Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)
Identifieur interne : 001408 ( Ncbi/Merge ); précédent : 001407; suivant : 001409Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)
Auteurs : Martin Mascher [Allemagne] ; Gary J. Muehlbauer [États-Unis] ; Daniel S. Rokhsar [États-Unis] ; Jarrod Chapman [États-Unis] ; Jeremy Schmutz [États-Unis] ; Kerrie Barry [États-Unis] ; María Mu Oz-Amatriaín [États-Unis] ; Timothy J. Close [États-Unis] ; Roger P. Wise [États-Unis] ; Alan H. Schulman [Finlande] ; Axel Himmelbach [Allemagne] ; Klaus Fx Mayer [Allemagne] ; Uwe Scholz [Allemagne] ; Jesse A. Poland [États-Unis] ; Nils Stein [Allemagne] ; Robbie Waugh [Royaume-Uni]Source :
- The Plant Journal [ 0960-7412 ] ; 2013.
Abstract
Next-generation whole-genome shotgun assemblies of complex genomes are highly useful, but fail to link nearby sequence contigs with each other or provide a linear order of contigs along individual chromosomes. Here, we introduce a strategy based on sequencing progeny of a segregating population that allows
Url:
DOI: 10.1111/tpj.12319
PubMed: 23998490
PubMed Central: 4298792
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Close</name><affiliation wicri:level="1"><nlm:aff id="au7"><institution>Department of Botany & Plant Sciences, University of California</institution><addr-line>Riverside, CA, 92521, USA</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Riverside, CA, 92521</wicri:regionArea><wicri:noRegion>92521</wicri:noRegion></affiliation></author><author><name sortKey="Wise, Roger P" sort="Wise, Roger P" uniqKey="Wise R" first="Roger P" last="Wise">Roger P. Wise</name><affiliation wicri:level="1"><nlm:aff id="au8"><institution>US Department of Agriculture/Agricultural Research Service, Department of Plant Pathology & Microbiology, Iowa State University</institution><addr-line>Ames, IA, 50011–1020, USA</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Ames, IA, 50011–1020</wicri:regionArea><wicri:noRegion>50011–1020</wicri:noRegion></affiliation></author><author><name sortKey="Schulman, Alan H" sort="Schulman, Alan H" uniqKey="Schulman A" first="Alan H" last="Schulman">Alan H. Schulman</name><affiliation wicri:level="1"><nlm:aff id="au9"><institution>Institute of Biotechnology, University of Helsinki/MTT Agrifood Research</institution><addr-line>PO Box 65, 00014, Helsinki, Finland</addr-line></nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>PO Box 65, 00014, Helsinki</wicri:regionArea><wicri:noRegion>Helsinki</wicri:noRegion></affiliation></author><author><name sortKey="Himmelbach, Axel" sort="Himmelbach, Axel" uniqKey="Himmelbach A" first="Axel" last="Himmelbach">Axel Himmelbach</name><affiliation wicri:level="1"><nlm:aff id="au1"><institution>Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)</institution><addr-line>D–06466 Seeland OT, Gatersleben, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>D–06466 Seeland OT, Gatersleben</wicri:regionArea><wicri:noRegion>Gatersleben</wicri:noRegion><wicri:noRegion>Gatersleben</wicri:noRegion><wicri:noRegion>Gatersleben</wicri:noRegion></affiliation></author><author><name sortKey="Mayer, Klaus Fx" sort="Mayer, Klaus Fx" uniqKey="Mayer K" first="Klaus Fx" last="Mayer">Klaus Fx Mayer</name><affiliation wicri:level="1"><nlm:aff id="au10"><institution>Munich Information Center for Protein Sequences/Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München</institution><addr-line>D–85764, Neuherberg, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>D–85764, Neuherberg</wicri:regionArea><wicri:noRegion>85764, Neuherberg</wicri:noRegion><wicri:noRegion>85764, Neuherberg</wicri:noRegion><wicri:noRegion>Neuherberg</wicri:noRegion></affiliation></author><author><name sortKey="Scholz, Uwe" sort="Scholz, Uwe" uniqKey="Scholz U" first="Uwe" last="Scholz">Uwe Scholz</name><affiliation wicri:level="1"><nlm:aff id="au1"><institution>Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)</institution><addr-line>D–06466 Seeland OT, Gatersleben, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>D–06466 Seeland OT, Gatersleben</wicri:regionArea><wicri:noRegion>Gatersleben</wicri:noRegion><wicri:noRegion>Gatersleben</wicri:noRegion><wicri:noRegion>Gatersleben</wicri:noRegion></affiliation></author><author><name sortKey="Poland, Jesse A" sort="Poland, Jesse A" uniqKey="Poland J" first="Jesse A" last="Poland">Jesse A. Poland</name><affiliation wicri:level="1"><nlm:aff id="au11"><institution>US Department of Agriculture/Agricultural Research Service, Hard Winter Wheat Genetics Research Unit and Department of Agronomy, Kansas State University</institution><addr-line>Manhattan, KS, 65506, USA</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Manhattan, KS, 65506</wicri:regionArea><wicri:noRegion>65506</wicri:noRegion></affiliation></author><author><name sortKey="Stein, Nils" sort="Stein, Nils" uniqKey="Stein N" first="Nils" last="Stein">Nils Stein</name><affiliation wicri:level="1"><nlm:aff id="au1"><institution>Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)</institution><addr-line>D–06466 Seeland OT, Gatersleben, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>D–06466 Seeland OT, Gatersleben</wicri:regionArea><wicri:noRegion>Gatersleben</wicri:noRegion><wicri:noRegion>Gatersleben</wicri:noRegion><wicri:noRegion>Gatersleben</wicri:noRegion></affiliation></author><author><name sortKey="Waugh, Robbie" sort="Waugh, Robbie" uniqKey="Waugh R" first="Robbie" last="Waugh">Robbie Waugh</name><affiliation wicri:level="1"><nlm:aff id="au12"><institution>Division of Plant Sciences, University of Dundee at the James Hutton Institute</institution><addr-line>Invergowrie, Dundee, DD2 5DA, UK</addr-line></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Invergowrie, Dundee, DD2 5DA</wicri:regionArea><wicri:noRegion>DD2 5DA</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">23998490</idno><idno type="pmc">4298792</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4298792</idno><idno type="RBID">PMC:4298792</idno><idno type="doi">10.1111/tpj.12319</idno><date when="2013">2013</date><idno type="wicri:Area/Pmc/Corpus">001262</idno><idno type="wicri:Area/Pmc/Curation">001260</idno><idno type="wicri:Area/Pmc/Checkpoint">000B53</idno><idno type="wicri:Area/Ncbi/Merge">001408</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)</title><author><name sortKey="Mascher, Martin" sort="Mascher, Martin" uniqKey="Mascher M" first="Martin" last="Mascher">Martin Mascher</name><affiliation wicri:level="1"><nlm:aff id="au1"><institution>Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)</institution><addr-line>D–06466 Seeland OT, Gatersleben, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>D–06466 Seeland OT, Gatersleben</wicri:regionArea><wicri:noRegion>Gatersleben</wicri:noRegion><wicri:noRegion>Gatersleben</wicri:noRegion><wicri:noRegion>Gatersleben</wicri:noRegion></affiliation></author><author><name sortKey="Muehlbauer, Gary J" sort="Muehlbauer, Gary J" uniqKey="Muehlbauer G" first="Gary J" last="Muehlbauer">Gary J. Muehlbauer</name><affiliation wicri:level="1"><nlm:aff id="au2"><institution>University of Minnesota, Department of Agronomy and Plant Genetics</institution><addr-line>St Paul, MN, 55108, USA</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>St Paul, MN, 55108</wicri:regionArea><wicri:noRegion>55108</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="au3"><institution>University of Minnesota, Department of Plant Biology</institution><addr-line>St Paul, MN 55108, USA</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>St Paul, MN 55108</wicri:regionArea><wicri:noRegion>MN 55108</wicri:noRegion></affiliation></author><author><name sortKey="Rokhsar, Daniel S" sort="Rokhsar, Daniel S" uniqKey="Rokhsar D" first="Daniel S" last="Rokhsar">Daniel S. Rokhsar</name><affiliation wicri:level="1"><nlm:aff id="au4"><institution>Department of Energy Joint Genome Institute</institution><addr-line>2800 Mitchell Drive, Walnut Creek, CA, 94598, USA</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>2800 Mitchell Drive, Walnut Creek, CA, 94598</wicri:regionArea><wicri:noRegion>94598</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="au5"><institution>Department of Molecular and Cell Biology, University of California</institution><addr-line>Berkeley, CA, 94720, USA</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Berkeley, CA, 94720</wicri:regionArea><wicri:noRegion>94720</wicri:noRegion></affiliation></author><author><name sortKey="Chapman, Jarrod" sort="Chapman, Jarrod" uniqKey="Chapman J" first="Jarrod" last="Chapman">Jarrod Chapman</name><affiliation wicri:level="1"><nlm:aff id="au4"><institution>Department of Energy Joint Genome Institute</institution><addr-line>2800 Mitchell Drive, Walnut Creek, CA, 94598, USA</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>2800 Mitchell Drive, Walnut Creek, CA, 94598</wicri:regionArea><wicri:noRegion>94598</wicri:noRegion></affiliation></author><author><name sortKey="Schmutz, Jeremy" sort="Schmutz, Jeremy" uniqKey="Schmutz J" first="Jeremy" last="Schmutz">Jeremy Schmutz</name><affiliation wicri:level="1"><nlm:aff id="au4"><institution>Department of Energy Joint Genome Institute</institution><addr-line>2800 Mitchell Drive, Walnut Creek, CA, 94598, USA</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>2800 Mitchell Drive, Walnut Creek, CA, 94598</wicri:regionArea><wicri:noRegion>94598</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="au6"><institution>HudsonAlpha Institute of Biotechnology</institution><addr-line>Huntsville, AL, 35806, USA</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Huntsville, AL, 35806</wicri:regionArea><wicri:noRegion>35806</wicri:noRegion></affiliation></author><author><name sortKey="Barry, Kerrie" sort="Barry, Kerrie" uniqKey="Barry K" first="Kerrie" last="Barry">Kerrie Barry</name><affiliation wicri:level="1"><nlm:aff id="au4"><institution>Department of Energy Joint Genome Institute</institution><addr-line>2800 Mitchell Drive, Walnut Creek, CA, 94598, USA</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>2800 Mitchell Drive, Walnut Creek, CA, 94598</wicri:regionArea><wicri:noRegion>94598</wicri:noRegion></affiliation></author><author><name sortKey="Mu Oz Amatriain, Maria" sort="Mu Oz Amatriain, Maria" uniqKey="Mu Oz Amatriain M" first="María" last="Mu Oz-Amatriaín">María Mu Oz-Amatriaín</name><affiliation wicri:level="1"><nlm:aff id="au2"><institution>University of Minnesota, Department of Agronomy and Plant Genetics</institution><addr-line>St Paul, MN, 55108, USA</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>St Paul, MN, 55108</wicri:regionArea><wicri:noRegion>55108</wicri:noRegion></affiliation></author><author><name sortKey="Close, Timothy J" sort="Close, Timothy J" uniqKey="Close T" first="Timothy J" last="Close">Timothy J. Close</name><affiliation wicri:level="1"><nlm:aff id="au7"><institution>Department of Botany & Plant Sciences, University of California</institution><addr-line>Riverside, CA, 92521, USA</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Riverside, CA, 92521</wicri:regionArea><wicri:noRegion>92521</wicri:noRegion></affiliation></author><author><name sortKey="Wise, Roger P" sort="Wise, Roger P" uniqKey="Wise R" first="Roger P" last="Wise">Roger P. Wise</name><affiliation wicri:level="1"><nlm:aff id="au8"><institution>US Department of Agriculture/Agricultural Research Service, Department of Plant Pathology & Microbiology, Iowa State University</institution><addr-line>Ames, IA, 50011–1020, USA</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Ames, IA, 50011–1020</wicri:regionArea><wicri:noRegion>50011–1020</wicri:noRegion></affiliation></author><author><name sortKey="Schulman, Alan H" sort="Schulman, Alan H" uniqKey="Schulman A" first="Alan H" last="Schulman">Alan H. Schulman</name><affiliation wicri:level="1"><nlm:aff id="au9"><institution>Institute of Biotechnology, University of Helsinki/MTT Agrifood Research</institution><addr-line>PO Box 65, 00014, Helsinki, Finland</addr-line></nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>PO Box 65, 00014, Helsinki</wicri:regionArea><wicri:noRegion>Helsinki</wicri:noRegion></affiliation></author><author><name sortKey="Himmelbach, Axel" sort="Himmelbach, Axel" uniqKey="Himmelbach A" first="Axel" last="Himmelbach">Axel Himmelbach</name><affiliation wicri:level="1"><nlm:aff id="au1"><institution>Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)</institution><addr-line>D–06466 Seeland OT, Gatersleben, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>D–06466 Seeland OT, Gatersleben</wicri:regionArea><wicri:noRegion>Gatersleben</wicri:noRegion><wicri:noRegion>Gatersleben</wicri:noRegion><wicri:noRegion>Gatersleben</wicri:noRegion></affiliation></author><author><name sortKey="Mayer, Klaus Fx" sort="Mayer, Klaus Fx" uniqKey="Mayer K" first="Klaus Fx" last="Mayer">Klaus Fx Mayer</name><affiliation wicri:level="1"><nlm:aff id="au10"><institution>Munich Information Center for Protein Sequences/Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München</institution><addr-line>D–85764, Neuherberg, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>D–85764, Neuherberg</wicri:regionArea><wicri:noRegion>85764, Neuherberg</wicri:noRegion><wicri:noRegion>85764, Neuherberg</wicri:noRegion><wicri:noRegion>Neuherberg</wicri:noRegion></affiliation></author><author><name sortKey="Scholz, Uwe" sort="Scholz, Uwe" uniqKey="Scholz U" first="Uwe" last="Scholz">Uwe Scholz</name><affiliation wicri:level="1"><nlm:aff id="au1"><institution>Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)</institution><addr-line>D–06466 Seeland OT, Gatersleben, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>D–06466 Seeland OT, Gatersleben</wicri:regionArea><wicri:noRegion>Gatersleben</wicri:noRegion><wicri:noRegion>Gatersleben</wicri:noRegion><wicri:noRegion>Gatersleben</wicri:noRegion></affiliation></author><author><name sortKey="Poland, Jesse A" sort="Poland, Jesse A" uniqKey="Poland J" first="Jesse A" last="Poland">Jesse A. Poland</name><affiliation wicri:level="1"><nlm:aff id="au11"><institution>US Department of Agriculture/Agricultural Research Service, Hard Winter Wheat Genetics Research Unit and Department of Agronomy, Kansas State University</institution><addr-line>Manhattan, KS, 65506, USA</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Manhattan, KS, 65506</wicri:regionArea><wicri:noRegion>65506</wicri:noRegion></affiliation></author><author><name sortKey="Stein, Nils" sort="Stein, Nils" uniqKey="Stein N" first="Nils" last="Stein">Nils Stein</name><affiliation wicri:level="1"><nlm:aff id="au1"><institution>Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)</institution><addr-line>D–06466 Seeland OT, Gatersleben, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>D–06466 Seeland OT, Gatersleben</wicri:regionArea><wicri:noRegion>Gatersleben</wicri:noRegion><wicri:noRegion>Gatersleben</wicri:noRegion><wicri:noRegion>Gatersleben</wicri:noRegion></affiliation></author><author><name sortKey="Waugh, Robbie" sort="Waugh, Robbie" uniqKey="Waugh R" first="Robbie" last="Waugh">Robbie Waugh</name><affiliation wicri:level="1"><nlm:aff id="au12"><institution>Division of Plant Sciences, University of Dundee at the James Hutton Institute</institution><addr-line>Invergowrie, Dundee, DD2 5DA, UK</addr-line></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Invergowrie, Dundee, DD2 5DA</wicri:regionArea><wicri:noRegion>DD2 5DA</wicri:noRegion></affiliation></author></analytic><series><title level="j">The Plant Journal</title><idno type="ISSN">0960-7412</idno><idno type="eISSN">1365-313X</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Next-generation whole-genome shotgun assemblies of complex genomes are highly useful, but fail to link nearby sequence contigs with each other or provide a linear order of contigs along individual chromosomes. Here, we introduce a strategy based on sequencing progeny of a segregating population that allows <italic>de novo</italic> production of a genetically anchored linear assembly of the gene space of an organism. We demonstrate the power of the approach by reconstructing the chromosomal organization of the gene space of barley, a large, complex and highly repetitive 5.1 Gb genome. We evaluate the robustness of the new assembly by comparison to a recently released physical and genetic framework of the barley genome, and to various genetically ordered sequence-based genotypic datasets. The method is independent of the need for any prior sequence resources, and will enable rapid and cost-efficient establishment of powerful genomic information for many species.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Andolfatto, P" uniqKey="Andolfatto P">P Andolfatto</name></author><author><name sortKey="Davison, D" uniqKey="Davison D">D Davison</name></author><author><name sortKey="Erezyilmaz, D" uniqKey="Erezyilmaz D">D Erezyilmaz</name></author><author><name sortKey="Hu, Tt" uniqKey="Hu T">TT Hu</name></author><author><name sortKey="Mast, J" uniqKey="Mast J">J Mast</name></author><author><name sortKey="Sunayama Morita, T" uniqKey="Sunayama Morita T">T Sunayama-Morita</name></author><author><name sortKey="Stern, Dl" uniqKey="Stern D">DL Stern</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Brenchley, R" uniqKey="Brenchley R">R Brenchley</name></author><author><name sortKey="Spannagl, 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Plant J</journal-id><journal-id journal-id-type="iso-abbrev">Plant J</journal-id><journal-id journal-id-type="publisher-id">tpj</journal-id><journal-title-group><journal-title>The Plant Journal</journal-title></journal-title-group><issn pub-type="ppub">0960-7412</issn><issn pub-type="epub">1365-313X</issn><publisher><publisher-name>BlackWell Publishing Ltd</publisher-name><publisher-loc>Oxford, UK</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">23998490</article-id><article-id pub-id-type="pmc">4298792</article-id><article-id pub-id-type="doi">10.1111/tpj.12319</article-id><article-categories><subj-group subj-group-type="heading"><subject>Technical Advance</subject></subj-group></article-categories><title-group><article-title>Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Mascher</surname><given-names>Martin</given-names></name><xref ref-type="aff" rid="au1">1</xref><xref ref-type="corresp" rid="cor1">†</xref></contrib><contrib contrib-type="author"><name><surname>Muehlbauer</surname><given-names>Gary J</given-names></name><xref ref-type="aff" rid="au2">2</xref><xref ref-type="aff" rid="au3">3</xref><xref ref-type="corresp" rid="cor1">†</xref></contrib><contrib contrib-type="author"><name><surname>Rokhsar</surname><given-names>Daniel S</given-names></name><xref ref-type="aff" rid="au4">4</xref><xref ref-type="aff" rid="au5">5</xref></contrib><contrib contrib-type="author"><name><surname>Chapman</surname><given-names>Jarrod</given-names></name><xref ref-type="aff" rid="au4">4</xref></contrib><contrib contrib-type="author"><name><surname>Schmutz</surname><given-names>Jeremy</given-names></name><xref ref-type="aff" rid="au4">4</xref><xref ref-type="aff" rid="au6">6</xref></contrib><contrib contrib-type="author"><name><surname>Barry</surname><given-names>Kerrie</given-names></name><xref ref-type="aff" rid="au4">4</xref></contrib><contrib contrib-type="author"><name><surname>Muñoz-Amatriaín</surname><given-names>María</given-names></name><xref ref-type="aff" rid="au2">2</xref></contrib><contrib contrib-type="author"><name><surname>Close</surname><given-names>Timothy J</given-names></name><xref ref-type="aff" rid="au7">7</xref></contrib><contrib contrib-type="author"><name><surname>Wise</surname><given-names>Roger P</given-names></name><xref ref-type="aff" rid="au8">8</xref></contrib><contrib contrib-type="author"><name><surname>Schulman</surname><given-names>Alan H</given-names></name><xref ref-type="aff" rid="au9">9</xref></contrib><contrib contrib-type="author"><name><surname>Himmelbach</surname><given-names>Axel</given-names></name><xref ref-type="aff" rid="au1">1</xref></contrib><contrib contrib-type="author"><name><surname>Mayer</surname><given-names>Klaus FX</given-names></name><xref ref-type="aff" rid="au10">10</xref></contrib><contrib contrib-type="author"><name><surname>Scholz</surname><given-names>Uwe</given-names></name><xref ref-type="aff" rid="au1">1</xref></contrib><contrib contrib-type="author"><name><surname>Poland</surname><given-names>Jesse A</given-names></name><xref ref-type="aff" rid="au11">11</xref></contrib><contrib contrib-type="author"><name><surname>Stein</surname><given-names>Nils</given-names></name><xref ref-type="aff" rid="au1">1</xref><xref ref-type="author-notes" rid="fn1">*</xref></contrib><contrib contrib-type="author"><name><surname>Waugh</surname><given-names>Robbie</given-names></name><xref ref-type="aff" rid="au12">12</xref><xref ref-type="author-notes" rid="fn1">*</xref></contrib><aff id="au1"><label>1</label><institution>Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)</institution><addr-line>D–06466 Seeland OT, Gatersleben, Germany</addr-line></aff><aff id="au2"><label>2</label><institution>University of Minnesota, Department of Agronomy and Plant Genetics</institution><addr-line>St Paul, MN, 55108, USA</addr-line></aff><aff id="au3"><label>3</label><institution>University of Minnesota, Department of Plant Biology</institution><addr-line>St Paul, MN 55108, USA</addr-line></aff><aff id="au4"><label>4</label><institution>Department of Energy Joint Genome Institute</institution><addr-line>2800 Mitchell Drive, Walnut Creek, CA, 94598, USA</addr-line></aff><aff id="au5"><label>5</label><institution>Department of Molecular and Cell Biology, University of California</institution><addr-line>Berkeley, CA, 94720, USA</addr-line></aff><aff id="au6"><label>6</label><institution>HudsonAlpha Institute of Biotechnology</institution><addr-line>Huntsville, AL, 35806, USA</addr-line></aff><aff id="au7"><label>7</label><institution>Department of Botany & Plant Sciences, University of California</institution><addr-line>Riverside, CA, 92521, USA</addr-line></aff><aff id="au8"><label>8</label><institution>US Department of Agriculture/Agricultural Research Service, Department of Plant Pathology & Microbiology, Iowa State University</institution><addr-line>Ames, IA, 50011–1020, USA</addr-line></aff><aff id="au9"><label>9</label><institution>Institute of Biotechnology, University of Helsinki/MTT Agrifood Research</institution><addr-line>PO Box 65, 00014, Helsinki, Finland</addr-line></aff><aff id="au10"><label>10</label><institution>Munich Information Center for Protein Sequences/Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München</institution><addr-line>D–85764, Neuherberg, Germany</addr-line></aff><aff id="au11"><label>11</label><institution>US Department of Agriculture/Agricultural Research Service, Hard Winter Wheat Genetics Research Unit and Department of Agronomy, Kansas State University</institution><addr-line>Manhattan, KS, 65506, USA</addr-line></aff><aff id="au12"><label>12</label><institution>Division of Plant Sciences, University of Dundee at the James Hutton Institute</institution><addr-line>Invergowrie, Dundee, DD2 5DA, UK</addr-line></aff></contrib-group><author-notes><corresp id="cor1">For correspondence (e-mails <email>stein@ipk-gatersleben.de</email>; <email>robbie.waugh@hutton.ac.uk</email>).
</corresp><fn id="fn1"><p>These authors contributed equally to this work.</p></fn></author-notes><pub-date pub-type="ppub"><month>11</month><year>2013</year></pub-date><pub-date pub-type="epub"><day>10</day><month>10</month><year>2013</year></pub-date><volume>76</volume><issue>4</issue><fpage>718</fpage><lpage>727</lpage><history><date date-type="received"><day>25</day><month>6</month><year>2013</year></date><date date-type="rev-recd"><day>07</day><month>8</month><year>2013</year></date><date date-type="accepted"><day>02</day><month>9</month><year>2013</year></date></history><permissions><copyright-statement>© 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd</copyright-statement><copyright-year>2013</copyright-year><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/3.0/"><license-p>This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><abstract><p>Next-generation whole-genome shotgun assemblies of complex genomes are highly useful, but fail to link nearby sequence contigs with each other or provide a linear order of contigs along individual chromosomes. Here, we introduce a strategy based on sequencing progeny of a segregating population that allows <italic>de novo</italic> production of a genetically anchored linear assembly of the gene space of an organism. We demonstrate the power of the approach by reconstructing the chromosomal organization of the gene space of barley, a large, complex and highly repetitive 5.1 Gb genome. We evaluate the robustness of the new assembly by comparison to a recently released physical and genetic framework of the barley genome, and to various genetically ordered sequence-based genotypic datasets. The method is independent of the need for any prior sequence resources, and will enable rapid and cost-efficient establishment of powerful genomic information for many species.</p></abstract><kwd-group><kwd>next-generation sequencing</kwd><kwd>genome assembly</kwd><kwd>genetic mapping</kwd><kwd>barley</kwd><kwd><italic>Hordeum vulgare</italic></kwd><kwd>population sequencing</kwd><kwd>technical advance</kwd></kwd-group></article-meta></front></pmc><affiliations><list><country><li>Allemagne</li><li>Finlande</li><li>Royaume-Uni</li><li>États-Unis</li></country></list><tree><country name="Allemagne"><noRegion><name sortKey="Mascher, Martin" sort="Mascher, Martin" uniqKey="Mascher M" first="Martin" last="Mascher">Martin Mascher</name></noRegion><name sortKey="Himmelbach, Axel" sort="Himmelbach, Axel" uniqKey="Himmelbach A" first="Axel" last="Himmelbach">Axel Himmelbach</name><name sortKey="Mayer, Klaus Fx" sort="Mayer, Klaus Fx" uniqKey="Mayer K" first="Klaus Fx" last="Mayer">Klaus Fx Mayer</name><name sortKey="Scholz, Uwe" sort="Scholz, Uwe" uniqKey="Scholz U" first="Uwe" last="Scholz">Uwe Scholz</name><name sortKey="Stein, Nils" sort="Stein, Nils" uniqKey="Stein N" first="Nils" last="Stein">Nils Stein</name></country><country name="États-Unis"><noRegion><name sortKey="Muehlbauer, Gary J" sort="Muehlbauer, Gary J" uniqKey="Muehlbauer G" first="Gary J" last="Muehlbauer">Gary J. Muehlbauer</name></noRegion><name sortKey="Barry, Kerrie" sort="Barry, Kerrie" uniqKey="Barry K" first="Kerrie" last="Barry">Kerrie Barry</name><name sortKey="Chapman, Jarrod" sort="Chapman, Jarrod" uniqKey="Chapman J" first="Jarrod" last="Chapman">Jarrod Chapman</name><name sortKey="Close, Timothy J" sort="Close, Timothy J" uniqKey="Close T" first="Timothy J" last="Close">Timothy J. Close</name><name sortKey="Mu Oz Amatriain, Maria" sort="Mu Oz Amatriain, Maria" uniqKey="Mu Oz Amatriain M" first="María" last="Mu Oz-Amatriaín">María Mu Oz-Amatriaín</name><name sortKey="Muehlbauer, Gary J" sort="Muehlbauer, Gary J" uniqKey="Muehlbauer G" first="Gary J" last="Muehlbauer">Gary J. Muehlbauer</name><name sortKey="Poland, Jesse A" sort="Poland, Jesse A" uniqKey="Poland J" first="Jesse A" last="Poland">Jesse A. Poland</name><name sortKey="Rokhsar, Daniel S" sort="Rokhsar, Daniel S" uniqKey="Rokhsar D" first="Daniel S" last="Rokhsar">Daniel S. Rokhsar</name><name sortKey="Rokhsar, Daniel S" sort="Rokhsar, Daniel S" uniqKey="Rokhsar D" first="Daniel S" last="Rokhsar">Daniel S. Rokhsar</name><name sortKey="Schmutz, Jeremy" sort="Schmutz, Jeremy" uniqKey="Schmutz J" first="Jeremy" last="Schmutz">Jeremy Schmutz</name><name sortKey="Schmutz, Jeremy" sort="Schmutz, Jeremy" uniqKey="Schmutz J" first="Jeremy" last="Schmutz">Jeremy Schmutz</name><name sortKey="Wise, Roger P" sort="Wise, Roger P" uniqKey="Wise R" first="Roger P" last="Wise">Roger P. Wise</name></country><country name="Finlande"><noRegion><name sortKey="Schulman, Alan H" sort="Schulman, Alan H" uniqKey="Schulman A" first="Alan H" last="Schulman">Alan H. Schulman</name></noRegion></country><country name="Royaume-Uni"><noRegion><name sortKey="Waugh, Robbie" sort="Waugh, Robbie" uniqKey="Waugh R" first="Robbie" last="Waugh">Robbie Waugh</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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