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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Differential Accumulation of Retroelements and Diversification of NB-LRR Disease Resistance Genes in Duplicated Regions following Polyploidy in the Ancestor of Soybean<xref ref-type="fn" rid="fn1">1</xref><xref ref-type="fn" rid="fn3">[W]</xref><xref ref-type="fn" rid="fn4">[OA]</xref></title><author><name sortKey="Innes, Roger W" sort="Innes, Roger W" uniqKey="Innes R" first="Roger W." last="Innes">Roger W. Innes</name></author><author><name sortKey="Ameline Torregrosa, Carine" sort="Ameline Torregrosa, Carine" uniqKey="Ameline Torregrosa C" first="Carine" last="Ameline-Torregrosa">Carine Ameline-Torregrosa</name></author><author><name sortKey="Ashfield, Tom" sort="Ashfield, Tom" uniqKey="Ashfield T" first="Tom" last="Ashfield">Tom Ashfield</name></author><author><name sortKey="Cannon, Ethalinda" sort="Cannon, Ethalinda" uniqKey="Cannon E" first="Ethalinda" last="Cannon">Ethalinda Cannon</name></author><author><name sortKey="Cannon, Steven B" sort="Cannon, Steven B" uniqKey="Cannon S" first="Steven B." last="Cannon">Steven B. Cannon</name></author><author><name sortKey="Chacko, Ben" sort="Chacko, Ben" uniqKey="Chacko B" first="Ben" last="Chacko">Ben Chacko</name></author><author><name sortKey="Chen, Nicolas W G" sort="Chen, Nicolas W G" uniqKey="Chen N" first="Nicolas W. G." last="Chen">Nicolas W. G. Chen</name></author><author><name sortKey="Couloux, Arnaud" sort="Couloux, Arnaud" uniqKey="Couloux A" first="Arnaud" last="Couloux">Arnaud Couloux</name></author><author><name sortKey="Dalwani, Anita" sort="Dalwani, Anita" uniqKey="Dalwani A" first="Anita" last="Dalwani">Anita Dalwani</name></author><author><name sortKey="Denny, Roxanne" sort="Denny, Roxanne" uniqKey="Denny R" first="Roxanne" last="Denny">Roxanne Denny</name></author><author><name sortKey="Deshpande, Shweta" sort="Deshpande, Shweta" uniqKey="Deshpande S" first="Shweta" last="Deshpande">Shweta Deshpande</name></author><author><name sortKey="Egan, Ashley N" sort="Egan, Ashley N" uniqKey="Egan A" first="Ashley N." last="Egan">Ashley N. Egan</name></author><author><name sortKey="Glover, Natasha" sort="Glover, Natasha" uniqKey="Glover N" first="Natasha" last="Glover">Natasha Glover</name></author><author><name sortKey="Hans, Christian S" sort="Hans, Christian S" uniqKey="Hans C" first="Christian S." last="Hans">Christian S. Hans</name></author><author><name sortKey="Howell, Stacy" sort="Howell, Stacy" uniqKey="Howell S" first="Stacy" last="Howell">Stacy Howell</name></author><author><name sortKey="Ilut, Dan" sort="Ilut, Dan" uniqKey="Ilut D" first="Dan" last="Ilut">Dan Ilut</name></author><author><name sortKey="Jackson, Scott" sort="Jackson, Scott" uniqKey="Jackson S" first="Scott" last="Jackson">Scott Jackson</name></author><author><name sortKey="Lai, Hongshing" sort="Lai, Hongshing" uniqKey="Lai H" first="Hongshing" last="Lai">Hongshing Lai</name></author><author><name sortKey="Mammadov, Jafar" sort="Mammadov, Jafar" uniqKey="Mammadov J" first="Jafar" last="Mammadov">Jafar Mammadov</name></author><author><name sortKey="Del Campo, Sara Martin" sort="Del Campo, Sara Martin" uniqKey="Del Campo S" first="Sara Martin" last="Del Campo">Sara Martin Del Campo</name></author><author><name sortKey="Metcalf, Michelle" sort="Metcalf, Michelle" uniqKey="Metcalf M" first="Michelle" last="Metcalf">Michelle Metcalf</name></author><author><name sortKey="Nguyen, Ashley" sort="Nguyen, Ashley" uniqKey="Nguyen A" first="Ashley" last="Nguyen">Ashley Nguyen</name></author><author><name sortKey="O Bleness, Majesta" sort="O Bleness, Majesta" uniqKey="O Bleness M" first="Majesta" last="O'Bleness">Majesta O'Bleness</name></author><author><name sortKey="Pfeil, Bernard E" sort="Pfeil, Bernard E" uniqKey="Pfeil B" first="Bernard E." last="Pfeil">Bernard E. Pfeil</name></author><author><name sortKey="Podicheti, Ram" sort="Podicheti, Ram" uniqKey="Podicheti R" first="Ram" last="Podicheti">Ram Podicheti</name></author><author><name sortKey="Ratnaparkhe, Milind B" sort="Ratnaparkhe, Milind B" uniqKey="Ratnaparkhe M" first="Milind B." last="Ratnaparkhe">Milind B. Ratnaparkhe</name></author><author><name sortKey="Samain, Sylvie" sort="Samain, Sylvie" uniqKey="Samain S" first="Sylvie" last="Samain">Sylvie Samain</name></author><author><name sortKey="Sanders, Iryna" sort="Sanders, Iryna" uniqKey="Sanders I" first="Iryna" last="Sanders">Iryna Sanders</name></author><author><name sortKey="Segurens, Beatrice" sort="Segurens, Beatrice" uniqKey="Segurens B" first="Béatrice" last="Ségurens">Béatrice Ségurens</name></author><author><name sortKey="Sevignac, Mireille" sort="Sevignac, Mireille" uniqKey="Sevignac M" first="Mireille" last="Sévignac">Mireille Sévignac</name></author><author><name sortKey="Sherman Broyles, Sue" sort="Sherman Broyles, Sue" uniqKey="Sherman Broyles S" first="Sue" last="Sherman-Broyles">Sue Sherman-Broyles</name></author><author><name sortKey="Thareau, Vincent" sort="Thareau, Vincent" uniqKey="Thareau V" first="Vincent" last="Thareau">Vincent Thareau</name></author><author><name sortKey="Tucker, Dominic M" sort="Tucker, Dominic M" uniqKey="Tucker D" first="Dominic M." last="Tucker">Dominic M. Tucker</name></author><author><name sortKey="Walling, Jason" sort="Walling, Jason" uniqKey="Walling J" first="Jason" last="Walling">Jason Walling</name></author><author><name sortKey="Wawrzynski, Adam" sort="Wawrzynski, Adam" uniqKey="Wawrzynski A" first="Adam" last="Wawrzynski">Adam Wawrzynski</name></author><author><name sortKey="Yi, Jing" sort="Yi, Jing" uniqKey="Yi J" first="Jing" last="Yi">Jing Yi</name></author><author><name sortKey="Doyle, Jeff J" sort="Doyle, Jeff J" uniqKey="Doyle J" first="Jeff J." last="Doyle">Jeff J. Doyle</name></author><author><name sortKey="Geffroy, Valerie" sort="Geffroy, Valerie" uniqKey="Geffroy V" first="Valérie" last="Geffroy">Valérie Geffroy</name></author><author><name sortKey="Roe, Bruce A" sort="Roe, Bruce A" uniqKey="Roe B" first="Bruce A." last="Roe">Bruce A. Roe</name></author><author><name sortKey="Maroof, M A Saghai" sort="Maroof, M A Saghai" uniqKey="Maroof M" first="M. A. Saghai" last="Maroof">M. A. Saghai Maroof</name></author><author><name sortKey="Young, Nevin D" sort="Young, Nevin D" uniqKey="Young N" first="Nevin D." last="Young">Nevin D. Young</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">18842825</idno><idno type="pmc">2593655</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2593655</idno><idno type="RBID">PMC:2593655</idno><idno type="doi">10.1104/pp.108.127902</idno><date when="2008">2008</date><idno type="wicri:Area/Pmc/Corpus">001056</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001056</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Differential Accumulation of Retroelements and Diversification of NB-LRR Disease Resistance Genes in Duplicated Regions following Polyploidy in the Ancestor of Soybean<xref ref-type="fn" rid="fn1">1</xref><xref ref-type="fn" rid="fn3">[W]</xref><xref ref-type="fn" rid="fn4">[OA]</xref></title><author><name sortKey="Innes, Roger W" sort="Innes, Roger W" uniqKey="Innes R" first="Roger W." last="Innes">Roger W. Innes</name></author><author><name sortKey="Ameline Torregrosa, Carine" sort="Ameline Torregrosa, Carine" uniqKey="Ameline Torregrosa C" first="Carine" last="Ameline-Torregrosa">Carine Ameline-Torregrosa</name></author><author><name sortKey="Ashfield, Tom" sort="Ashfield, Tom" uniqKey="Ashfield T" first="Tom" last="Ashfield">Tom Ashfield</name></author><author><name sortKey="Cannon, Ethalinda" sort="Cannon, Ethalinda" uniqKey="Cannon E" first="Ethalinda" last="Cannon">Ethalinda Cannon</name></author><author><name sortKey="Cannon, Steven B" sort="Cannon, Steven B" uniqKey="Cannon S" first="Steven B." last="Cannon">Steven B. Cannon</name></author><author><name sortKey="Chacko, Ben" sort="Chacko, Ben" uniqKey="Chacko B" first="Ben" last="Chacko">Ben Chacko</name></author><author><name sortKey="Chen, Nicolas W G" sort="Chen, Nicolas W G" uniqKey="Chen N" first="Nicolas W. G." last="Chen">Nicolas W. G. Chen</name></author><author><name sortKey="Couloux, Arnaud" sort="Couloux, Arnaud" uniqKey="Couloux A" first="Arnaud" last="Couloux">Arnaud Couloux</name></author><author><name sortKey="Dalwani, Anita" sort="Dalwani, Anita" uniqKey="Dalwani A" first="Anita" last="Dalwani">Anita Dalwani</name></author><author><name sortKey="Denny, Roxanne" sort="Denny, Roxanne" uniqKey="Denny R" first="Roxanne" last="Denny">Roxanne Denny</name></author><author><name sortKey="Deshpande, Shweta" sort="Deshpande, Shweta" uniqKey="Deshpande S" first="Shweta" last="Deshpande">Shweta Deshpande</name></author><author><name sortKey="Egan, Ashley N" sort="Egan, Ashley N" uniqKey="Egan A" first="Ashley N." last="Egan">Ashley N. Egan</name></author><author><name sortKey="Glover, Natasha" sort="Glover, Natasha" uniqKey="Glover N" first="Natasha" last="Glover">Natasha Glover</name></author><author><name sortKey="Hans, Christian S" sort="Hans, Christian S" uniqKey="Hans C" first="Christian S." last="Hans">Christian S. Hans</name></author><author><name sortKey="Howell, Stacy" sort="Howell, Stacy" uniqKey="Howell S" first="Stacy" last="Howell">Stacy Howell</name></author><author><name sortKey="Ilut, Dan" sort="Ilut, Dan" uniqKey="Ilut D" first="Dan" last="Ilut">Dan Ilut</name></author><author><name sortKey="Jackson, Scott" sort="Jackson, Scott" uniqKey="Jackson S" first="Scott" last="Jackson">Scott Jackson</name></author><author><name sortKey="Lai, Hongshing" sort="Lai, Hongshing" uniqKey="Lai H" first="Hongshing" last="Lai">Hongshing Lai</name></author><author><name sortKey="Mammadov, Jafar" sort="Mammadov, Jafar" uniqKey="Mammadov J" first="Jafar" last="Mammadov">Jafar Mammadov</name></author><author><name sortKey="Del Campo, Sara Martin" sort="Del Campo, Sara Martin" uniqKey="Del Campo S" first="Sara Martin" last="Del Campo">Sara Martin Del Campo</name></author><author><name sortKey="Metcalf, Michelle" sort="Metcalf, Michelle" uniqKey="Metcalf M" first="Michelle" last="Metcalf">Michelle Metcalf</name></author><author><name sortKey="Nguyen, Ashley" sort="Nguyen, Ashley" uniqKey="Nguyen A" first="Ashley" last="Nguyen">Ashley Nguyen</name></author><author><name sortKey="O Bleness, Majesta" sort="O Bleness, Majesta" uniqKey="O Bleness M" first="Majesta" last="O'Bleness">Majesta O'Bleness</name></author><author><name sortKey="Pfeil, Bernard E" sort="Pfeil, Bernard E" uniqKey="Pfeil B" first="Bernard E." last="Pfeil">Bernard E. Pfeil</name></author><author><name sortKey="Podicheti, Ram" sort="Podicheti, Ram" uniqKey="Podicheti R" first="Ram" last="Podicheti">Ram Podicheti</name></author><author><name sortKey="Ratnaparkhe, Milind B" sort="Ratnaparkhe, Milind B" uniqKey="Ratnaparkhe M" first="Milind B." last="Ratnaparkhe">Milind B. Ratnaparkhe</name></author><author><name sortKey="Samain, Sylvie" sort="Samain, Sylvie" uniqKey="Samain S" first="Sylvie" last="Samain">Sylvie Samain</name></author><author><name sortKey="Sanders, Iryna" sort="Sanders, Iryna" uniqKey="Sanders I" first="Iryna" last="Sanders">Iryna Sanders</name></author><author><name sortKey="Segurens, Beatrice" sort="Segurens, Beatrice" uniqKey="Segurens B" first="Béatrice" last="Ségurens">Béatrice Ségurens</name></author><author><name sortKey="Sevignac, Mireille" sort="Sevignac, Mireille" uniqKey="Sevignac M" first="Mireille" last="Sévignac">Mireille Sévignac</name></author><author><name sortKey="Sherman Broyles, Sue" sort="Sherman Broyles, Sue" uniqKey="Sherman Broyles S" first="Sue" last="Sherman-Broyles">Sue Sherman-Broyles</name></author><author><name sortKey="Thareau, Vincent" sort="Thareau, Vincent" uniqKey="Thareau V" first="Vincent" last="Thareau">Vincent Thareau</name></author><author><name sortKey="Tucker, Dominic M" sort="Tucker, Dominic M" uniqKey="Tucker D" first="Dominic M." last="Tucker">Dominic M. Tucker</name></author><author><name sortKey="Walling, Jason" sort="Walling, Jason" uniqKey="Walling J" first="Jason" last="Walling">Jason Walling</name></author><author><name sortKey="Wawrzynski, Adam" sort="Wawrzynski, Adam" uniqKey="Wawrzynski A" first="Adam" last="Wawrzynski">Adam Wawrzynski</name></author><author><name sortKey="Yi, Jing" sort="Yi, Jing" uniqKey="Yi J" first="Jing" last="Yi">Jing Yi</name></author><author><name sortKey="Doyle, Jeff J" sort="Doyle, Jeff J" uniqKey="Doyle J" first="Jeff J." last="Doyle">Jeff J. Doyle</name></author><author><name sortKey="Geffroy, Valerie" sort="Geffroy, Valerie" uniqKey="Geffroy V" first="Valérie" last="Geffroy">Valérie Geffroy</name></author><author><name sortKey="Roe, Bruce A" sort="Roe, Bruce A" uniqKey="Roe B" first="Bruce A." last="Roe">Bruce A. Roe</name></author><author><name sortKey="Maroof, M A Saghai" sort="Maroof, M A Saghai" uniqKey="Maroof M" first="M. A. Saghai" last="Maroof">M. A. Saghai Maroof</name></author><author><name sortKey="Young, Nevin D" sort="Young, Nevin D" uniqKey="Young N" first="Nevin D." last="Young">Nevin D. Young</name></author></analytic><series><title level="j">Plant Physiology</title><idno type="ISSN">0032-0889</idno><idno type="eISSN">1532-2548</idno><imprint><date when="2008">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The genomes of most, if not all, flowering plants have undergone whole genome duplication events during their evolution. The impact of such polyploidy events is poorly understood, as is the fate of most duplicated genes. We sequenced an approximately 1 million-bp region in soybean (<italic>Glycine max</italic>) centered on the <italic>Rpg1-b</italic> disease resistance gene and compared this region with a region duplicated 10 to 14 million years ago. These two regions were also compared with homologous regions in several related legume species (a second soybean genotype, <italic>Glycine tomentella</italic>, <italic>Phaseolus vulgaris</italic>, and <italic>Medicago truncatula</italic>), which enabled us to determine how each of the duplicated regions (homoeologues) in soybean has changed following polyploidy. The biggest change was in retroelement content, with homoeologue 2 having expanded to 3-fold the size of homoeologue 1. Despite this accumulation of retroelements, over 77% of the duplicated low-copy genes have been retained in the same order and appear to be functional. This finding contrasts with recent analyses of the maize (<italic>Zea mays</italic>) genome, in which only about one-third of duplicated genes appear to have been retained over a similar time period. Fluorescent in situ hybridization revealed that the homoeologue 2 region is located very near a centromere. Thus, pericentromeric localization, per se, does not result in a high rate of gene inactivation, despite greatly accelerated retrotransposon accumulation. In contrast to low-copy genes, nucleotide-binding-leucine-rich repeat disease resistance gene clusters have undergone dramatic species/homoeologue-specific duplications and losses, with some evidence for partitioning of subfamilies between homoeologues.</p></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Plant Physiol</journal-id><journal-id journal-id-type="publisher-id">plantphysiol</journal-id><journal-title>Plant Physiology</journal-title><issn pub-type="ppub">0032-0889</issn><issn pub-type="epub">1532-2548</issn><publisher><publisher-name>American Society of Plant Biologists</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">18842825</article-id><article-id pub-id-type="pmc">2593655</article-id><article-id pub-id-type="publisher-id">127902</article-id><article-id pub-id-type="doi">10.1104/pp.108.127902</article-id><article-categories><subj-group subj-group-type="heading"><subject>Genome Analysis</subject></subj-group></article-categories><title-group><article-title>Differential Accumulation of Retroelements and Diversification of NB-LRR Disease Resistance Genes in Duplicated Regions following Polyploidy in the Ancestor of Soybean<xref ref-type="fn" rid="fn1">1</xref><xref ref-type="fn" rid="fn3">[W]</xref><xref ref-type="fn" rid="fn4">[OA]</xref></article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Innes</surname><given-names>Roger W.</given-names></name><xref ref-type="corresp" rid="cor1">*</xref></contrib><contrib contrib-type="author"><name><surname>Ameline-Torregrosa</surname><given-names>Carine</given-names></name></contrib><contrib contrib-type="author"><name><surname>Ashfield</surname><given-names>Tom</given-names></name></contrib><contrib contrib-type="author"><name><surname>Cannon</surname><given-names>Ethalinda</given-names></name></contrib><contrib contrib-type="author"><name><surname>Cannon</surname><given-names>Steven B.</given-names></name></contrib><contrib contrib-type="author"><name><surname>Chacko</surname><given-names>Ben</given-names></name></contrib><contrib contrib-type="author"><name><surname>Chen</surname><given-names>Nicolas W.G.</given-names></name></contrib><contrib contrib-type="author"><name><surname>Couloux</surname><given-names>Arnaud</given-names></name></contrib><contrib contrib-type="author"><name><surname>Dalwani</surname><given-names>Anita</given-names></name></contrib><contrib contrib-type="author"><name><surname>Denny</surname><given-names>Roxanne</given-names></name></contrib><contrib contrib-type="author"><name><surname>Deshpande</surname><given-names>Shweta</given-names></name></contrib><contrib contrib-type="author"><name><surname>Egan</surname><given-names>Ashley N.</given-names></name></contrib><contrib contrib-type="author"><name><surname>Glover</surname><given-names>Natasha</given-names></name></contrib><contrib contrib-type="author"><name><surname>Hans</surname><given-names>Christian S.</given-names></name></contrib><contrib contrib-type="author"><name><surname>Howell</surname><given-names>Stacy</given-names></name></contrib><contrib contrib-type="author"><name><surname>Ilut</surname><given-names>Dan</given-names></name></contrib><contrib contrib-type="author"><name><surname>Jackson</surname><given-names>Scott</given-names></name></contrib><contrib contrib-type="author"><name><surname>Lai</surname><given-names>Hongshing</given-names></name></contrib><contrib contrib-type="author"><name><surname>Mammadov</surname><given-names>Jafar</given-names></name><xref ref-type="fn" rid="fn2">2</xref></contrib><contrib contrib-type="author"><name><surname>del Campo</surname><given-names>Sara Martin</given-names></name></contrib><contrib contrib-type="author"><name><surname>Metcalf</surname><given-names>Michelle</given-names></name></contrib><contrib contrib-type="author"><name><surname>Nguyen</surname><given-names>Ashley</given-names></name></contrib><contrib contrib-type="author"><name><surname>O'Bleness</surname><given-names>Majesta</given-names></name></contrib><contrib contrib-type="author"><name><surname>Pfeil</surname><given-names>Bernard E.</given-names></name></contrib><contrib contrib-type="author"><name><surname>Podicheti</surname><given-names>Ram</given-names></name></contrib><contrib contrib-type="author"><name><surname>Ratnaparkhe</surname><given-names>Milind B.</given-names></name></contrib><contrib contrib-type="author"><name><surname>Samain</surname><given-names>Sylvie</given-names></name></contrib><contrib contrib-type="author"><name><surname>Sanders</surname><given-names>Iryna</given-names></name></contrib><contrib contrib-type="author"><name><surname>Ségurens</surname><given-names>Béatrice</given-names></name></contrib><contrib contrib-type="author"><name><surname>Sévignac</surname><given-names>Mireille</given-names></name></contrib><contrib contrib-type="author"><name><surname>Sherman-Broyles</surname><given-names>Sue</given-names></name></contrib><contrib contrib-type="author"><name><surname>Thareau</surname><given-names>Vincent</given-names></name></contrib><contrib contrib-type="author"><name><surname>Tucker</surname><given-names>Dominic M.</given-names></name></contrib><contrib contrib-type="author"><name><surname>Walling</surname><given-names>Jason</given-names></name></contrib><contrib contrib-type="author"><name><surname>Wawrzynski</surname><given-names>Adam</given-names></name></contrib><contrib contrib-type="author"><name><surname>Yi</surname><given-names>Jing</given-names></name></contrib><contrib contrib-type="author"><name><surname>Doyle</surname><given-names>Jeff J.</given-names></name></contrib><contrib contrib-type="author"><name><surname>Geffroy</surname><given-names>Valérie</given-names></name></contrib><contrib contrib-type="author"><name><surname>Roe</surname><given-names>Bruce A.</given-names></name></contrib><contrib contrib-type="author"><name><surname>Maroof</surname><given-names>M.A. Saghai</given-names></name></contrib><contrib contrib-type="author"><name><surname>Young</surname><given-names>Nevin D.</given-names></name></contrib></contrib-group><aff id="N0x1cf93f0N0x1ef4b48">Department of Biology, Indiana University, Bloomington, Indiana 47405 (R.W.I., T.A., A.D., S.H., S.M.d.C., M.M., R.P., A.W.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., E.C., S.B.C., B.C., R.D., N.D.Y.); Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011 (E.C.); United States Department of Agriculture-Agricultural Research Service and Department of Agronomy, Iowa State University, Ames, Iowa 50011 (S.B.C.); Institut de Biotechnologie des Plantes, UMR CNRS 8618, INRA, Université Paris Sud, 91 405 Orsay, France (N.W.G.C., M.S., V.T., V.G.); Genoscope/Commissariat à l'Energie Atomique-Centre National de Séquençage, 91 057 Evry, France (A.C., S.S., B.S.); Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019 (S.D., H.L., M.O., I.S., J.Y., B.A.R.); L.H. Bailey Hortorium, Department of Plant Biology, Cornell University, Ithaca, New York 14853 (A.N.E., D.I., B.E.P., S.S.-B., J.J.D.); Department of Crop and Soil Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061 (N.G., J.M., A.N., M.B.R., D.M.T., M.A.S.M.); Department of Agronomy, Purdue University, West Lafayette, Indiana 47907 (C.S.H., S.J., J.W.); Commonwealth Scientific and Industrial Research Organization Plant Industry, Canberra, Australian Capital Territory 2601, Australia (B.E.P.); and Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211 (M.B.R.)</aff><author-notes><fn id="cor1"><label>*</label><p>Corresponding author; e-mail <email>rinnes@indiana.edu</email>.</p></fn><fn id="fn2"><label>2</label><p>Present address: Trait Genetics and Technology, Dow AgroSciences LLC, Indianapolis, IN 46268.</p></fn></author-notes><pub-date pub-type="ppub"><month>12</month><year>2008</year></pub-date><volume>148</volume><issue>4</issue><fpage>1740</fpage><lpage>1759</lpage><history><date date-type="received"><day>10</day><month>8</month><year>2008</year></date><date date-type="accepted"><day>6</day><month>10</month><year>2008</year></date></history><permissions><copyright-statement>Copyright © 2008, American Society of Plant Biologists</copyright-statement></permissions><abstract><p>The genomes of most, if not all, flowering plants have undergone whole genome duplication events during their evolution. The impact of such polyploidy events is poorly understood, as is the fate of most duplicated genes. We sequenced an approximately 1 million-bp region in soybean (<italic>Glycine max</italic>) centered on the <italic>Rpg1-b</italic> disease resistance gene and compared this region with a region duplicated 10 to 14 million years ago. These two regions were also compared with homologous regions in several related legume species (a second soybean genotype, <italic>Glycine tomentella</italic>, <italic>Phaseolus vulgaris</italic>, and <italic>Medicago truncatula</italic>), which enabled us to determine how each of the duplicated regions (homoeologues) in soybean has changed following polyploidy. The biggest change was in retroelement content, with homoeologue 2 having expanded to 3-fold the size of homoeologue 1. Despite this accumulation of retroelements, over 77% of the duplicated low-copy genes have been retained in the same order and appear to be functional. This finding contrasts with recent analyses of the maize (<italic>Zea mays</italic>) genome, in which only about one-third of duplicated genes appear to have been retained over a similar time period. Fluorescent in situ hybridization revealed that the homoeologue 2 region is located very near a centromere. Thus, pericentromeric localization, per se, does not result in a high rate of gene inactivation, despite greatly accelerated retrotransposon accumulation. In contrast to low-copy genes, nucleotide-binding-leucine-rich repeat disease resistance gene clusters have undergone dramatic species/homoeologue-specific duplications and losses, with some evidence for partitioning of subfamilies between homoeologues.</p></abstract></article-meta><notes><fn-group><fn id="fn1"><label>1</label><p>This work was supported by the National Science Foundation Plant Genome Research Program (grant no. DBI–0321664 to R.W.I., M.A.S.M., N.D.Y., B.A.R., and J.J.D.) and by a grant from Genoscope/Commissariat à l'Energie Atomique-Centre National de Séquençage (to V.G.). A.N.E. was supported by a National Science Foundation Systematics Award (grant no. DEB–0516673).</p></fn><fn><p>The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (<ext-link ext-link-type="uri" xlink:href="www.plantphysiol.org">www.plantphysiol.org</ext-link>) is: Roger W. Innes (<email>rinnes@indiana.edu</email>).</p></fn><fn id="fn3"><label>[W]</label><p>The online version of this article contains Web-only data.</p></fn><fn id="fn4"><label>[OA]</label><p>Open Access articles can be viewed online without a subscription.</p></fn><fn><p><ext-link ext-link-type="uri" xlink:href="www.plantphysiol.org/cgi/doi/10.1104/pp.108.127902">www.plantphysiol.org/cgi/doi/10.1104/pp.108.127902</ext-link></p></fn></fn-group></notes></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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