The development of an Arabidopsis model system for genome‐wide analysis of polyploidy effects
Identifieur interne : 000492 ( Istex/Corpus ); précédent : 000491; suivant : 000493The development of an Arabidopsis model system for genome‐wide analysis of polyploidy effects
Auteurs : Z. Jeffrey Chen ; Jianlin Wang ; Lu Tian ; Hyeon-Se Lee ; Jiyuan J. Wang ; Meng Chen ; Jinsuk J. Lee ; Caroline Josefsson ; Andreas Madlung ; Brian Watson ; Zach Lippman ; Matt Vaughn ; J. Chris Pires ; Vincent Colot ; R. W. Doerge ; Robert A. Martienssen ; Luca Comai ; Thomas C. OsbornSource :
- 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
Links to Exploration step
ISTEX:106146BAD678BB4E14BDC457E6822196B66B0020Le document en format XML
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Jeffrey Chen</name><affiliation><mods:affiliation>Intercollegiate Program in Genetics and Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843–2474, USA</mods:affiliation></affiliation><affiliation><mods:affiliation>E-mail: zjchen@tamu.edu</mods:affiliation></affiliation></author><author><name sortKey="Wang, Jianlin" sort="Wang, Jianlin" uniqKey="Wang J" first="Jianlin" last="Wang">Jianlin Wang</name><affiliation><mods:affiliation>Intercollegiate Program in Genetics and Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843–2474, USA</mods:affiliation></affiliation></author><author><name sortKey="Tian, Lu" sort="Tian, Lu" uniqKey="Tian L" first="Lu" last="Tian">Lu Tian</name><affiliation><mods:affiliation>Intercollegiate Program in Genetics and Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843–2474, USA</mods:affiliation></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><mods:affiliation>Intercollegiate Program in Genetics and Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843–2474, USA</mods:affiliation></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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Jeffrey Chen</name><affiliation><mods:affiliation>Intercollegiate Program in Genetics and Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843–2474, USA</mods:affiliation></affiliation><affiliation><mods:affiliation>E-mail: zjchen@tamu.edu</mods:affiliation></affiliation></author><author><name sortKey="Wang, Jianlin" sort="Wang, Jianlin" uniqKey="Wang J" first="Jianlin" last="Wang">Jianlin Wang</name><affiliation><mods:affiliation>Intercollegiate Program in Genetics and Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843–2474, USA</mods:affiliation></affiliation></author><author><name sortKey="Tian, Lu" sort="Tian, Lu" uniqKey="Tian L" first="Lu" last="Tian">Lu Tian</name><affiliation><mods:affiliation>Intercollegiate Program in Genetics and Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843–2474, USA</mods:affiliation></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><mods:affiliation>Intercollegiate Program in Genetics and Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843–2474, USA</mods:affiliation></affiliation></author><author><name sortKey="Wang, Jiyuan J" sort="Wang, Jiyuan J" uniqKey="Wang J" first="Jiyuan J." last="Wang">Jiyuan J. Wang</name><affiliation><mods:affiliation>Intercollegiate Program in Genetics and Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843–2474, USA</mods:affiliation></affiliation></author><author><name sortKey="Chen, Meng" sort="Chen, Meng" uniqKey="Chen M" first="Meng" last="Chen">Meng Chen</name><affiliation><mods:affiliation>Intercollegiate Program in Genetics and Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843–2474, USA</mods:affiliation></affiliation></author><author><name sortKey="Lee, Jinsuk J" sort="Lee, Jinsuk J" uniqKey="Lee J" first="Jinsuk J." last="Lee">Jinsuk J. Lee</name><affiliation><mods:affiliation>Intercollegiate Program in Genetics and Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843–2474, USA</mods:affiliation></affiliation></author><author><name sortKey="Josefsson, Caroline" sort="Josefsson, Caroline" uniqKey="Josefsson C" first="Caroline" last="Josefsson">Caroline Josefsson</name><affiliation><mods:affiliation>Department of Botany, University of Washington, Seattle, WA 98195, USA</mods:affiliation></affiliation></author><author><name sortKey="Madlung, Andreas" sort="Madlung, Andreas" uniqKey="Madlung A" first="Andreas" last="Madlung">Andreas Madlung</name><affiliation><mods:affiliation>Department of Botany, University of Washington, Seattle, WA 98195, USA</mods:affiliation></affiliation></author><author><name sortKey="Watson, Brian" sort="Watson, Brian" uniqKey="Watson B" first="Brian" last="Watson">Brian Watson</name><affiliation><mods:affiliation>Department of Botany, University of Washington, Seattle, WA 98195, USA</mods:affiliation></affiliation></author><author><name sortKey="Lippman, Zach" sort="Lippman, Zach" uniqKey="Lippman Z" first="Zach" last="Lippman">Zach Lippman</name><affiliation><mods:affiliation>Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA</mods:affiliation></affiliation></author><author><name sortKey="Vaughn, Matt" sort="Vaughn, Matt" uniqKey="Vaughn M" first="Matt" last="Vaughn">Matt Vaughn</name><affiliation><mods:affiliation>Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA</mods:affiliation></affiliation></author><author><name sortKey="Pires, J Chris" sort="Pires, J Chris" uniqKey="Pires J" first="J. Chris" last="Pires">J. Chris Pires</name><affiliation><mods:affiliation>Department of Agronomy, University of Wisconsin, Madison, WI 53706, USA</mods:affiliation></affiliation></author><author><name sortKey="Colot, Vincent" sort="Colot, Vincent" uniqKey="Colot V" first="Vincent" last="Colot">Vincent Colot</name><affiliation><mods:affiliation>Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA</mods:affiliation></affiliation></author><author><name sortKey="Doerge, R W" sort="Doerge, R W" uniqKey="Doerge R" first="R. W." last="Doerge">R. W. Doerge</name><affiliation><mods:affiliation>Departments of Statistics, Agronomy, and Computational Genomics, Purdue University, West Lafayette, IN 47907, USA</mods:affiliation></affiliation></author><author><name sortKey="Martienssen, Robert A" sort="Martienssen, Robert A" uniqKey="Martienssen R" first="Robert A." last="Martienssen">Robert A. Martienssen</name><affiliation><mods:affiliation>Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA</mods:affiliation></affiliation></author><author><name sortKey="Comai, Luca" sort="Comai, Luca" uniqKey="Comai L" first="Luca" last="Comai">Luca Comai</name><affiliation><mods:affiliation>Department of Botany, University of Washington, Seattle, WA 98195, USA</mods:affiliation></affiliation></author><author><name sortKey="Osborn, Thomas C" sort="Osborn, Thomas C" uniqKey="Osborn T" first="Thomas C." last="Osborn">Thomas C. Osborn</name><affiliation><mods:affiliation>Department of Agronomy, University of Wisconsin, Madison, WI 53706, USA</mods:affiliation></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><istex><corpusName>wiley</corpusName><keywords><teeft><json:string>arabidopsis</json:string><json:string>genome</json:string><json:string>polyploid</json:string><json:string>microarray</json:string><json:string>linnean</json:string><json:string>linnean society</json:string><json:string>microarrays</json:string><json:string>thaliana</json:string><json:string>diploid</json:string><json:string>genetics</json:string><json:string>chromosome</json:string><json:string>gene expression</json:string><json:string>genomic</json:string><json:string>cdna</json:string><json:string>comai</json:string><json:string>polyploidy</json:string><json:string>autotetraploid</json:string><json:string>biological journal</json:string><json:string>arenosa</json:string><json:string>suecica</json:string><json:string>hybridization</json:string><json:string>pikaard</json:string><json:string>chromatin</json:string><json:string>homoeologous</json:string><json:string>oligos</json:string><json:string>methylation</json:string><json:string>allopolyploids</json:string><json:string>feldman</json:string><json:string>national academy</json:string><json:string>polyploidy effects</json:string><json:string>hochberg</json:string><json:string>osborn</json:string><json:string>allotetraploid</json:string><json:string>allotetraploids</json:string><json:string>ploidy</json:string><json:string>nature genetics</json:string><json:string>nucleolar</json:string><json:string>madlung</json:string><json:string>doerge</json:string><json:string>meyerowitz</json:string><json:string>histone</json:string><json:string>nucleolar dominance</json:string><json:string>wendel</json:string><json:string>arabidopsis model system</json:string><json:string>imprinting</json:string><json:string>wang</json:string><json:string>autotetraploid diploid</json:string><json:string>tetraploid</json:string><json:string>arabidopsis polyploids</json:string><json:string>chromatin structure</json:string><json:string>microarray experiments</json:string><json:string>gene</json:string><json:string>brassica</json:string><json:string>epigenetic</json:string><json:string>homoeologous genes</json:string><json:string>model system</json:string><json:string>hybrid</json:string><json:string>chen</json:string><json:string>gene expression changes</json:string><json:string>genome duplication</json:string><json:string>mittelsten scheid</json:string><json:string>gene activation</json:string><json:string>black doerge</json:string><json:string>genome organization</json:string><json:string>arabidopsis thaliana</json:string><json:string>arabidopsis genome</json:string><json:string>gene expression studies</json:string><json:string>short oligos</json:string><json:string>linear model</json:string><json:string>experimental design</json:string><json:string>cdna amplicons</json:string><json:string>predesigned chips</json:string><json:string>benjamini hochberg</json:string><json:string>hybridization intensities</json:string><json:string>arabidopsis suecica</json:string><json:string>microarray analysis</json:string><json:string>epigenetic changes</json:string><json:string>microarray data</json:string><json:string>differential gene expression</json:string><json:string>phenotypic variation</json:string><json:string>arabidopsis allopolyploids</json:string><json:string>arabidopsis species</json:string><json:string>arabidopsis genome initiative</json:string><json:string>nature biotechnology</json:string><json:string>plant cell</json:string><json:string>current opinions</json:string><json:string>plant physiology</json:string><json:string>nature review</json:string></teeft></keywords><author><json:item><name>Z. JEFFREY CHEN</name><affiliations><json:string>Intercollegiate Program in Genetics and Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843–2474, USA</json:string><json:string>E-mail: zjchen@tamu.edu</json:string></affiliations></json:item><json:item><name>JIANLIN WANG</name><affiliations><json:string>Intercollegiate Program in Genetics and Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843–2474, USA</json:string></affiliations></json:item><json:item><name>LU TIAN</name><affiliations><json:string>Intercollegiate Program in Genetics and Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843–2474, USA</json:string></affiliations></json:item><json:item><name>HYEON‐SE LEE</name><affiliations><json:string>Intercollegiate Program in Genetics and Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843–2474, USA</json:string></affiliations></json:item><json:item><name>JIYUAN J. WANG</name><affiliations><json:string>Intercollegiate Program in Genetics and Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843–2474, USA</json:string></affiliations></json:item><json:item><name>MENG CHEN</name><affiliations><json:string>Intercollegiate Program in Genetics and Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843–2474, USA</json:string></affiliations></json:item><json:item><name>JINSUK J. LEE</name><affiliations><json:string>Intercollegiate Program in Genetics and Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843–2474, USA</json:string></affiliations></json:item><json:item><name>CAROLINE JOSEFSSON</name><affiliations><json:string>Department of Botany, University of Washington, Seattle, WA 98195, USA</json:string></affiliations></json:item><json:item><name>ANDREAS MADLUNG</name><affiliations><json:string>Department of Botany, University of Washington, Seattle, WA 98195, USA</json:string></affiliations></json:item><json:item><name>BRIAN WATSON</name><affiliations><json:string>Department of Botany, University of Washington, Seattle, WA 98195, USA</json:string></affiliations></json:item><json:item><name>ZACH LIPPMAN</name><affiliations><json:string>Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA</json:string></affiliations></json:item><json:item><name>MATT VAUGHN</name><affiliations><json:string>Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA</json:string></affiliations></json:item><json:item><name>J. CHRIS PIRES</name><affiliations><json:string>Department of Agronomy, University of Wisconsin, Madison, WI 53706, USA</json:string></affiliations></json:item><json:item><name>VINCENT COLOT</name><affiliations><json:string>Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA</json:string></affiliations></json:item><json:item><name>R. W. DOERGE</name><affiliations><json:string>Departments of Statistics, Agronomy, and Computational Genomics, Purdue University, West Lafayette, IN 47907, USA</json:string></affiliations></json:item><json:item><name>ROBERT A. MARTIENSSEN</name><affiliations><json:string>Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA</json:string></affiliations></json:item><json:item><name>LUCA COMAI</name><affiliations><json:string>Department of Botany, University of Washington, Seattle, WA 98195, USA</json:string></affiliations></json:item><json:item><name>THOMAS C. OSBORN</name><affiliations><json:string>Department of Agronomy, University of Wisconsin, Madison, WI 53706, USA</json:string></affiliations></json:item></author><subject><json:item><lang><json:string>eng</json:string></lang><value>Brassicaceae</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>chromatin</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>epigenetics</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>gene silencing</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>genome dosage</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>genome duplication</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>microarray</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>RNAi</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>transcriptome</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>transposons</value></json:item></subject><articleId><json:string>BIJ351</json:string></articleId><arkIstex>ark:/67375/WNG-M8V968KM-0</arkIstex><language><json:string>eng</json:string></language><originalGenre><json:string>article</json:string></originalGenre><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.</abstract><qualityIndicators><score>9.544</score><pdfWordCount>7769</pdfWordCount><pdfCharCount>50652</pdfCharCount><pdfVersion>1.4</pdfVersion><pdfPageCount>12</pdfPageCount><pdfPageSize>592.165 x 790.976 pts</pdfPageSize><pdfWordsPerPage>647</pdfWordsPerPage><pdfText>true</pdfText><refBibsNative>true</refBibsNative><abstractWordCount>212</abstractWordCount><abstractCharCount>1549</abstractCharCount><keywordCount>10</keywordCount></qualityIndicators><title>The development of an Arabidopsis model system for genome‐wide analysis of polyploidy effects</title><pmid><json:string>18079994</json:string></pmid><genre><json:string>article</json:string></genre><host><title>Biological Journal of the Linnean Society</title><language><json:string>unknown</json:string></language><doi><json:string>10.1111/(ISSN)1095-8312</json:string></doi><issn><json:string>0024-4066</json:string></issn><eissn><json:string>1095-8312</json:string></eissn><publisherId><json:string>BIJ</json:string></publisherId><volume>82</volume><issue>4</issue><pages><first>689</first><last>700</last><total>12</total></pages><genre><json:string>journal</json:string></genre></host><namedEntities><unitex><date><json:string>1979</json:string><json:string>2004</json:string></date><geogName></geogName><orgName><json:string>Axon Instruments</json:string><json:string>NCBI</json:string><json:string>Institute for Genomic Research</json:string><json:string>TIGR</json:string><json:string>Purdue University</json:string><json:string>National Institutes of Health, National Science Foundation</json:string><json:string>Arabidopsis Biological Resource Center</json:string><json:string>Department of Agronomy, University of Wisconsin, Madison, WI</json:string><json:string>National Center of Biological Institutes</json:string><json:string>Department of Biology, University of Puget Sound, Tacoma, WA</json:string><json:string>Arabidopsis Genome Initiative</json:string><json:string>National Institutes of Health</json:string><json:string>Cold Spring Harbor Laboratory, Cold Spring Harbor, NY</json:string><json:string>Department of Botany, University of Washington, Seattle, WA</json:string></orgName><orgName_funder></orgName_funder><orgName_provider></orgName_provider><persName><json:string>An Arabidopsis</json:string><json:string>D. 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EFFECTS</title><author xml:id="author-0000" role="corresp"><persName><forename type="first">Z. JEFFREY</forename><surname>CHEN</surname></persName><affiliation><orgName type="division">Intercollegiate Program in Genetics and Department of Soil and Crop Sciences</orgName><orgName type="institution">Texas A&M University</orgName><address><addrLine>College Station</addrLine><addrLine>TX 77843–2474, USA</addrLine><country key="US" xml:lang="en">UNITED STATES</country></address></affiliation></author><author xml:id="author-0001"><persName><forename type="first">JIANLIN</forename><surname>WANG</surname></persName><affiliation><orgName type="division">Intercollegiate Program in Genetics and Department of Soil and Crop Sciences</orgName><orgName type="institution">Texas A&M University</orgName><address><addrLine>College Station</addrLine><addrLine>TX 77843–2474, USA</addrLine><country key="US" xml:lang="en">UNITED STATES</country></address></affiliation></author><author xml:id="author-0002"><persName><forename type="first">LU</forename><surname>TIAN</surname></persName><affiliation><orgName type="division">Intercollegiate Program in Genetics and Department of Soil and Crop Sciences</orgName><orgName type="institution">Texas A&M University</orgName><address><addrLine>College Station</addrLine><addrLine>TX 77843–2474, USA</addrLine><country key="US" xml:lang="en">UNITED STATES</country></address></affiliation></author><author xml:id="author-0003"><persName><forename type="first">HYEON‐SE</forename><surname>LEE</surname></persName><affiliation><orgName type="division">Intercollegiate Program in Genetics and Department of Soil and Crop Sciences</orgName><orgName type="institution">Texas A&M University</orgName><address><addrLine>College Station</addrLine><addrLine>TX 77843–2474, USA</addrLine><country key="US" xml:lang="en">UNITED STATES</country></address></affiliation></author><author xml:id="author-0004"><persName><forename type="first">JIYUAN 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J.</forename><surname>LEE</surname></persName><affiliation><orgName type="division">Intercollegiate Program in Genetics and Department of Soil and Crop Sciences</orgName><orgName type="institution">Texas A&M University</orgName><address><addrLine>College Station</addrLine><addrLine>TX 77843–2474, USA</addrLine><country key="US" xml:lang="en">UNITED STATES</country></address></affiliation></author><author xml:id="author-0007"><persName><forename type="first">CAROLINE</forename><surname>JOSEFSSON</surname></persName><affiliation><orgName type="division">Department of Botany</orgName><orgName type="institution">University of Washington</orgName><address><addrLine>Seattle</addrLine><addrLine>WA 98195, USA</addrLine><country key="US" xml:lang="en">UNITED STATES</country></address></affiliation></author><author xml:id="author-0008"><persName><forename type="first">ANDREAS</forename><surname>MADLUNG</surname></persName><affiliation><orgName type="division">Department of Botany</orgName><orgName type="institution">University of Washington</orgName><address><addrLine>Seattle</addrLine><addrLine>WA 98195, USA</addrLine><country key="US" xml:lang="en">UNITED STATES</country></address></affiliation></author><author xml:id="author-0009"><persName><forename type="first">BRIAN</forename><surname>WATSON</surname></persName><affiliation><orgName type="division">Department of Botany</orgName><orgName type="institution">University of Washington</orgName><address><addrLine>Seattle</addrLine><addrLine>WA 98195, USA</addrLine><country key="US" xml:lang="en">UNITED STATES</country></address></affiliation></author><author xml:id="author-0010"><persName><forename type="first">ZACH</forename><surname>LIPPMAN</surname></persName><affiliation><orgName type="laboratory">Cold Spring Harbor Laboratory</orgName><address><addrLine>Cold Spring Harbor</addrLine><addrLine>NY 11724, USA</addrLine><country key="US" xml:lang="en">UNITED STATES</country></address></affiliation></author><author xml:id="author-0011"><persName><forename type="first">MATT</forename><surname>VAUGHN</surname></persName><affiliation><orgName type="laboratory">Cold Spring Harbor Laboratory</orgName><address><addrLine>Cold Spring Harbor</addrLine><addrLine>NY 11724, USA</addrLine><country key="US" xml:lang="en">UNITED STATES</country></address></affiliation></author><author xml:id="author-0012"><persName><forename type="first">J. CHRIS</forename><surname>PIRES</surname></persName><affiliation><orgName type="division">Department of Agronomy</orgName><orgName type="institution">University of Wisconsin</orgName><address><addrLine>Madison</addrLine><addrLine>WI 53706, USA</addrLine><country key="US" xml:lang="en">UNITED STATES</country></address></affiliation></author><author xml:id="author-0013"><persName><forename type="first">VINCENT</forename><surname>COLOT</surname></persName><affiliation><orgName type="laboratory">Cold Spring Harbor Laboratory</orgName><address><addrLine>Cold Spring Harbor</addrLine><addrLine>NY 11724, USA</addrLine><country key="US" xml:lang="en">UNITED STATES</country></address></affiliation></author><author xml:id="author-0014"><persName><forename type="first">R. W.</forename><surname>DOERGE</surname></persName><affiliation><orgName type="division">Departments of Statistics</orgName><address><addrLine>Agronomy</addrLine><addrLine>and Computational Genomics, Purdue University, West Lafayette, IN 47907, USA</addrLine><country key="US" xml:lang="en">UNITED STATES</country></address></affiliation></author><author xml:id="author-0015"><persName><forename type="first">ROBERT A.</forename><surname>MARTIENSSEN</surname></persName><affiliation><orgName type="laboratory">Cold Spring Harbor Laboratory</orgName><address><addrLine>Cold Spring Harbor</addrLine><addrLine>NY 11724, USA</addrLine><country key="US" xml:lang="en">UNITED STATES</country></address></affiliation></author><author xml:id="author-0016"><persName><forename type="first">LUCA</forename><surname>COMAI</surname></persName><affiliation><orgName type="division">Department of Botany</orgName><orgName type="institution">University of Washington</orgName><address><addrLine>Seattle</addrLine><addrLine>WA 98195, USA</addrLine><country key="US" xml:lang="en">UNITED STATES</country></address></affiliation></author><author xml:id="author-0017"><persName><forename type="first">THOMAS C.</forename><surname>OSBORN</surname></persName><affiliation><orgName type="division">Department of Agronomy</orgName><orgName type="institution">University of Wisconsin</orgName><address><addrLine>Madison</addrLine><addrLine>WI 53706, USA</addrLine><country key="US" xml:lang="en">UNITED STATES</country></address></affiliation></author><idno type="istex">106146BAD678BB4E14BDC457E6822196B66B0020</idno><idno type="ark">ark:/67375/WNG-M8V968KM-0</idno><idno type="DOI">10.1111/j.1095-8312.2004.00351.x</idno><idno type="unit">BIJ351</idno><idno type="toTypesetVersion">file:BIJ.BIJ351.pdf</idno></analytic><monogr><title level="j" type="main">Biological Journal of the Linnean Society</title><title level="j" type="alt">BIOLOGICAL JOURNAL LINNEAN SOCIETY</title><idno type="pISSN">0024-4066</idno><idno type="eISSN">1095-8312</idno><idno type="book-DOI">10.1111/(ISSN)1095-8312</idno><idno type="book-part-DOI">10.1111/bij.2004.82.issue-4</idno><idno type="product">BIJ</idno><idno type="publisherDivision">ST</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"></date></imprint></monogr></biblStruct></sourceDesc></fileDesc><encodingDesc><schemaRef type="ODD" url="https://xml-schema.delivery.istex.fr/tei-istex.odd"></schemaRef><appInfo><application ident="pub2tei" version="1.0.10" when="2019-12-20"><label>pub2TEI-ISTEX</label><desc>A set of style sheets for converting XML documents encoded in various scientific publisher formats into a common TEI format.
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<hi rend="italic">Arabidopsis</hi> 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 <hi rend="italic">Arabidopsis</hi> 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 <hi rend="italic">Arabidopsis</hi> offer an exceptional means by which regulatory mechanisms of gene and genome duplication may be revealed. Moreover, the <hi rend="italic">Arabidopsis</hi> genome is completely sequenced; both coding and non‐coding sequences are available. We have developed spotted oligo‐gene and chromosome microarrays using the complete <hi rend="italic">Arabidopsis</hi> genome sequence. The oligo‐gene microarray consists of ∼26 000 70‐mer oligonucleotides that are designed from all annotated genes in <hi rend="italic">Arabidopsis</hi>, 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 <hi rend="italic">Arabidopsis</hi> polyploids and related species. © 2004 The Linnean Society of London, <hi rend="italic">Biological Journal of the Linnean Society</hi>, 2004, <hi rend="bold">82</hi>, 689–700.</p></abstract><textClass><keywords xml:lang="en"><term xml:id="k1">Brassicaceae</term><term xml:id="k2">chromatin</term><term xml:id="k3">epigenetics</term><term xml:id="k4">gene silencing</term><term xml:id="k5">genome dosage</term><term xml:id="k6">genome duplication</term><term xml:id="k7">microarray</term><term xml:id="k8">RNAi</term><term xml:id="k9">transcriptome</term><term xml:id="k10">transposons</term></keywords><keywords rend="tocHeading1"><term>Original Articles</term></keywords></textClass><langUsage><language ident="en"></language></langUsage></profileDesc><revisionDesc><change when="2019-12-20" who="#istex" xml:id="pub2tei">formatting</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><extension>txt</extension><original>false</original><mimetype>text/plain</mimetype><uri>https://api.istex.fr/ark:/67375/WNG-M8V968KM-0/fulltext.txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="Wiley, elements deleted: body"><istex:xmlDeclaration>version="1.0" encoding="UTF-8" standalone="yes"</istex:xmlDeclaration><istex:document><component version="2.0" type="serialArticle" xml:lang="en"><header><publicationMeta level="product"><publisherInfo><publisherName>Blackwell Science Ltd</publisherName><publisherLoc>Oxford, UK</publisherLoc></publisherInfo><doi origin="wiley" registered="yes">10.1111/(ISSN)1095-8312</doi><issn type="print">0024-4066</issn><issn type="electronic">1095-8312</issn><idGroup><id type="product" value="BIJ"></id><id type="publisherDivision" value="ST"></id></idGroup><titleGroup><title type="main" sort="BIOLOGICAL JOURNAL LINNEAN SOCIETY">Biological Journal of the Linnean Society</title></titleGroup></publicationMeta><publicationMeta level="part" position="08004"><doi origin="wiley">10.1111/bij.2004.82.issue-4</doi><numberingGroup><numbering type="journalVolume" number="82">82</numbering><numbering type="journalIssue" number="4">4</numbering></numberingGroup><coverDate startDate="2004-08">August 2004</coverDate></publicationMeta><publicationMeta level="unit" type="article" position="26" status="forIssue"><doi origin="wiley">10.1111/j.1095-8312.2004.00351.x</doi><idGroup><id type="unit" value="BIJ351"></id></idGroup><countGroup><count type="pageTotal" number="12"></count></countGroup><titleGroup><title type="tocHeading1">Original Articles</title></titleGroup><eventGroup><event type="firstOnline" date="2004-08-09"></event><event type="publishedOnlineFinalForm" date="2004-08-09"></event><event type="xmlConverted" agent="Converter:BPG_TO_WML3G version:2.3.15 mode:FullText" date="2010-07-15"></event><event type="xmlConverted" agent="Converter:WILEY_ML3G_TO_WILEY_ML3GV2 version:3.8.8" date="2014-02-22"></event><event type="xmlConverted" agent="Converter:WML3G_To_WML3G version:4.1.7 mode:FullText,remove_FC" date="2014-10-15"></event></eventGroup><numberingGroup><numbering type="pageFirst" number="689">689</numbering><numbering type="pageLast" number="700">700</numbering></numberingGroup><correspondenceTo>
E‐mail: <email>zjchen@tamu.edu</email></correspondenceTo><linkGroup><link type="toTypesetVersion" href="file:BIJ.BIJ351.pdf"></link></linkGroup></publicationMeta><contentMeta><unparsedEditorialHistory>Received 19 June 2003; accepted for publication 5 January 2004</unparsedEditorialHistory><countGroup><count type="figureTotal" number="4"></count><count type="tableTotal" number="1"></count><count type="formulaTotal" number="0"></count><count type="referenceTotal" number="109"></count><count type="wordTotal" number="5781"></count><count type="linksPubMed" number="0"></count><count type="linksCrossRef" number="0"></count></countGroup><titleGroup><title type="main">The development of an <i>Arabidopsis</i> model system for genome‐wide analysis of polyploidy effects</title><title type="shortAuthors">Z. J. CHEN <i>Et al.</i></title><title type="short"><i>ARABIDOPSIS</i> MODEL SYSTEM FOR ANALYSIS OF POLYPLOIDY EFFECTS</title></titleGroup><creators><creator creatorRole="author" xml:id="cr1" affiliationRef="#a1" corresponding="yes"><personName><givenNames>Z. JEFFREY</givenNames><familyName>CHEN</familyName></personName></creator><creator creatorRole="author" xml:id="cr2" affiliationRef="#a1"><personName><givenNames>JIANLIN</givenNames><familyName>WANG</familyName></personName></creator><creator creatorRole="author" xml:id="cr3" affiliationRef="#a1"><personName><givenNames>LU</givenNames><familyName>TIAN</familyName></personName></creator><creator creatorRole="author" xml:id="cr4" affiliationRef="#a1"><personName><givenNames>HYEON‐SE</givenNames><familyName>LEE</familyName></personName></creator><creator creatorRole="author" xml:id="cr5" affiliationRef="#a1"><personName><givenNames>JIYUAN J.</givenNames><familyName>WANG</familyName></personName></creator><creator creatorRole="author" xml:id="cr6" affiliationRef="#a1"><personName><givenNames>MENG</givenNames><familyName>CHEN</familyName></personName></creator><creator creatorRole="author" xml:id="cr7" affiliationRef="#a1"><personName><givenNames>JINSUK J.</givenNames><familyName>LEE</familyName></personName></creator><creator creatorRole="author" xml:id="cr8" affiliationRef="#a2"><personName><givenNames>CAROLINE</givenNames><familyName>JOSEFSSON</familyName></personName></creator><creator creatorRole="author" xml:id="cr9" affiliationRef="#a2" noteRef="#fn1"><personName><givenNames>ANDREAS</givenNames><familyName>MADLUNG</familyName></personName></creator><creator creatorRole="author" xml:id="cr10" affiliationRef="#a2"><personName><givenNames>BRIAN</givenNames><familyName>WATSON</familyName></personName></creator><creator creatorRole="author" xml:id="cr11" affiliationRef="#a3"><personName><givenNames>ZACH</givenNames><familyName>LIPPMAN</familyName></personName></creator><creator creatorRole="author" xml:id="cr12" affiliationRef="#a3"><personName><givenNames>MATT</givenNames><familyName>VAUGHN</familyName></personName></creator><creator creatorRole="author" xml:id="cr13" affiliationRef="#a4"><personName><givenNames>J. CHRIS</givenNames><familyName>PIRES</familyName></personName></creator><creator creatorRole="author" xml:id="cr14" affiliationRef="#a3" noteRef="#fn2"><personName><givenNames>VINCENT</givenNames><familyName>COLOT</familyName></personName></creator><creator creatorRole="author" xml:id="cr15" affiliationRef="#a5"><personName><givenNames>R. W.</givenNames><familyName>DOERGE</familyName></personName></creator><creator creatorRole="author" xml:id="cr16" affiliationRef="#a3"><personName><givenNames>ROBERT A.</givenNames><familyName>MARTIENSSEN</familyName></personName></creator><creator creatorRole="author" xml:id="cr17" affiliationRef="#a2"><personName><givenNames>LUCA</givenNames><familyName>COMAI</familyName></personName></creator><creator creatorRole="author" xml:id="cr18" affiliationRef="#a4"><personName><givenNames>THOMAS C.</givenNames><familyName>OSBORN</familyName></personName></creator></creators><affiliationGroup><affiliation xml:id="a1" countryCode="US"><unparsedAffiliation>Intercollegiate Program in Genetics and Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843–2474, USA</unparsedAffiliation></affiliation><affiliation xml:id="a2" countryCode="US"><unparsedAffiliation>Department of Botany, University of Washington, Seattle, WA 98195, USA</unparsedAffiliation></affiliation><affiliation xml:id="a3" countryCode="US"><unparsedAffiliation>Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA</unparsedAffiliation></affiliation><affiliation xml:id="a4" countryCode="US"><unparsedAffiliation>Department of Agronomy, University of Wisconsin, Madison, WI 53706, USA</unparsedAffiliation></affiliation><affiliation xml:id="a5" countryCode="US"><unparsedAffiliation>Departments of Statistics, Agronomy, and Computational Genomics, Purdue University, West Lafayette, IN 47907, USA</unparsedAffiliation></affiliation></affiliationGroup><keywordGroup xml:lang="en"><keyword xml:id="k1">Brassicaceae</keyword><keyword xml:id="k2">chromatin</keyword><keyword xml:id="k3">epigenetics</keyword><keyword xml:id="k4">gene silencing</keyword><keyword xml:id="k5">genome dosage</keyword><keyword xml:id="k6">genome duplication</keyword><keyword xml:id="k7">microarray</keyword><keyword xml:id="k8">RNAi</keyword><keyword xml:id="k9">transcriptome</keyword><keyword xml:id="k10">transposons</keyword></keywordGroup><abstractGroup><abstract type="main" xml:lang="en"><p> <i>Arabidopsis</i> 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 <i>Arabidopsis</i> 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 <i>Arabidopsis</i> offer an exceptional means by which regulatory mechanisms of gene and genome duplication may be revealed. Moreover, the <i>Arabidopsis</i> genome is completely sequenced; both coding and non‐coding sequences are available. We have developed spotted oligo‐gene and chromosome microarrays using the complete <i>Arabidopsis</i> genome sequence. The oligo‐gene microarray consists of ∼26 000 70‐mer oligonucleotides that are designed from all annotated genes in <i>Arabidopsis</i>, 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 <i>Arabidopsis</i> polyploids and related species. © 2004 The Linnean Society of London, <i>Biological Journal of the Linnean Society</i>, 2004, <b>82</b>, 689–700.</p></abstract></abstractGroup></contentMeta><noteGroup><note xml:id="fn1"><label>†</label><p>
Department of Biology, University of Puget Sound, Tacoma, WA 98416, USA; </p></note><note xml:id="fn2"><label>‡</label><p>
Unité de Recherche en Génomique Végétale, Evry, Paris, France.</p></note></noteGroup></header></component></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>The development of an Arabidopsis model system for genome‐wide analysis of polyploidy effects</title></titleInfo><titleInfo type="abbreviated" lang="en"><title>ARABIDOPSIS MODEL SYSTEM FOR ANALYSIS OF POLYPLOIDY EFFECTS</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>The development of an Arabidopsis model system for genome‐wide analysis of polyploidy effects</title></titleInfo><name type="personal"><namePart type="given">Z. JEFFREY</namePart><namePart type="family">CHEN</namePart><affiliation>Intercollegiate Program in Genetics and Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843–2474, USA</affiliation><affiliation>E-mail: zjchen@tamu.edu</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">JIANLIN</namePart><namePart type="family">WANG</namePart><affiliation>Intercollegiate Program in Genetics and Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843–2474, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">LU</namePart><namePart type="family">TIAN</namePart><affiliation>Intercollegiate Program in Genetics and Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843–2474, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">HYEON‐SE</namePart><namePart type="family">LEE</namePart><affiliation>Intercollegiate Program in Genetics and Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843–2474, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">JIYUAN J.</namePart><namePart type="family">WANG</namePart><affiliation>Intercollegiate Program in Genetics and Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843–2474, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">MENG</namePart><namePart type="family">CHEN</namePart><affiliation>Intercollegiate Program in Genetics and Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843–2474, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">JINSUK J.</namePart><namePart type="family">LEE</namePart><affiliation>Intercollegiate Program in Genetics and Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843–2474, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">CAROLINE</namePart><namePart type="family">JOSEFSSON</namePart><affiliation>Department of Botany, University of Washington, Seattle, WA 98195, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">ANDREAS</namePart><namePart type="family">MADLUNG</namePart><affiliation>Department of Botany, University of Washington, Seattle, WA 98195, USA</affiliation><description>Department of Biology, University of Puget Sound, Tacoma, WA 98416, USA;</description><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">BRIAN</namePart><namePart type="family">WATSON</namePart><affiliation>Department of Botany, University of Washington, Seattle, WA 98195, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">ZACH</namePart><namePart type="family">LIPPMAN</namePart><affiliation>Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">MATT</namePart><namePart type="family">VAUGHN</namePart><affiliation>Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">J. CHRIS</namePart><namePart type="family">PIRES</namePart><affiliation>Department of Agronomy, University of Wisconsin, Madison, WI 53706, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">VINCENT</namePart><namePart type="family">COLOT</namePart><affiliation>Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA</affiliation><description>Unité de Recherche en Génomique Végétale, Evry, Paris, France.</description><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">R. W.</namePart><namePart type="family">DOERGE</namePart><affiliation>Departments of Statistics, Agronomy, and Computational Genomics, Purdue University, West Lafayette, IN 47907, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">ROBERT A.</namePart><namePart type="family">MARTIENSSEN</namePart><affiliation>Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">LUCA</namePart><namePart type="family">COMAI</namePart><affiliation>Department of Botany, University of Washington, Seattle, WA 98195, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">THOMAS C.</namePart><namePart type="family">OSBORN</namePart><affiliation>Department of Agronomy, University of Wisconsin, Madison, WI 53706, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="article" displayLabel="article" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-6N5SZHKN-D">article</genre><originInfo><publisher>Blackwell Science Ltd</publisher><place><placeTerm type="text">Oxford, UK</placeTerm></place><dateIssued encoding="w3cdtf">2004-08</dateIssued><edition>Received 19 June 2003; accepted for publication 5 January 2004</edition><copyrightDate encoding="w3cdtf">2004</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><physicalDescription><extent unit="figures">4</extent><extent unit="tables">1</extent><extent unit="formulas">0</extent><extent unit="references">109</extent><extent unit="linksCrossRef">0</extent><extent unit="words">5781</extent></physicalDescription><abstract 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.</abstract><subject lang="en"><genre>keywords</genre><topic>Brassicaceae</topic><topic>chromatin</topic><topic>epigenetics</topic><topic>gene silencing</topic><topic>genome dosage</topic><topic>genome duplication</topic><topic>microarray</topic><topic>RNAi</topic><topic>transcriptome</topic><topic>transposons</topic></subject><relatedItem type="host"><titleInfo><title>Biological Journal of the Linnean Society</title></titleInfo><genre type="journal" authority="ISTEX" authorityURI="https://publication-type.data.istex.fr" valueURI="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</genre><identifier type="ISSN">0024-4066</identifier><identifier type="eISSN">1095-8312</identifier><identifier type="DOI">10.1111/(ISSN)1095-8312</identifier><identifier type="PublisherID">BIJ</identifier><part><date>2004</date><detail type="volume"><caption>vol.</caption><number>82</number></detail><detail type="issue"><caption>no.</caption><number>4</number></detail><extent unit="pages"><start>689</start><end>700</end><total>12</total></extent></part></relatedItem><relatedItem type="references" displayLabel="cit1"><titleInfo><title>Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ‐specific reciprocal silencing</title></titleInfo><name type="personal"><namePart type="given">KL</namePart><namePart type="family">Adams</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">R</namePart><namePart type="family">Cronn</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">R</namePart><namePart type="family">Percifield</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">JF</namePart><namePart type="family">Wendel</namePart><role><roleTerm type="text">author</roleTerm></role></name><genre>journal-article</genre><note type="citation/reference">Adams KL, Cronn R, Percifield R, Wendel JF. 2003. 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