Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea
Identifieur interne : 003395 ( Main/Exploration ); précédent : 003394; suivant : 003396Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea
Auteurs : Isobel Ap Parkin [Canada] ; Chushin Koh [Canada] ; Haibao Tang [États-Unis] ; Stephen J. Robinson [Canada] ; Sateesh Kagale [Canada] ; Wayne E. Clarke [Canada] ; Chris D. Town [États-Unis] ; John Nixon [Canada] ; Vivek Krishnakumar [États-Unis] ; Shelby L. Bidwell [États-Unis] ; France Denoeud [France] ; Harry Belcram [France] ; Matthew G. Links [Canada] ; Jérémy Just [France] ; Carling Clarke [Canada] ; Tricia Bender [Canada] ; Terry Huebert [Canada] ; Annaliese S. Mason [Australie] ; J Chris Pires [États-Unis] ; Guy Barker [Royaume-Uni] ; Jonathan Moore [Royaume-Uni] ; Peter G. Walley [Royaume-Uni] ; Sahana Manoli [Australie] ; Jacqueline Batley [Australie] ; David Edwards [Australie] ; Matthew N. Nelson [Australie] ; Xiyin Wang [États-Unis] ; Andrew H. Paterson [États-Unis] ; Graham King [Australie] ; Ian Bancroft [Royaume-Uni] ; Boulos Chalhoub [France] ; Andrew G. Sharpe [Canada]Source :
- Genome Biology [ 1465-6906 ] ; 2014.
Abstract
We generate an assembly representing 75% of the predicted
Differential expression of the triplicated syntelogs and cytosine methylation levels across the sub-genomes suggest residual marks of the genome dominance that led to the current genome architecture. Although cytosine methylation does not correlate with individual gene dominance, the independent methylation patterns of triplicated copies suggest epigenetic mechanisms play a role in the functional diversification of duplicate genes.
Url:
DOI: 10.1186/gb-2014-15-6-r77
PubMed: 24916971
PubMed Central: 4097860
Affiliations:
- Australie, Canada, France, Royaume-Uni, États-Unis
- Maryland, Missouri (État), Île-de-France
- Évry (Essonne)
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 001641
- to stream Pmc, to step Curation: 001501
- to stream Pmc, to step Checkpoint: 001279
- to stream Ncbi, to step Merge: 001B08
- to stream Ncbi, to step Curation: 001B08
- to stream Ncbi, to step Checkpoint: 001B08
- to stream Main, to step Merge: 003407
- to stream Main, to step Curation: 003395
Le document en format XML
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<author><name sortKey="Wang, Xiyin" sort="Wang, Xiyin" uniqKey="Wang X" first="Xiyin" last="Wang">Xiyin Wang</name>
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<author><name sortKey="Bancroft, Ian" sort="Bancroft, Ian" uniqKey="Bancroft I" first="Ian" last="Bancroft">Ian Bancroft</name>
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<author><name sortKey="Chalhoub, Boulos" sort="Chalhoub, Boulos" uniqKey="Chalhoub B" first="Boulos" last="Chalhoub">Boulos Chalhoub</name>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid <italic>Brassica oleracea</italic>
</title>
<author><name sortKey="Parkin, Isobel Ap" sort="Parkin, Isobel Ap" uniqKey="Parkin I" first="Isobel Ap" last="Parkin">Isobel Ap Parkin</name>
<affiliation wicri:level="1"><nlm:aff id="I1">Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N0X2, Canada</nlm:aff>
<country xml:lang="fr">Canada</country>
<wicri:regionArea>Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N0X2</wicri:regionArea>
<wicri:noRegion>S7N0X2</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Koh, Chushin" sort="Koh, Chushin" uniqKey="Koh C" first="Chushin" last="Koh">Chushin Koh</name>
<affiliation wicri:level="1"><nlm:aff id="I2">National Research Council Canada, 110 Gymnasium Place, Saskatoon S7N0W9, Canada</nlm:aff>
<country xml:lang="fr">Canada</country>
<wicri:regionArea>National Research Council Canada, 110 Gymnasium Place, Saskatoon S7N0W9</wicri:regionArea>
<wicri:noRegion>Saskatoon S7N0W9</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Tang, Haibao" sort="Tang, Haibao" uniqKey="Tang H" first="Haibao" last="Tang">Haibao Tang</name>
<affiliation wicri:level="2"><nlm:aff id="I3">J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Robinson, Stephen J" sort="Robinson, Stephen J" uniqKey="Robinson S" first="Stephen J" last="Robinson">Stephen J. Robinson</name>
<affiliation wicri:level="1"><nlm:aff id="I1">Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N0X2, Canada</nlm:aff>
<country xml:lang="fr">Canada</country>
<wicri:regionArea>Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N0X2</wicri:regionArea>
<wicri:noRegion>S7N0X2</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Kagale, Sateesh" sort="Kagale, Sateesh" uniqKey="Kagale S" first="Sateesh" last="Kagale">Sateesh Kagale</name>
<affiliation wicri:level="1"><nlm:aff id="I1">Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N0X2, Canada</nlm:aff>
<country xml:lang="fr">Canada</country>
<wicri:regionArea>Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N0X2</wicri:regionArea>
<wicri:noRegion>S7N0X2</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="I2">National Research Council Canada, 110 Gymnasium Place, Saskatoon S7N0W9, Canada</nlm:aff>
<country xml:lang="fr">Canada</country>
<wicri:regionArea>National Research Council Canada, 110 Gymnasium Place, Saskatoon S7N0W9</wicri:regionArea>
<wicri:noRegion>Saskatoon S7N0W9</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Clarke, Wayne E" sort="Clarke, Wayne E" uniqKey="Clarke W" first="Wayne E" last="Clarke">Wayne E. Clarke</name>
<affiliation wicri:level="1"><nlm:aff id="I1">Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N0X2, Canada</nlm:aff>
<country xml:lang="fr">Canada</country>
<wicri:regionArea>Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N0X2</wicri:regionArea>
<wicri:noRegion>S7N0X2</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Town, Chris D" sort="Town, Chris D" uniqKey="Town C" first="Chris D" last="Town">Chris D. Town</name>
<affiliation wicri:level="2"><nlm:aff id="I3">J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Nixon, John" sort="Nixon, John" uniqKey="Nixon J" first="John" last="Nixon">John Nixon</name>
<affiliation wicri:level="1"><nlm:aff id="I1">Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N0X2, Canada</nlm:aff>
<country xml:lang="fr">Canada</country>
<wicri:regionArea>Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N0X2</wicri:regionArea>
<wicri:noRegion>S7N0X2</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Krishnakumar, Vivek" sort="Krishnakumar, Vivek" uniqKey="Krishnakumar V" first="Vivek" last="Krishnakumar">Vivek Krishnakumar</name>
<affiliation wicri:level="2"><nlm:aff id="I3">J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Bidwell, Shelby L" sort="Bidwell, Shelby L" uniqKey="Bidwell S" first="Shelby L" last="Bidwell">Shelby L. Bidwell</name>
<affiliation wicri:level="2"><nlm:aff id="I3">J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Denoeud, France" sort="Denoeud, France" uniqKey="Denoeud F" first="France" last="Denoeud">France Denoeud</name>
<affiliation wicri:level="3"><nlm:aff id="I4">Commissariat à l’Energie Atomique (CEA), Institut de Génomique, BP5706, Evry, 91057, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>Commissariat à l’Energie Atomique (CEA), Institut de Génomique, BP5706, Evry, 91057</wicri:regionArea>
<placeName><region type="region" nuts="2">Île-de-France</region>
</placeName>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="I5">Centre National de Recherche Scientifique (CNRS), UMR 8030, CP5706 Evry, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>Centre National de Recherche Scientifique (CNRS), UMR 8030, CP5706 Evry</wicri:regionArea>
<wicri:noRegion>CP5706 Evry</wicri:noRegion>
<wicri:noRegion>CP5706 Evry</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="I6">Université d’Evry, UMR 8030, Evry, CP5706, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>Université d’Evry, UMR 8030, Evry, CP5706</wicri:regionArea>
<wicri:noRegion>CP5706</wicri:noRegion>
<wicri:noRegion>CP5706</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Belcram, Harry" sort="Belcram, Harry" uniqKey="Belcram H" first="Harry" last="Belcram">Harry Belcram</name>
<affiliation wicri:level="3"><nlm:aff id="I7">Organization and Evolution of Plant Genomes, Unité de Recherche en Génomique Végétale, Unité Mixte de Rechercheé 1165, (Inland Northwest Research Alliance Institut National de Recherche Agronomique - Centre National de la Recherche Scientifique, Université Evry Val d’Essonne), Evry, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>Organization and Evolution of Plant Genomes, Unité de Recherche en Génomique Végétale, Unité Mixte de Rechercheé 1165, (Inland Northwest Research Alliance Institut National de Recherche Agronomique - Centre National de la Recherche Scientifique, Université Evry Val d’Essonne), Evry</wicri:regionArea>
<placeName><region type="region">Île-de-France</region>
<region type="old region">Île-de-France</region>
<settlement type="city">Évry (Essonne)</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Links, Matthew G" sort="Links, Matthew G" uniqKey="Links M" first="Matthew G" last="Links">Matthew G. Links</name>
<affiliation wicri:level="1"><nlm:aff id="I1">Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N0X2, Canada</nlm:aff>
<country xml:lang="fr">Canada</country>
<wicri:regionArea>Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N0X2</wicri:regionArea>
<wicri:noRegion>S7N0X2</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Just, Jeremy" sort="Just, Jeremy" uniqKey="Just J" first="Jérémy" last="Just">Jérémy Just</name>
<affiliation wicri:level="3"><nlm:aff id="I7">Organization and Evolution of Plant Genomes, Unité de Recherche en Génomique Végétale, Unité Mixte de Rechercheé 1165, (Inland Northwest Research Alliance Institut National de Recherche Agronomique - Centre National de la Recherche Scientifique, Université Evry Val d’Essonne), Evry, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>Organization and Evolution of Plant Genomes, Unité de Recherche en Génomique Végétale, Unité Mixte de Rechercheé 1165, (Inland Northwest Research Alliance Institut National de Recherche Agronomique - Centre National de la Recherche Scientifique, Université Evry Val d’Essonne), Evry</wicri:regionArea>
<placeName><region type="region">Île-de-France</region>
<region type="old region">Île-de-France</region>
<settlement type="city">Évry (Essonne)</settlement>
</placeName>
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</author>
<author><name sortKey="Clarke, Carling" sort="Clarke, Carling" uniqKey="Clarke C" first="Carling" last="Clarke">Carling Clarke</name>
<affiliation wicri:level="1"><nlm:aff id="I2">National Research Council Canada, 110 Gymnasium Place, Saskatoon S7N0W9, Canada</nlm:aff>
<country xml:lang="fr">Canada</country>
<wicri:regionArea>National Research Council Canada, 110 Gymnasium Place, Saskatoon S7N0W9</wicri:regionArea>
<wicri:noRegion>Saskatoon S7N0W9</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Bender, Tricia" sort="Bender, Tricia" uniqKey="Bender T" first="Tricia" last="Bender">Tricia Bender</name>
<affiliation wicri:level="1"><nlm:aff id="I1">Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N0X2, Canada</nlm:aff>
<country xml:lang="fr">Canada</country>
<wicri:regionArea>Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N0X2</wicri:regionArea>
<wicri:noRegion>S7N0X2</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Huebert, Terry" sort="Huebert, Terry" uniqKey="Huebert T" first="Terry" last="Huebert">Terry Huebert</name>
<affiliation wicri:level="1"><nlm:aff id="I1">Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N0X2, Canada</nlm:aff>
<country xml:lang="fr">Canada</country>
<wicri:regionArea>Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N0X2</wicri:regionArea>
<wicri:noRegion>S7N0X2</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Mason, Annaliese S" sort="Mason, Annaliese S" uniqKey="Mason A" first="Annaliese S" last="Mason">Annaliese S. Mason</name>
<affiliation wicri:level="1"><nlm:aff id="I8">School of Agriculture and Food Sciences, The University of Queensland, Brisbane 4072, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Agriculture and Food Sciences, The University of Queensland, Brisbane 4072</wicri:regionArea>
<wicri:noRegion>Brisbane 4072</wicri:noRegion>
</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 wicri:level="2"><nlm:aff id="I9">Division of Biological Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211-7310, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Division of Biological Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211-7310</wicri:regionArea>
<placeName><region type="state">Missouri (État)</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Barker, Guy" sort="Barker, Guy" uniqKey="Barker G" first="Guy" last="Barker">Guy Barker</name>
<affiliation wicri:level="1"><nlm:aff id="I10">Warwick Life Sciences, The University of Warwick, Warwick CV35 9EF, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Warwick Life Sciences, The University of Warwick, Warwick CV35 9EF</wicri:regionArea>
<wicri:noRegion>Warwick CV35 9EF</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Moore, Jonathan" sort="Moore, Jonathan" uniqKey="Moore J" first="Jonathan" last="Moore">Jonathan Moore</name>
<affiliation wicri:level="1"><nlm:aff id="I10">Warwick Life Sciences, The University of Warwick, Warwick CV35 9EF, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Warwick Life Sciences, The University of Warwick, Warwick CV35 9EF</wicri:regionArea>
<wicri:noRegion>Warwick CV35 9EF</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Walley, Peter G" sort="Walley, Peter G" uniqKey="Walley P" first="Peter G" last="Walley">Peter G. Walley</name>
<affiliation wicri:level="1"><nlm:aff id="I10">Warwick Life Sciences, The University of Warwick, Warwick CV35 9EF, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Warwick Life Sciences, The University of Warwick, Warwick CV35 9EF</wicri:regionArea>
<wicri:noRegion>Warwick CV35 9EF</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Manoli, Sahana" sort="Manoli, Sahana" uniqKey="Manoli S" first="Sahana" last="Manoli">Sahana Manoli</name>
<affiliation wicri:level="1"><nlm:aff id="I8">School of Agriculture and Food Sciences, The University of Queensland, Brisbane 4072, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Agriculture and Food Sciences, The University of Queensland, Brisbane 4072</wicri:regionArea>
<wicri:noRegion>Brisbane 4072</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Batley, Jacqueline" sort="Batley, Jacqueline" uniqKey="Batley J" first="Jacqueline" last="Batley">Jacqueline Batley</name>
<affiliation wicri:level="1"><nlm:aff id="I8">School of Agriculture and Food Sciences, The University of Queensland, Brisbane 4072, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Agriculture and Food Sciences, The University of Queensland, Brisbane 4072</wicri:regionArea>
<wicri:noRegion>Brisbane 4072</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Edwards, David" sort="Edwards, David" uniqKey="Edwards D" first="David" last="Edwards">David Edwards</name>
<affiliation wicri:level="1"><nlm:aff id="I8">School of Agriculture and Food Sciences, The University of Queensland, Brisbane 4072, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Agriculture and Food Sciences, The University of Queensland, Brisbane 4072</wicri:regionArea>
<wicri:noRegion>Brisbane 4072</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Nelson, Matthew N" sort="Nelson, Matthew N" uniqKey="Nelson M" first="Matthew N" last="Nelson">Matthew N. Nelson</name>
<affiliation wicri:level="1"><nlm:aff id="I11">School of Plant Biology/ The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Plant Biology/ The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009</wicri:regionArea>
<wicri:noRegion>WA 6009</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Wang, Xiyin" sort="Wang, Xiyin" uniqKey="Wang X" first="Xiyin" last="Wang">Xiyin Wang</name>
<affiliation wicri:level="1"><nlm:aff id="I12">Plant Genome Mapping Laboratory, University of Georgia, Athens GA 30602, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Plant Genome Mapping Laboratory, University of Georgia, Athens GA 30602</wicri:regionArea>
<wicri:noRegion>Athens GA 30602</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Paterson, Andrew H" sort="Paterson, Andrew H" uniqKey="Paterson A" first="Andrew H" last="Paterson">Andrew H. Paterson</name>
<affiliation wicri:level="1"><nlm:aff id="I12">Plant Genome Mapping Laboratory, University of Georgia, Athens GA 30602, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Plant Genome Mapping Laboratory, University of Georgia, Athens GA 30602</wicri:regionArea>
<wicri:noRegion>Athens GA 30602</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="King, Graham" sort="King, Graham" uniqKey="King G" first="Graham" last="King">Graham King</name>
<affiliation wicri:level="1"><nlm:aff id="I13">Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480</wicri:regionArea>
<wicri:noRegion>NSW 2480</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Bancroft, Ian" sort="Bancroft, Ian" uniqKey="Bancroft I" first="Ian" last="Bancroft">Ian Bancroft</name>
<affiliation wicri:level="1"><nlm:aff id="I14">Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD</wicri:regionArea>
<wicri:noRegion>York YO10 5DD</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Chalhoub, Boulos" sort="Chalhoub, Boulos" uniqKey="Chalhoub B" first="Boulos" last="Chalhoub">Boulos Chalhoub</name>
<affiliation wicri:level="3"><nlm:aff id="I7">Organization and Evolution of Plant Genomes, Unité de Recherche en Génomique Végétale, Unité Mixte de Rechercheé 1165, (Inland Northwest Research Alliance Institut National de Recherche Agronomique - Centre National de la Recherche Scientifique, Université Evry Val d’Essonne), Evry, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>Organization and Evolution of Plant Genomes, Unité de Recherche en Génomique Végétale, Unité Mixte de Rechercheé 1165, (Inland Northwest Research Alliance Institut National de Recherche Agronomique - Centre National de la Recherche Scientifique, Université Evry Val d’Essonne), Evry</wicri:regionArea>
<placeName><region type="region">Île-de-France</region>
<region type="old region">Île-de-France</region>
<settlement type="city">Évry (Essonne)</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Sharpe, Andrew G" sort="Sharpe, Andrew G" uniqKey="Sharpe A" first="Andrew G" last="Sharpe">Andrew G. Sharpe</name>
<affiliation wicri:level="1"><nlm:aff id="I2">National Research Council Canada, 110 Gymnasium Place, Saskatoon S7N0W9, Canada</nlm:aff>
<country xml:lang="fr">Canada</country>
<wicri:regionArea>National Research Council Canada, 110 Gymnasium Place, Saskatoon S7N0W9</wicri:regionArea>
<wicri:noRegion>Saskatoon S7N0W9</wicri:noRegion>
</affiliation>
</author>
</analytic>
<series><title level="j">Genome Biology</title>
<idno type="ISSN">1465-6906</idno>
<idno type="eISSN">1465-6914</idno>
<imprint><date when="2014">2014</date>
</imprint>
</series>
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<profileDesc><textClass></textClass>
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</teiHeader>
<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p><italic>Brassica oleracea</italic>
is a valuable vegetable species that has contributed to human health and nutrition for hundreds of years and comprises multiple distinct cultivar groups with diverse morphological and phytochemical attributes. In addition to this phenotypic wealth, <italic>B. oleracea</italic>
offers unique insights into polyploid evolution, as it results from multiple ancestral polyploidy events and a final Brassiceae-specific triplication event. Further, <italic>B. oleracea</italic>
represents one of the diploid genomes that formed the economically important allopolyploid oilseed, <italic>Brassica napus</italic>
. A deeper understanding of <italic>B. oleracea</italic>
genome architecture provides a foundation for crop improvement strategies throughout the <italic>Brassica</italic>
genus.</p>
</sec>
<sec><title>Results</title>
<p>We generate an assembly representing 75% of the predicted <italic>B. oleracea</italic>
genome using a hybrid Illumina/Roche 454 approach. Two dense genetic maps are generated to anchor almost 92% of the assembled scaffolds to nine pseudo-chromosomes. Over 50,000 genes are annotated and 40% of the genome predicted to be repetitive, thus contributing to the increased genome size of <italic>B. oleracea</italic>
compared to its close relative <italic>B. rapa</italic>
. A snapshot of both the leaf transcriptome and methylome allows comparisons to be made across the triplicated sub-genomes, which resulted from the most recent Brassiceae-specific polyploidy event.</p>
</sec>
<sec><title>Conclusions</title>
<p>Differential expression of the triplicated syntelogs and cytosine methylation levels across the sub-genomes suggest residual marks of the genome dominance that led to the current genome architecture. Although cytosine methylation does not correlate with individual gene dominance, the independent methylation patterns of triplicated copies suggest epigenetic mechanisms play a role in the functional diversification of duplicate genes.</p>
</sec>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Wang, X" uniqKey="Wang X">X Wang</name>
</author>
<author><name sortKey="Wang, H" uniqKey="Wang H">H Wang</name>
</author>
<author><name sortKey="Wang, J" uniqKey="Wang J">J Wang</name>
</author>
<author><name sortKey="Sun, R" uniqKey="Sun R">R Sun</name>
</author>
<author><name sortKey="Wu, J" uniqKey="Wu J">J Wu</name>
</author>
<author><name sortKey="Liu, S" uniqKey="Liu S">S Liu</name>
</author>
<author><name sortKey="Bai, Y" uniqKey="Bai Y">Y Bai</name>
</author>
<author><name sortKey="Mun, Jh" uniqKey="Mun J">JH Mun</name>
</author>
<author><name sortKey="Bancroft, I" uniqKey="Bancroft I">I Bancroft</name>
</author>
<author><name sortKey="Cheng, F" uniqKey="Cheng F">F Cheng</name>
</author>
<author><name sortKey="Huang, S" uniqKey="Huang S">S Huang</name>
</author>
<author><name sortKey="Li, X" uniqKey="Li X">X Li</name>
</author>
<author><name sortKey="Hua, W" uniqKey="Hua W">W Hua</name>
</author>
<author><name sortKey="Wang, J" uniqKey="Wang J">J Wang</name>
</author>
<author><name sortKey="Wang, X" uniqKey="Wang X">X Wang</name>
</author>
<author><name sortKey="Freeling, M" uniqKey="Freeling M">M Freeling</name>
</author>
<author><name sortKey="Pires, Jc" uniqKey="Pires J">JC Pires</name>
</author>
<author><name sortKey="Paterson, Ah" uniqKey="Paterson A">AH Paterson</name>
</author>
<author><name sortKey="Chalhoub, B" uniqKey="Chalhoub B">B Chalhoub</name>
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</div1>
</back>
</TEI>
<affiliations><list><country><li>Australie</li>
<li>Canada</li>
<li>France</li>
<li>Royaume-Uni</li>
<li>États-Unis</li>
</country>
<region><li>Maryland</li>
<li>Missouri (État)</li>
<li>Île-de-France</li>
</region>
<settlement><li>Évry (Essonne)</li>
</settlement>
</list>
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<name sortKey="Clarke, Wayne E" sort="Clarke, Wayne E" uniqKey="Clarke W" first="Wayne E" last="Clarke">Wayne E. Clarke</name>
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<name sortKey="Kagale, Sateesh" sort="Kagale, Sateesh" uniqKey="Kagale S" first="Sateesh" last="Kagale">Sateesh Kagale</name>
<name sortKey="Kagale, Sateesh" sort="Kagale, Sateesh" uniqKey="Kagale S" first="Sateesh" last="Kagale">Sateesh Kagale</name>
<name sortKey="Koh, Chushin" sort="Koh, Chushin" uniqKey="Koh C" first="Chushin" last="Koh">Chushin Koh</name>
<name sortKey="Links, Matthew G" sort="Links, Matthew G" uniqKey="Links M" first="Matthew G" last="Links">Matthew G. Links</name>
<name sortKey="Nixon, John" sort="Nixon, John" uniqKey="Nixon J" first="John" last="Nixon">John Nixon</name>
<name sortKey="Robinson, Stephen J" sort="Robinson, Stephen J" uniqKey="Robinson S" first="Stephen J" last="Robinson">Stephen J. Robinson</name>
<name sortKey="Sharpe, Andrew G" sort="Sharpe, Andrew G" uniqKey="Sharpe A" first="Andrew G" last="Sharpe">Andrew G. Sharpe</name>
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<name sortKey="Paterson, Andrew H" sort="Paterson, Andrew H" uniqKey="Paterson A" first="Andrew H" last="Paterson">Andrew H. Paterson</name>
<name sortKey="Pires, J Chris" sort="Pires, J Chris" uniqKey="Pires J" first="J Chris" last="Pires">J Chris Pires</name>
<name sortKey="Town, Chris D" sort="Town, Chris D" uniqKey="Town C" first="Chris D" last="Town">Chris D. Town</name>
<name sortKey="Wang, Xiyin" sort="Wang, Xiyin" uniqKey="Wang X" first="Xiyin" last="Wang">Xiyin Wang</name>
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<country name="France"><region name="Île-de-France"><name sortKey="Denoeud, France" sort="Denoeud, France" uniqKey="Denoeud F" first="France" last="Denoeud">France Denoeud</name>
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<name sortKey="Belcram, Harry" sort="Belcram, Harry" uniqKey="Belcram H" first="Harry" last="Belcram">Harry Belcram</name>
<name sortKey="Chalhoub, Boulos" sort="Chalhoub, Boulos" uniqKey="Chalhoub B" first="Boulos" last="Chalhoub">Boulos Chalhoub</name>
<name sortKey="Denoeud, France" sort="Denoeud, France" uniqKey="Denoeud F" first="France" last="Denoeud">France Denoeud</name>
<name sortKey="Denoeud, France" sort="Denoeud, France" uniqKey="Denoeud F" first="France" last="Denoeud">France Denoeud</name>
<name sortKey="Just, Jeremy" sort="Just, Jeremy" uniqKey="Just J" first="Jérémy" last="Just">Jérémy Just</name>
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<country name="Australie"><noRegion><name sortKey="Mason, Annaliese S" sort="Mason, Annaliese S" uniqKey="Mason A" first="Annaliese S" last="Mason">Annaliese S. Mason</name>
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<name sortKey="Batley, Jacqueline" sort="Batley, Jacqueline" uniqKey="Batley J" first="Jacqueline" last="Batley">Jacqueline Batley</name>
<name sortKey="Edwards, David" sort="Edwards, David" uniqKey="Edwards D" first="David" last="Edwards">David Edwards</name>
<name sortKey="King, Graham" sort="King, Graham" uniqKey="King G" first="Graham" last="King">Graham King</name>
<name sortKey="Manoli, Sahana" sort="Manoli, Sahana" uniqKey="Manoli S" first="Sahana" last="Manoli">Sahana Manoli</name>
<name sortKey="Nelson, Matthew N" sort="Nelson, Matthew N" uniqKey="Nelson M" first="Matthew N" last="Nelson">Matthew N. Nelson</name>
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<country name="Royaume-Uni"><noRegion><name sortKey="Barker, Guy" sort="Barker, Guy" uniqKey="Barker G" first="Guy" last="Barker">Guy Barker</name>
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<name sortKey="Bancroft, Ian" sort="Bancroft, Ian" uniqKey="Bancroft I" first="Ian" last="Bancroft">Ian Bancroft</name>
<name sortKey="Moore, Jonathan" sort="Moore, Jonathan" uniqKey="Moore J" first="Jonathan" last="Moore">Jonathan Moore</name>
<name sortKey="Walley, Peter G" sort="Walley, Peter G" uniqKey="Walley P" first="Peter G" last="Walley">Peter G. Walley</name>
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</tree>
</affiliations>
</record>
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