" uniqKey="Jansson S">S. Jansson</name></author><author><name sortKey="Taylor, G" uniqKey="Taylor G">G. Taylor</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Allemagne</li><li>France</li></country><region><li>District de Giessen</li><li>Hesse (Land)</li><li>Provence-Alpes-Côte d'Azur</li></region><settlement><li>Avignon</li><li>Marbourg</li></settlement></list><tree><country name="Allemagne"><region name="Hesse (Land)"><name sortKey="Roschanski, Anna M" sort="Roschanski, Anna M" uniqKey="Roschanski A" first="Anna M." last="Roschanski">Anna M. Roschanski</name></region><name sortKey="Liepelt, Sascha" sort="Liepelt, Sascha" uniqKey="Liepelt S" first="Sascha" last="Liepelt">Sascha Liepelt</name><name sortKey="Ziegenhagen, Birgit" sort="Ziegenhagen, Birgit" uniqKey="Ziegenhagen B" first="Birgit" last="Ziegenhagen">Birgit Ziegenhagen</name></country><country name="France"><region name="Provence-Alpes-Côte d'Azur"><name sortKey="Fady, Bruno" sort="Fady, Bruno" uniqKey="Fady B" first="Bruno" last="Fady">Bruno Fady</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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