Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses.
Identifieur interne : 003C13 ( Main/Exploration ); précédent : 003C12; suivant : 003C14Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses.
Auteurs : Helge Küster [Allemagne] ; Anke Becker ; Christian Firnhaber ; Natalija Hohnjec ; Katja Manthey ; Andreas M. Perlick ; Thomas Bekel ; Michael Dondrup ; Kolja Henckel ; Alexander Goesmann ; Folker Meyer ; Daniel Wipf ; Natalia Requena ; Ulrich Hildebrandt ; Rüdiger Hampp ; Uwe Nehls ; Franziska Krajinski ; Philipp Franken ; Alfred PühlerSource :
- Phytochemistry [ 0031-9422 ] ; 2007.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- genetics : Mycorrhizae, Symbiosis, Transcription, Genetic.
- methods : Computational Biology, Oligonucleotide Array Sequence Analysis.
- Expressed Sequence Tags.
Abstract
The great majority of terrestrial plants enters a beneficial arbuscular mycorrhiza (AM) or ectomycorrhiza (ECM) symbiosis with soil fungi. In the SPP 1084 "MolMyk: Molecular Basics of Mycorrhizal Symbioses", high-throughput EST-sequencing was performed to obtain snapshots of the plant and fungal transcriptome in mycorrhizal roots and in extraradical hyphae. To focus activities, the interactions between Medicago truncatula and Glomus intraradices as well as Populus tremula and Amanita muscaria were selected as models for AM and ECM symbioses, respectively. Together, almost, 20.000 expressed sequence tags (ESTs) were generated from different random and suppressive subtractive hybridization (SSH) cDNA libraries, providing a comprehensive overview of the mycorrhizal transcriptome. To automatically cluster and annotate EST-sequences, the BioMake and SAMS software tools were developed. In connection with the eNorthern software SteN, plant genes with a predicted mycorrhiza-induced expression were identified. To support experimental transcriptome profiling, macro- and microarray tools have been constructed for the two model mycorrhizae, based either on PCR-amplified cDNAs or 70mer oligonucleotides. These arrays were used to profile the transcriptome of AM and ECM roots under different conditions, and the data obtained were uploaded to the ArrayLIMS and EMMA databases that are designed to store and evaluate expression profiles from DNA arrays. Together, the EST- and transcriptome databases can be mined to identify candidate genes for targeted functional studies.
DOI: 10.1016/j.phytochem.2006.09.026
PubMed: 17081576
Affiliations:
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Helge.Kuester@Genetik.Uni-Bielefeld.DE</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute for Genome Research, Center for Biotechnology (CeBiTec), Universität Bielefeld, Universitätsstrasse 25, 33594 Bielefeld</wicri:regionArea><wicri:noRegion>33594 Bielefeld</wicri:noRegion><wicri:noRegion>33594 Bielefeld</wicri:noRegion><wicri:noRegion>33594 Bielefeld</wicri:noRegion></affiliation></author><author><name sortKey="Becker, Anke" sort="Becker, Anke" uniqKey="Becker A" first="Anke" last="Becker">Anke Becker</name></author><author><name sortKey="Firnhaber, Christian" sort="Firnhaber, Christian" uniqKey="Firnhaber C" first="Christian" last="Firnhaber">Christian Firnhaber</name></author><author><name sortKey="Hohnjec, Natalija" sort="Hohnjec, Natalija" uniqKey="Hohnjec N" first="Natalija" last="Hohnjec">Natalija Hohnjec</name></author><author><name sortKey="Manthey, Katja" sort="Manthey, Katja" uniqKey="Manthey K" first="Katja" last="Manthey">Katja Manthey</name></author><author><name sortKey="Perlick, Andreas M" sort="Perlick, Andreas M" uniqKey="Perlick A" first="Andreas M" last="Perlick">Andreas M. Perlick</name></author><author><name sortKey="Bekel, Thomas" sort="Bekel, Thomas" uniqKey="Bekel T" first="Thomas" last="Bekel">Thomas Bekel</name></author><author><name sortKey="Dondrup, Michael" sort="Dondrup, Michael" uniqKey="Dondrup M" first="Michael" last="Dondrup">Michael Dondrup</name></author><author><name sortKey="Henckel, Kolja" sort="Henckel, Kolja" uniqKey="Henckel K" first="Kolja" last="Henckel">Kolja Henckel</name></author><author><name sortKey="Goesmann, Alexander" sort="Goesmann, Alexander" uniqKey="Goesmann A" first="Alexander" last="Goesmann">Alexander Goesmann</name></author><author><name sortKey="Meyer, Folker" sort="Meyer, Folker" uniqKey="Meyer F" first="Folker" last="Meyer">Folker Meyer</name></author><author><name sortKey="Wipf, Daniel" sort="Wipf, Daniel" uniqKey="Wipf D" first="Daniel" last="Wipf">Daniel Wipf</name></author><author><name sortKey="Requena, Natalia" sort="Requena, Natalia" uniqKey="Requena N" first="Natalia" last="Requena">Natalia Requena</name></author><author><name sortKey="Hildebrandt, Ulrich" sort="Hildebrandt, Ulrich" uniqKey="Hildebrandt U" first="Ulrich" last="Hildebrandt">Ulrich Hildebrandt</name></author><author><name sortKey="Hampp, Rudiger" sort="Hampp, Rudiger" uniqKey="Hampp R" first="Rüdiger" last="Hampp">Rüdiger Hampp</name></author><author><name sortKey="Nehls, Uwe" sort="Nehls, Uwe" uniqKey="Nehls U" first="Uwe" last="Nehls">Uwe Nehls</name></author><author><name sortKey="Krajinski, Franziska" sort="Krajinski, Franziska" uniqKey="Krajinski F" first="Franziska" last="Krajinski">Franziska Krajinski</name></author><author><name sortKey="Franken, Philipp" sort="Franken, Philipp" uniqKey="Franken P" first="Philipp" last="Franken">Philipp Franken</name></author><author><name sortKey="Puhler, Alfred" sort="Puhler, Alfred" uniqKey="Puhler A" first="Alfred" last="Pühler">Alfred Pühler</name></author></analytic><series><title level="j">Phytochemistry</title><idno type="ISSN">0031-9422</idno><imprint><date when="2007" type="published">2007</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Computational Biology (methods)</term><term>Expressed Sequence Tags (MeSH)</term><term>Mycorrhizae (genetics)</term><term>Oligonucleotide Array Sequence Analysis (methods)</term><term>Symbiosis (genetics)</term><term>Transcription, Genetic (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Biologie informatique (méthodes)</term><term>Mycorhizes (génétique)</term><term>Symbiose (génétique)</term><term>Séquençage par oligonucléotides en batterie (méthodes)</term><term>Transcription génétique (génétique)</term><term>Étiquettes de séquences exprimées (MeSH)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Mycorrhizae</term><term>Symbiosis</term><term>Transcription, Genetic</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Mycorhizes</term><term>Symbiose</term><term>Transcription génétique</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term><term>Oligonucleotide Array Sequence Analysis</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Biologie informatique</term><term>Séquençage par oligonucléotides en batterie</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Expressed Sequence Tags</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Étiquettes de séquences exprimées</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The great majority of terrestrial plants enters a beneficial arbuscular mycorrhiza (AM) or ectomycorrhiza (ECM) symbiosis with soil fungi. In the SPP 1084 "MolMyk: Molecular Basics of Mycorrhizal Symbioses", high-throughput EST-sequencing was performed to obtain snapshots of the plant and fungal transcriptome in mycorrhizal roots and in extraradical hyphae. To focus activities, the interactions between Medicago truncatula and Glomus intraradices as well as Populus tremula and Amanita muscaria were selected as models for AM and ECM symbioses, respectively. Together, almost, 20.000 expressed sequence tags (ESTs) were generated from different random and suppressive subtractive hybridization (SSH) cDNA libraries, providing a comprehensive overview of the mycorrhizal transcriptome. To automatically cluster and annotate EST-sequences, the BioMake and SAMS software tools were developed. In connection with the eNorthern software SteN, plant genes with a predicted mycorrhiza-induced expression were identified. To support experimental transcriptome profiling, macro- and microarray tools have been constructed for the two model mycorrhizae, based either on PCR-amplified cDNAs or 70mer oligonucleotides. These arrays were used to profile the transcriptome of AM and ECM roots under different conditions, and the data obtained were uploaded to the ArrayLIMS and EMMA databases that are designed to store and evaluate expression profiles from DNA arrays. Together, the EST- and transcriptome databases can be mined to identify candidate genes for targeted functional studies.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">17081576</PMID><DateCompleted><Year>2007</Year><Month>04</Month><Day>11</Day></DateCompleted><DateRevised><Year>2006</Year><Month>12</Month><Day>25</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0031-9422</ISSN><JournalIssue CitedMedium="Print"><Volume>68</Volume><Issue>1</Issue><PubDate><Year>2007</Year><Month>Jan</Month></PubDate></JournalIssue><Title>Phytochemistry</Title><ISOAbbreviation>Phytochemistry</ISOAbbreviation></Journal><ArticleTitle>Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses.</ArticleTitle><Pagination><MedlinePgn>19-32</MedlinePgn></Pagination><Abstract><AbstractText>The great majority of terrestrial plants enters a beneficial arbuscular mycorrhiza (AM) or ectomycorrhiza (ECM) symbiosis with soil fungi. In the SPP 1084 "MolMyk: Molecular Basics of Mycorrhizal Symbioses", high-throughput EST-sequencing was performed to obtain snapshots of the plant and fungal transcriptome in mycorrhizal roots and in extraradical hyphae. To focus activities, the interactions between Medicago truncatula and Glomus intraradices as well as Populus tremula and Amanita muscaria were selected as models for AM and ECM symbioses, respectively. Together, almost, 20.000 expressed sequence tags (ESTs) were generated from different random and suppressive subtractive hybridization (SSH) cDNA libraries, providing a comprehensive overview of the mycorrhizal transcriptome. To automatically cluster and annotate EST-sequences, the BioMake and SAMS software tools were developed. In connection with the eNorthern software SteN, plant genes with a predicted mycorrhiza-induced expression were identified. To support experimental transcriptome profiling, macro- and microarray tools have been constructed for the two model mycorrhizae, based either on PCR-amplified cDNAs or 70mer oligonucleotides. These arrays were used to profile the transcriptome of AM and ECM roots under different conditions, and the data obtained were uploaded to the ArrayLIMS and EMMA databases that are designed to store and evaluate expression profiles from DNA arrays. Together, the EST- and transcriptome databases can be mined to identify candidate genes for targeted functional studies.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Küster</LastName><ForeName>Helge</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Institute for Genome Research, Center for Biotechnology (CeBiTec), Universität Bielefeld, Universitätsstrasse 25, 33594 Bielefeld, Germany. Helge.Kuester@Genetik.Uni-Bielefeld.DE</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Becker</LastName><ForeName>Anke</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Firnhaber</LastName><ForeName>Christian</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Hohnjec</LastName><ForeName>Natalija</ForeName><Initials>N</Initials></Author><Author ValidYN="Y"><LastName>Manthey</LastName><ForeName>Katja</ForeName><Initials>K</Initials></Author><Author ValidYN="Y"><LastName>Perlick</LastName><ForeName>Andreas M</ForeName><Initials>AM</Initials></Author><Author ValidYN="Y"><LastName>Bekel</LastName><ForeName>Thomas</ForeName><Initials>T</Initials></Author><Author ValidYN="Y"><LastName>Dondrup</LastName><ForeName>Michael</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Henckel</LastName><ForeName>Kolja</ForeName><Initials>K</Initials></Author><Author ValidYN="Y"><LastName>Goesmann</LastName><ForeName>Alexander</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Meyer</LastName><ForeName>Folker</ForeName><Initials>F</Initials></Author><Author ValidYN="Y"><LastName>Wipf</LastName><ForeName>Daniel</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>Requena</LastName><ForeName>Natalia</ForeName><Initials>N</Initials></Author><Author ValidYN="Y"><LastName>Hildebrandt</LastName><ForeName>Ulrich</ForeName><Initials>U</Initials></Author><Author ValidYN="Y"><LastName>Hampp</LastName><ForeName>Rüdiger</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Nehls</LastName><ForeName>Uwe</ForeName><Initials>U</Initials></Author><Author ValidYN="Y"><LastName>Krajinski</LastName><ForeName>Franziska</ForeName><Initials>F</Initials></Author><Author ValidYN="Y"><LastName>Franken</LastName><ForeName>Philipp</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Pühler</LastName><ForeName>Alfred</ForeName><Initials>A</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D016454">Review</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2006</Year><Month>11</Month><Day>01</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Phytochemistry</MedlineTA><NlmUniqueID>0151434</NlmUniqueID><ISSNLinking>0031-9422</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D019295" MajorTopicYN="N">Computational Biology</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020224" MajorTopicYN="Y">Expressed Sequence Tags</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D038821" MajorTopicYN="N">Mycorrhizae</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020411" MajorTopicYN="N">Oligonucleotide Array Sequence Analysis</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013559" MajorTopicYN="N">Symbiosis</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014158" MajorTopicYN="N">Transcription, Genetic</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList><NumberOfReferences>80</NumberOfReferences></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2006</Year><Month>04</Month><Day>27</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2006</Year><Month>06</Month><Day>09</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2006</Year><Month>09</Month><Day>19</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2006</Year><Month>11</Month><Day>4</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2007</Year><Month>4</Month><Day>12</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2006</Year><Month>11</Month><Day>4</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">17081576</ArticleId><ArticleId IdType="pii">S0031-9422(06)00593-0</ArticleId><ArticleId IdType="doi">10.1016/j.phytochem.2006.09.026</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Allemagne</li></country></list><tree><noCountry><name sortKey="Becker, Anke" sort="Becker, Anke" uniqKey="Becker A" first="Anke" last="Becker">Anke Becker</name><name sortKey="Bekel, Thomas" sort="Bekel, Thomas" uniqKey="Bekel T" first="Thomas" last="Bekel">Thomas Bekel</name><name sortKey="Dondrup, Michael" sort="Dondrup, Michael" uniqKey="Dondrup M" first="Michael" last="Dondrup">Michael Dondrup</name><name sortKey="Firnhaber, Christian" sort="Firnhaber, Christian" uniqKey="Firnhaber C" first="Christian" last="Firnhaber">Christian Firnhaber</name><name sortKey="Franken, Philipp" sort="Franken, Philipp" uniqKey="Franken P" first="Philipp" last="Franken">Philipp Franken</name><name sortKey="Goesmann, Alexander" sort="Goesmann, Alexander" uniqKey="Goesmann A" first="Alexander" last="Goesmann">Alexander Goesmann</name><name sortKey="Hampp, Rudiger" sort="Hampp, Rudiger" uniqKey="Hampp R" first="Rüdiger" last="Hampp">Rüdiger Hampp</name><name sortKey="Henckel, Kolja" sort="Henckel, Kolja" uniqKey="Henckel K" first="Kolja" last="Henckel">Kolja Henckel</name><name sortKey="Hildebrandt, Ulrich" sort="Hildebrandt, Ulrich" uniqKey="Hildebrandt U" first="Ulrich" last="Hildebrandt">Ulrich Hildebrandt</name><name sortKey="Hohnjec, Natalija" sort="Hohnjec, Natalija" uniqKey="Hohnjec N" first="Natalija" last="Hohnjec">Natalija Hohnjec</name><name sortKey="Krajinski, Franziska" sort="Krajinski, Franziska" uniqKey="Krajinski F" first="Franziska" last="Krajinski">Franziska Krajinski</name><name sortKey="Manthey, Katja" sort="Manthey, Katja" uniqKey="Manthey K" first="Katja" last="Manthey">Katja Manthey</name><name sortKey="Meyer, Folker" sort="Meyer, Folker" uniqKey="Meyer F" first="Folker" last="Meyer">Folker Meyer</name><name sortKey="Nehls, Uwe" sort="Nehls, Uwe" uniqKey="Nehls U" first="Uwe" last="Nehls">Uwe Nehls</name><name sortKey="Perlick, Andreas M" sort="Perlick, Andreas M" uniqKey="Perlick A" first="Andreas M" last="Perlick">Andreas M. Perlick</name><name sortKey="Puhler, Alfred" sort="Puhler, Alfred" uniqKey="Puhler A" first="Alfred" last="Pühler">Alfred Pühler</name><name sortKey="Requena, Natalia" sort="Requena, Natalia" uniqKey="Requena N" first="Natalia" last="Requena">Natalia Requena</name><name sortKey="Wipf, Daniel" sort="Wipf, Daniel" uniqKey="Wipf D" first="Daniel" last="Wipf">Daniel Wipf</name></noCountry><country name="Allemagne"><noRegion><name sortKey="Kuster, Helge" sort="Kuster, Helge" uniqKey="Kuster H" first="Helge" last="Küster">Helge Küster</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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