Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)
Identifieur interne : 000F63 ( Main/Merge ); précédent : 000F62; suivant : 000F64Anchoring 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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PMC:4298792Le document en format XML
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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><idno type="wicri:Area/Ncbi/Curation">001408</idno><idno type="wicri:Area/Ncbi/Checkpoint">001408</idno><idno type="wicri:doubleKey">0960-7412:2013:Mascher M:anchoring:and:ordering</idno><idno type="wicri:Area/Main/Merge">000F63</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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