Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)

Martin Mascher, Gary J. Muehlbauer, Daniel S. Rokhsar, Jarrod Chapman, Jeremy Schmutz, Kerrie Barry, Maria Munoz-Amatriain, Timothy J. Close, Roger P. Wise, Alan H. Schulman, Axel Himmelbach, Klaus F. X. Mayer, Uwe Scholz, Jesse A. Poland, Nils Stein (Lead / Corresponding author), Robbie Waugh (Lead / Corresponding author)

    Research output: Contribution to journalArticle

    170 Citations (Scopus)

    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.
    Original languageEnglish
    Pages (from-to)718-727
    Number of pages10
    JournalPlant Journal
    Volume76
    Issue number4
    DOIs
    Publication statusPublished - Nov 2013

    Keywords

    • next-generation sequencing
    • technical advance
    • population sequencing
    • Hordeum vulgare
    • barley
    • genetic mapping
    • genome assembly

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  • Cite this

    Mascher, M., Muehlbauer, G. J., Rokhsar, D. S., Chapman, J., Schmutz, J., Barry, K., Munoz-Amatriain, M., Close, T. J., Wise, R. P., Schulman, A. H., Himmelbach, A., Mayer, K. F. X., Scholz, U., Poland, J. A., Stein, N., & Waugh, R. (2013). Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). Plant Journal, 76(4), 718-727. https://doi.org/10.1111/tpj.12319