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

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 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, María Muñoz-Amatriaín, Timothy J. Close, Roger P. Wise, Alan H. Schulman, Axel Himmelbach, Klaus F.X. Mayer, Uwe Scholz, Jesse A. Poland, Nils Stein, Robbie Waugh

Research output: Contribution to journal › Article › peer-review

219 Scopus citations

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. © 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd.

Original language	English (US)
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
State	Published - Nov 1 2013
Externally published	Yes

Bibliographical note

Generated from Scopus record by KAUST IRTS on 2022-09-13

ASJC Scopus subject areas

Plant Science
Cell Biology
Genetics

Access to Document

10.1111/tpj.12319

Cite this

Mascher, M., Muehlbauer, G. J., Rokhsar, D. S., Chapman, J., Schmutz, J., Barry, K., Muñoz-Amatriaín, 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

@article{3711980ee7934b01b3a927edc51426c1,

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 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. {\textcopyright} 2013 The Authors The Plant Journal {\textcopyright} 2013 John Wiley & Sons Ltd.",

author = "Martin Mascher and Muehlbauer, {Gary J.} and Rokhsar, {Daniel S.} and Jarrod Chapman and Jeremy Schmutz and Kerrie Barry and Mar{\'i}a Mu{\~n}oz-Amatria{\'i}n 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",

note = "Generated from Scopus record by KAUST IRTS on 2022-09-13",

year = "2013",

month = nov,

day = "1",

doi = "10.1111/tpj.12319",

language = "English (US)",

volume = "76",

pages = "718--727",

journal = "Plant Journal",

issn = "0960-7412",

publisher = "Wiley",

number = "4",

}

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 - Muñoz-Amatriaín, María

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

N1 - Generated from Scopus record by KAUST IRTS on 2022-09-13

PY - 2013/11/1

Y1 - 2013/11/1

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 5.1 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. © 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd.

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. © 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd.

UR - https://onlinelibrary.wiley.com/doi/10.1111/tpj.12319

UR - http://www.scopus.com/inward/record.url?scp=84886793453&partnerID=8YFLogxK

U2 - 10.1111/tpj.12319

DO - 10.1111/tpj.12319

M3 - Article

SN - 0960-7412

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

Bibliographical note

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this