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; Robbie Waugh

doi:10.1111/tpj.12319

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 journal › Article › peer-review

225 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 5.1Â 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 language	English
Pages (from-to)	718-727
Number of pages	10
Journal	Plant Journal
Volume	76
Issue number	4
DOIs	https://doi.org/10.1111/tpj.12319
Publication status	Published - Nov 2013

Keywords

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

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10.1111/tpj.12319

http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291365-313X

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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

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title = "Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)",

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.",

keywords = "next-generation sequencing, technical advance, population sequencing, Hordeum vulgare, barley, genetic mapping, genome assembly",

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",

year = "2013",

month = nov,

doi = "10.1111/tpj.12319",

language = "English",

volume = "76",

pages = "718--727",

journal = "Plant Journal",

issn = "1365-313X",

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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

PY - 2013/11

Y1 - 2013/11

N2 - 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 5.1Â 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.

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 5.1Â 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.

KW - next-generation sequencing

KW - technical advance

KW - population sequencing

KW - Hordeum vulgare

KW - barley

KW - genetic mapping

KW - genome assembly

U2 - 10.1111/tpj.12319

DO - 10.1111/tpj.12319

M3 - Article

C2 - 23998490

SN - 1365-313X

VL - 76

SP - 718

EP - 727

JO - Plant Journal

JF - Plant Journal

IS - 4

ER -

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

Abstract

Keywords

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