Arabidopsis thaliana full genome longmer microarrays: a powerful gene discovery tool for agriculture and forestry.
Identifieur interne : 004105 ( Main/Exploration ); précédent : 004104; suivant : 004106Arabidopsis thaliana full genome longmer microarrays: a powerful gene discovery tool for agriculture and forestry.
Auteurs : Carl J. Douglas [Canada] ; Jürgen EhltingSource :
- Transgenic research [ 0962-8819 ] ; 2005.
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Abstract
Sequenced plant genomes provide a large reservoir of known genes with potential for use in crop and tree improvement, but assignment of specific functions to annotated genes in sequenced plant genomes remains a challenge. Furthermore, most plant genes belong to families encoding proteins with related but distinct functions. In this commentary, we discuss our development of Arabidopsis spotted whole genome longmer oligonucleotide microarrays, and their use in global transcription profiling. We show that longmer array based transcriptome analysis in Arabidopsis can be used as an efficient and effective gene discovery and functional genomics tool, particularly for functional analyses of members of large gene families. We discuss experiments that focus on gene families involved in phenylpropanoid natural product biosynthesis and fiber differentiation. These analyses have helped to elucidate functions of individual gene family members, and have identified new candidate genes involved in fiber development and differentiation. Results obtained by these studies in Arabidopsis can be used as the basis for gene discovery in commercially important plants, and we have focused our attention on Populus trichocarpa (poplar), a species important in forestry and agroforestry for which complete genome sequence information is available.
DOI: 10.1007/s11248-005-8926-x
PubMed: 16245146
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Douglas</name><affiliation wicri:level="4"><nlm:affiliation>Department of Botany, University of British Columbia, BC V6T 1Z4 Vancouver, Canada. cdouglas@interchange.ubc.ca</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Botany, University of British Columbia, BC V6T 1Z4 Vancouver</wicri:regionArea><orgName type="university">Université de la Colombie-Britannique</orgName><placeName><settlement type="city">Vancouver</settlement><region type="state">Colombie-Britannique </region></placeName></affiliation></author><author><name sortKey="Ehlting, Jurgen" sort="Ehlting, Jurgen" uniqKey="Ehlting J" first="Jürgen" last="Ehlting">Jürgen Ehlting</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2005">2005</date><idno type="RBID">pubmed:16245146</idno><idno type="pmid">16245146</idno><idno type="doi">10.1007/s11248-005-8926-x</idno><idno type="wicri:Area/Main/Corpus">003F35</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">003F35</idno><idno type="wicri:Area/Main/Curation">003F35</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">003F35</idno><idno type="wicri:Area/Main/Exploration">003F35</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Arabidopsis thaliana full genome longmer microarrays: a powerful gene discovery tool for agriculture and forestry.</title><author><name sortKey="Douglas, Carl J" sort="Douglas, Carl J" uniqKey="Douglas C" first="Carl J" last="Douglas">Carl J. Douglas</name><affiliation wicri:level="4"><nlm:affiliation>Department of Botany, University of British Columbia, BC V6T 1Z4 Vancouver, Canada. cdouglas@interchange.ubc.ca</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Botany, University of British Columbia, BC V6T 1Z4 Vancouver</wicri:regionArea><orgName type="university">Université de la Colombie-Britannique</orgName><placeName><settlement type="city">Vancouver</settlement><region type="state">Colombie-Britannique </region></placeName></affiliation></author><author><name sortKey="Ehlting, Jurgen" sort="Ehlting, Jurgen" uniqKey="Ehlting J" first="Jürgen" last="Ehlting">Jürgen Ehlting</name></author></analytic><series><title level="j">Transgenic research</title><idno type="ISSN">0962-8819</idno><imprint><date when="2005" type="published">2005</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Agriculture (MeSH)</term><term>Arabidopsis (genetics)</term><term>Forestry (MeSH)</term><term>Gene Expression Profiling (MeSH)</term><term>Genetic Techniques (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Oligonucleotide Array Sequence Analysis (MeSH)</term><term>Plants, Edible (genetics)</term><term>Populus (genetics)</term><term>Trees (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Agriculture (MeSH)</term><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Arabidopsis (génétique)</term><term>Arbres (génétique)</term><term>Génome végétal (MeSH)</term><term>Plantes comestibles (génétique)</term><term>Populus (génétique)</term><term>Science forêt (MeSH)</term><term>Séquençage par oligonucléotides en batterie (MeSH)</term><term>Techniques génétiques (MeSH)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term><term>Plants, Edible</term><term>Populus</term><term>Trees</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Arabidopsis</term><term>Arbres</term><term>Plantes comestibles</term><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Agriculture</term><term>Forestry</term><term>Gene Expression Profiling</term><term>Genetic Techniques</term><term>Genome, Plant</term><term>Oligonucleotide Array Sequence Analysis</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Agriculture</term><term>Analyse de profil d'expression de gènes</term><term>Génome végétal</term><term>Science forêt</term><term>Séquençage par oligonucléotides en batterie</term><term>Techniques génétiques</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Sequenced plant genomes provide a large reservoir of known genes with potential for use in crop and tree improvement, but assignment of specific functions to annotated genes in sequenced plant genomes remains a challenge. Furthermore, most plant genes belong to families encoding proteins with related but distinct functions. In this commentary, we discuss our development of Arabidopsis spotted whole genome longmer oligonucleotide microarrays, and their use in global transcription profiling. We show that longmer array based transcriptome analysis in Arabidopsis can be used as an efficient and effective gene discovery and functional genomics tool, particularly for functional analyses of members of large gene families. We discuss experiments that focus on gene families involved in phenylpropanoid natural product biosynthesis and fiber differentiation. These analyses have helped to elucidate functions of individual gene family members, and have identified new candidate genes involved in fiber development and differentiation. Results obtained by these studies in Arabidopsis can be used as the basis for gene discovery in commercially important plants, and we have focused our attention on Populus trichocarpa (poplar), a species important in forestry and agroforestry for which complete genome sequence information is available.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16245146</PMID><DateCompleted><Year>2006</Year><Month>01</Month><Day>25</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0962-8819</ISSN><JournalIssue CitedMedium="Print"><Volume>14</Volume><Issue>5</Issue><PubDate><Year>2005</Year><Month>Oct</Month></PubDate></JournalIssue><Title>Transgenic research</Title><ISOAbbreviation>Transgenic Res</ISOAbbreviation></Journal><ArticleTitle>Arabidopsis thaliana full genome longmer microarrays: a powerful gene discovery tool for agriculture and forestry.</ArticleTitle><Pagination><MedlinePgn>551-61</MedlinePgn></Pagination><Abstract><AbstractText>Sequenced plant genomes provide a large reservoir of known genes with potential for use in crop and tree improvement, but assignment of specific functions to annotated genes in sequenced plant genomes remains a challenge. Furthermore, most plant genes belong to families encoding proteins with related but distinct functions. In this commentary, we discuss our development of Arabidopsis spotted whole genome longmer oligonucleotide microarrays, and their use in global transcription profiling. We show that longmer array based transcriptome analysis in Arabidopsis can be used as an efficient and effective gene discovery and functional genomics tool, particularly for functional analyses of members of large gene families. We discuss experiments that focus on gene families involved in phenylpropanoid natural product biosynthesis and fiber differentiation. These analyses have helped to elucidate functions of individual gene family members, and have identified new candidate genes involved in fiber development and differentiation. Results obtained by these studies in Arabidopsis can be used as the basis for gene discovery in commercially important plants, and we have focused our attention on Populus trichocarpa (poplar), a species important in forestry and agroforestry for which complete genome sequence information is available.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Douglas</LastName><ForeName>Carl J</ForeName><Initials>CJ</Initials><AffiliationInfo><Affiliation>Department of Botany, University of British Columbia, BC V6T 1Z4 Vancouver, Canada. cdouglas@interchange.ubc.ca</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ehlting</LastName><ForeName>Jürgen</ForeName><Initials>J</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 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