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

    146 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

    Fingerprint

    Genome
    genome
    Hordeum
    Population
    barley
    Firearms
    Genes
    genes
    Chromosomes
    chromosomes
    genomics
    Costs and Cost Analysis
    organisms
    methodology
    Datasets

    Keywords

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

    Cite this

    Mascher, M., Muehlbauer, G. J., Rokhsar, D. S., Chapman, J., Schmutz, J., Barry, K., ... 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
    Mascher, Martin ; Muehlbauer, Gary J. ; Rokhsar, Daniel S. ; Chapman, Jarrod ; Schmutz, Jeremy ; Barry, Kerrie ; Munoz-Amatriain, Maria ; Close, Timothy J. ; Wise, Roger P. ; Schulman, Alan H. ; Himmelbach, Axel ; Mayer, Klaus F. X. ; Scholz, Uwe ; Poland, Jesse A. ; Stein, Nils ; Waugh, Robbie. / Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). In: Plant Journal. 2013 ; Vol. 76, No. 4. pp. 718-727.
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    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{\^A} 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.",
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    author = "Martin Mascher and Muehlbauer, {Gary J.} and Rokhsar, {Daniel S.} and Jarrod Chapman and Jeremy Schmutz and Kerrie Barry and Maria Munoz-Amatriain and Close, {Timothy J.} and Wise, {Roger P.} and Schulman, {Alan H.} and Axel Himmelbach and Mayer, {Klaus F. X.} and Uwe Scholz and Poland, {Jesse A.} and Nils Stein and Robbie Waugh",
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    Mascher, M, Muehlbauer, GJ, Rokhsar, DS, Chapman, J, Schmutz, J, Barry, K, Munoz-Amatriain, M, Close, TJ, Wise, RP, Schulman, AH, Himmelbach, A, Mayer, KFX, Scholz, U, Poland, JA, Stein, N & Waugh, R 2013, 'Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)', Plant Journal, vol. 76, no. 4, pp. 718-727. https://doi.org/10.1111/tpj.12319

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

    In: Plant Journal, Vol. 76, No. 4, 11.2013, p. 718-727.

    Research output: Contribution to journalArticle

    TY - JOUR

    T1 - Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)

    AU - Mascher, Martin

    AU - Muehlbauer, Gary J.

    AU - Rokhsar, Daniel S.

    AU - Chapman, Jarrod

    AU - Schmutz, Jeremy

    AU - Barry, Kerrie

    AU - Munoz-Amatriain, Maria

    AU - Close, Timothy J.

    AU - Wise, Roger P.

    AU - Schulman, Alan H.

    AU - Himmelbach, Axel

    AU - Mayer, Klaus F. X.

    AU - Scholz, Uwe

    AU - Poland, Jesse A.

    AU - Stein, Nils

    AU - Waugh, Robbie

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    AB - 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.

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    KW - technical advance

    KW - population sequencing

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    KW - barley

    KW - genetic mapping

    KW - genome assembly

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    DO - 10.1111/tpj.12319

    M3 - Article

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    JO - Plant Journal

    JF - Plant Journal

    SN - 0960-7412

    IS - 4

    ER -

    Mascher M, Muehlbauer GJ, Rokhsar DS, Chapman J, Schmutz J, Barry K et al. Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). Plant Journal. 2013 Nov;76(4):718-727. https://doi.org/10.1111/tpj.12319