The development of an Arabidopsis model system for genome‐wide analysis of polyploidy effects
Identifieur interne : 003111 ( Main/Exploration ); précédent : 003110; suivant : 003112The development of an Arabidopsis model system for genome‐wide analysis of polyploidy effects
Auteurs : Z. Jeffrey Chen [États-Unis] ; Jianlin Wang [États-Unis] ; Lu Tian [États-Unis] ; Hyeon-Se Lee [États-Unis] ; Jiyuan J. Wang [États-Unis] ; Meng Chen [États-Unis] ; Jinsuk J. Lee [États-Unis] ; Caroline Josefsson [États-Unis] ; Andreas Madlung [États-Unis] ; Brian Watson [États-Unis] ; Zach Lippman [États-Unis] ; Matt Vaughn [États-Unis] ; J. Chris Pires [États-Unis] ; Vincent Colot [États-Unis] ; R. W. Doerge [États-Unis] ; Robert A. Martienssen [États-Unis] ; Luca Comai [États-Unis] ; Thomas C. Osborn [États-Unis]Source :
- Biological Journal of the Linnean Society [ 0024-4066 ] ; 2004-08.
English descriptors
- Teeft :
- Allopolyploids, Allotetraploid, Allotetraploids, Arabidopsis, Arabidopsis allopolyploids, Arabidopsis genome, Arabidopsis genome initiative, Arabidopsis model system, Arabidopsis polyploids, Arabidopsis species, Arabidopsis suecica, Arabidopsis thaliana, Arenosa, Autotetraploid, Autotetraploid diploid, Benjamini hochberg, Biological journal, Black doerge, Brassica, Cdna, Cdna amplicons, Chen, Chromatin, Chromatin structure, Chromosome, Comai, Current opinions, Differential gene expression, Diploid, Doerge, Epigenetic, Epigenetic changes, Experimental design, Feldman, Gene, Gene activation, Gene expression, Gene expression changes, Gene expression studies, Genetics, Genome, Genome duplication, Genome organization, Genomic, Histone, Hochberg, Homoeologous, Homoeologous genes, Hybrid, Hybridization, Hybridization intensities, Imprinting, Linear model, Linnean, Linnean society, Madlung, Methylation, Meyerowitz, Microarray, Microarray analysis, Microarray data, Microarray experiments, Microarrays, Mittelsten scheid, Model system, National academy, Nature biotechnology, Nature genetics, Nature review, Nucleolar, Nucleolar dominance, Oligos, Osborn, Phenotypic variation, Pikaard, Plant cell, Plant physiology, Ploidy, Polyploid, Polyploidy, Polyploidy effects, Predesigned chips, Short oligos, Suecica, Tetraploid, Thaliana, Wang, Wendel.
Abstract
Arabidopsis is a model system not only for studying numerous aspects of plant biology, but also for understanding mechanisms of the rapid evolutionary process associated with genome duplication and polyploidization. Although in animals interspecific hybrids are often sterile and aneuploids are related to disease syndromes, both Arabidopsis autopolyploids and allopolyploids occur in nature and can be readily formed in the laboratory, providing an attractive system for comparing changes in gene expression and genome structure among relatively ‘young’ and ‘established’ or ‘ancient’ polyploids. Powerful reverse and forward genetics in Arabidopsis offer an exceptional means by which regulatory mechanisms of gene and genome duplication may be revealed. Moreover, the Arabidopsis genome is completely sequenced; both coding and non‐coding sequences are available. We have developed spotted oligo‐gene and chromosome microarrays using the complete Arabidopsis genome sequence. The oligo‐gene microarray consists of ∼26 000 70‐mer oligonucleotides that are designed from all annotated genes in Arabidopsis, and the chromosome microarray contains 1 kb genomic tiling fragments amplified from a chromosomal region or the complete sequence of chromosome 4. We have demonstrated the utility of microarrays for genome‐wide analysis of changes in gene expression, genome organization and chromatin structure in Arabidopsis polyploids and related species. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 82, 689–700.
Url:
DOI: 10.1111/j.1095-8312.2004.00351.x
Affiliations:
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Jeffrey Chen</name><affiliation wicri:level="1"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Intercollegiate Program in Genetics and Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843–2474</wicri:regionArea><wicri:noRegion>TX 77843–2474</wicri:noRegion></affiliation><affiliation wicri:level="1"><country wicri:rule="url">États-Unis</country></affiliation></author><author><name sortKey="Wang, Jianlin" sort="Wang, Jianlin" uniqKey="Wang J" first="Jianlin" last="Wang">Jianlin Wang</name><affiliation wicri:level="1"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Intercollegiate Program in Genetics and Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843–2474</wicri:regionArea><wicri:noRegion>TX 77843–2474</wicri:noRegion></affiliation></author><author><name sortKey="Tian, Lu" sort="Tian, Lu" uniqKey="Tian L" first="Lu" last="Tian">Lu Tian</name><affiliation wicri:level="1"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Intercollegiate Program in Genetics and Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843–2474</wicri:regionArea><wicri:noRegion>TX 77843–2474</wicri:noRegion></affiliation></author><author><name sortKey="Lee, Hyeon E" sort="Lee, Hyeon E" uniqKey="Lee H" first="Hyeon-Se" last="Lee">Hyeon-Se Lee</name><affiliation wicri:level="1"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Intercollegiate Program in Genetics and Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843–2474</wicri:regionArea><wicri:noRegion>TX 77843–2474</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Jiyuan J" sort="Wang, Jiyuan J" uniqKey="Wang J" first="Jiyuan J." last="Wang">Jiyuan J. 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Chris" last="Pires">J. Chris Pires</name><affiliation wicri:level="1"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Agronomy, University of Wisconsin, Madison, WI 53706</wicri:regionArea><wicri:noRegion>WI 53706</wicri:noRegion></affiliation></author><author><name sortKey="Colot, Vincent" sort="Colot, Vincent" uniqKey="Colot V" first="Vincent" last="Colot">Vincent Colot</name><affiliation wicri:level="1"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724</wicri:regionArea><wicri:noRegion>NY 11724</wicri:noRegion></affiliation></author><author><name sortKey="Doerge, R W" sort="Doerge, R W" uniqKey="Doerge R" first="R. W." last="Doerge">R. W. 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Osborn</name><affiliation wicri:level="1"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Agronomy, University of Wisconsin, Madison, WI 53706</wicri:regionArea><wicri:noRegion>WI 53706</wicri:noRegion></affiliation></author></analytic><monogr></monogr><series><title level="j" type="main">Biological Journal of the Linnean Society</title><title level="j" type="alt">BIOLOGICAL JOURNAL LINNEAN SOCIETY</title><idno type="ISSN">0024-4066</idno><idno type="eISSN">1095-8312</idno><imprint><biblScope unit="vol">82</biblScope><biblScope unit="issue">4</biblScope><biblScope unit="page" from="689">689</biblScope><biblScope unit="page" to="700">700</biblScope><biblScope unit="page-count">12</biblScope><publisher>Blackwell Science Ltd</publisher><pubPlace>Oxford, UK</pubPlace><date type="published" when="2004-08">2004-08</date></imprint><idno type="ISSN">0024-4066</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0024-4066</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="Teeft" xml:lang="en"><term>Allopolyploids</term><term>Allotetraploid</term><term>Allotetraploids</term><term>Arabidopsis</term><term>Arabidopsis allopolyploids</term><term>Arabidopsis genome</term><term>Arabidopsis genome initiative</term><term>Arabidopsis model system</term><term>Arabidopsis polyploids</term><term>Arabidopsis species</term><term>Arabidopsis suecica</term><term>Arabidopsis thaliana</term><term>Arenosa</term><term>Autotetraploid</term><term>Autotetraploid diploid</term><term>Benjamini hochberg</term><term>Biological journal</term><term>Black doerge</term><term>Brassica</term><term>Cdna</term><term>Cdna amplicons</term><term>Chen</term><term>Chromatin</term><term>Chromatin structure</term><term>Chromosome</term><term>Comai</term><term>Current opinions</term><term>Differential gene expression</term><term>Diploid</term><term>Doerge</term><term>Epigenetic</term><term>Epigenetic changes</term><term>Experimental design</term><term>Feldman</term><term>Gene</term><term>Gene activation</term><term>Gene expression</term><term>Gene expression changes</term><term>Gene expression studies</term><term>Genetics</term><term>Genome</term><term>Genome duplication</term><term>Genome organization</term><term>Genomic</term><term>Histone</term><term>Hochberg</term><term>Homoeologous</term><term>Homoeologous genes</term><term>Hybrid</term><term>Hybridization</term><term>Hybridization intensities</term><term>Imprinting</term><term>Linear model</term><term>Linnean</term><term>Linnean society</term><term>Madlung</term><term>Methylation</term><term>Meyerowitz</term><term>Microarray</term><term>Microarray analysis</term><term>Microarray data</term><term>Microarray experiments</term><term>Microarrays</term><term>Mittelsten scheid</term><term>Model system</term><term>National academy</term><term>Nature biotechnology</term><term>Nature genetics</term><term>Nature review</term><term>Nucleolar</term><term>Nucleolar dominance</term><term>Oligos</term><term>Osborn</term><term>Phenotypic variation</term><term>Pikaard</term><term>Plant cell</term><term>Plant physiology</term><term>Ploidy</term><term>Polyploid</term><term>Polyploidy</term><term>Polyploidy effects</term><term>Predesigned chips</term><term>Short oligos</term><term>Suecica</term><term>Tetraploid</term><term>Thaliana</term><term>Wang</term><term>Wendel</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Arabidopsis is a model system not only for studying numerous aspects of plant biology, but also for understanding mechanisms of the rapid evolutionary process associated with genome duplication and polyploidization. Although in animals interspecific hybrids are often sterile and aneuploids are related to disease syndromes, both Arabidopsis autopolyploids and allopolyploids occur in nature and can be readily formed in the laboratory, providing an attractive system for comparing changes in gene expression and genome structure among relatively ‘young’ and ‘established’ or ‘ancient’ polyploids. Powerful reverse and forward genetics in Arabidopsis offer an exceptional means by which regulatory mechanisms of gene and genome duplication may be revealed. Moreover, the Arabidopsis genome is completely sequenced; both coding and non‐coding sequences are available. We have developed spotted oligo‐gene and chromosome microarrays using the complete Arabidopsis genome sequence. The oligo‐gene microarray consists of ∼26 000 70‐mer oligonucleotides that are designed from all annotated genes in Arabidopsis, and the chromosome microarray contains 1 kb genomic tiling fragments amplified from a chromosomal region or the complete sequence of chromosome 4. We have demonstrated the utility of microarrays for genome‐wide analysis of changes in gene expression, genome organization and chromatin structure in Arabidopsis polyploids and related species. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 82, 689–700.</div></front></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Washington (État)</li></region><settlement><li>Seattle</li></settlement><orgName><li>Université de Washington</li></orgName></list><tree><country name="États-Unis"><noRegion><name sortKey="Chen, Z Jeffrey" sort="Chen, Z Jeffrey" uniqKey="Chen Z" first="Z. Jeffrey" last="Chen">Z. Jeffrey Chen</name></noRegion><name sortKey="Chen, Meng" sort="Chen, Meng" uniqKey="Chen M" first="Meng" last="Chen">Meng Chen</name><name sortKey="Chen, Z Jeffrey" sort="Chen, Z Jeffrey" uniqKey="Chen Z" first="Z. Jeffrey" last="Chen">Z. Jeffrey Chen</name><name sortKey="Colot, Vincent" sort="Colot, Vincent" uniqKey="Colot V" first="Vincent" last="Colot">Vincent Colot</name><name sortKey="Comai, Luca" sort="Comai, Luca" uniqKey="Comai L" first="Luca" last="Comai">Luca Comai</name><name sortKey="Doerge, R W" sort="Doerge, R W" uniqKey="Doerge R" first="R. W." last="Doerge">R. W. Doerge</name><name sortKey="Josefsson, Caroline" sort="Josefsson, Caroline" uniqKey="Josefsson C" first="Caroline" last="Josefsson">Caroline Josefsson</name><name sortKey="Lee, Hyeon E" sort="Lee, Hyeon E" uniqKey="Lee H" first="Hyeon-Se" last="Lee">Hyeon-Se Lee</name><name sortKey="Lee, Jinsuk J" sort="Lee, Jinsuk J" uniqKey="Lee J" first="Jinsuk J." last="Lee">Jinsuk J. Lee</name><name sortKey="Lippman, Zach" sort="Lippman, Zach" uniqKey="Lippman Z" first="Zach" last="Lippman">Zach Lippman</name><name sortKey="Madlung, Andreas" sort="Madlung, Andreas" uniqKey="Madlung A" first="Andreas" last="Madlung">Andreas Madlung</name><name sortKey="Martienssen, Robert A" sort="Martienssen, Robert A" uniqKey="Martienssen R" first="Robert A." last="Martienssen">Robert A. Martienssen</name><name sortKey="Osborn, Thomas C" sort="Osborn, Thomas C" uniqKey="Osborn T" first="Thomas C." last="Osborn">Thomas C. Osborn</name><name sortKey="Pires, J Chris" sort="Pires, J Chris" uniqKey="Pires J" first="J. Chris" last="Pires">J. Chris Pires</name><name sortKey="Tian, Lu" sort="Tian, Lu" uniqKey="Tian L" first="Lu" last="Tian">Lu Tian</name><name sortKey="Vaughn, Matt" sort="Vaughn, Matt" uniqKey="Vaughn M" first="Matt" last="Vaughn">Matt Vaughn</name><name sortKey="Wang, Jianlin" sort="Wang, Jianlin" uniqKey="Wang J" first="Jianlin" last="Wang">Jianlin Wang</name><name sortKey="Wang, Jiyuan J" sort="Wang, Jiyuan J" uniqKey="Wang J" first="Jiyuan J." last="Wang">Jiyuan J. Wang</name><name sortKey="Watson, Brian" sort="Watson, Brian" uniqKey="Watson B" first="Brian" last="Watson">Brian Watson</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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