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Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ) |
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| Authors: | Martin Mascher Gary J Muehlbauer Daniel S Rokhsar Jarrod Chapman Jeremy Schmutz Kerrie Barry María Muñoz‐Amatriaín Timothy J Close Roger P Wise Alan H Schulman Axel Himmelbach Klaus FX Mayer Uwe Scholz Jesse A Poland Nils Stein Robbie Waugh |
| Institution: | 1. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), , Gatersleben, Germany;2. University of Minnesota, Department of Agronomy and Plant Genetics, , MN, 55108 USA;3. University of Minnesota, Department of Plant Biology, , St Paul, MN 4. 55108, USA;5. Department of Energy Joint Genome Institute, , Walnut Creek, CA, 94598 USA;6. Department of Molecular and Cell Biology, University of California, , Berkeley, CA, 94720 USA;7. HudsonAlpha Institute of Biotechnology, , Huntsville, AL, 35806 USA;8. Department of Botany & Plant Sciences, University of California, , Riverside, CA, 92521 USA;9. US Department of Agriculture/Agricultural Research Service, Department of Plant Pathology & Microbiology, Iowa State University, , Ames, IA, 50011–1020 USA;10. Institute of Biotechnology, University of Helsinki/MTT Agrifood Research, , 00014 Helsinki, Finland;11. Munich Information Center for Protein Sequences/Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, , D–85764 Neuherberg, Germany;12. US Department of Agriculture/Agricultural Research Service, Hard Winter Wheat Genetics Research Unit and Department of Agronomy, Kansas State University, , Manhattan, KS, 65506 USA;13. Division of Plant Sciences, University of Dundee at the James Hutton Institute, , Invergowrie, Dundee, DD2 5DA UK |
| 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 de novo 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. |
| Keywords: | next‐generation sequencing genome assembly genetic mapping barley Hordeum vulgare population sequencing technical advance |