Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data

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Abstract

The Wheat@URGI portal has been developed to provide the international community of researchers and breeders with access to the bread wheat reference genome sequence produced by the International Wheat Genome Sequencing Consortium. Genome browsers, BLAST, and InterMine tools have been established for in-depth exploration of the genome sequence together with additional linked datasets including physical maps, sequence variations, gene expression, and genetic and phenomic data from other international collaborative projects already stored in the GnpIS information system. The portal provides enhanced search and browser features that will facilitate the deployment of the latest genomics resources in wheat improvement.

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The online version of this article (10.1186/s13059-018-1491-4) contains supplementary material, which is available to authorized users.

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The generic genome browser: a building block for a model organism system database.

Lincoln D. Stein, Christopher John Mungall, ShengQiang Shu … (2002)

The Generic Model Organism System Database Project (GMOD) seeks to develop reusable software components for model organism system databases. In this paper we describe the Generic Genome Browser (GBrowse), a Web-based application for displaying genomic annotations and other features. For the end user, features of the browser include the ability to scroll and zoom through arbitrary regions of a genome, to enter a region of the genome by searching for a landmark or performing a full text search of all features, and the ability to enable and disable tracks and change their relative order and appearance. The user can upload private annotations to view them in the context of the public ones, and publish those annotations to the community. For the data provider, features of the browser software include reliance on readily available open source components, simple installation, flexible configuration, and easy integration with other components of a model organism system Web site. GBrowse is freely available under an open source license. The software, its documentation, and support are available at http://www.gmod.org.

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Structural and functional partitioning of bread wheat chromosome 3B.

Frédéric Choulet, Adriana Alberti, Sébastien Theil … (2014)

We produced a reference sequence of the 1-gigabase chromosome 3B of hexaploid bread wheat. By sequencing 8452 bacterial artificial chromosomes in pools, we assembled a sequence of 774 megabases carrying 5326 protein-coding genes, 1938 pseudogenes, and 85% of transposable elements. The distribution of structural and functional features along the chromosome revealed partitioning correlated with meiotic recombination. Comparative analyses indicated high wheat-specific inter- and intrachromosomal gene duplication activities that are potential sources of variability for adaption. In addition to providing a better understanding of the organization, function, and evolution of a large and polyploid genome, the availability of a high-quality sequence anchored to genetic maps will accelerate the identification of genes underlying important agronomic traits. Copyright © 2014, American Association for the Advancement of Science.

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

Martin Mascher, Gary J Muehlbauer, Daniel S. Rokhsar … (2013)

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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Author and article information

Contributors

Michael Alaux:

ORCID: http://orcid.org/0000-0001-9356-4072

michael.alaux@inra.fr

Journal

Journal ID (nlm-ta): Genome Biol

Journal ID (iso-abbrev): Genome Biol

Title: Genome Biology

Publisher: BioMed Central (London )

ISSN (Print): 1474-7596

ISSN (Electronic): 1474-760X

Publication date (Electronic): 17 August 2018

Publication date PMC-release: 17 August 2018

Publication date Collection: 2018

Volume: 19

Electronic Location Identifier: 111

Affiliations

[1 ]GRID grid.418070.a, URGI, INRA, Université Paris-Saclay, ; 78026 Versailles, France

[2 ]International Wheat Genome Sequencing Consortium (IWGSC), 18 High Street, Little Eversden, Cambridge, CB23 1HE UK

[3 ]ISNI 0000 0001 2169 1988, GRID grid.414548.8, GDEC, INRA, Université Clermont Auvergne, ; 63000 Clermont-Ferrand, France

[4 ]ISNI 0000 0004 4910 6535, GRID grid.460789.4, Present address: GQE-Le Moulon UMR 320, INRA, Université Paris-Sud, Université Paris-Saclay, CNRS, AgroParisTech, Ferme du Moulon, ; 91190 Gif-sur-Yvette, France

[5 ]Present address: Inari Agriculture, 200 Sydney Street, Cambridge, MA 02139 USA

[6 ]International Wheat Genome Sequencing Consortium (IWGSC), 2841 NE Marywood Ct, Lee’s Summit, MO 64086 USA

[7 ]International Wheat Genome Sequencing Consortium (IWGSC), 5207 Wyoming Road, Bethesda, Maryland 20816 USA

Author information

Michael Alaux http://orcid.org/0000-0001-9356-4072

Article

Publisher ID: 1491

DOI: 10.1186/s13059-018-1491-4

PMC ID: 6097284

PubMed ID: 30115101

SO-VID: 90355e3e-00da-438f-a119-273a7b35bbfa

License:

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

History

Date received : 13 April 2018

Date accepted : 23 July 2018

Funding

Funded by: FundRef http://dx.doi.org/10.13039/501100001665, Agence Nationale de la Recherche;

Award ID: ANR-10-BTBR-03

Award ID: ANR-09-GENM-025

Award Recipient : Michael Alaux Catherine Feuillet

Funded by: FundRef http://dx.doi.org/10.13039/100011102, Seventh Framework Programme;

Award ID: FP7-613556

Award ID: FP7-KBBE-212019

Award ID: FP7-283496

Award Recipient : Michael Alaux Catherine Feuillet Hadi Quesneville

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ScienceOpen disciplines: Genetics

Keywords: data integration,information system,big data,wheat genomics, genetics and phenomics

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ScienceOpen disciplines: Genetics

Keywords: data integration, information system, big data, wheat genomics, genetics and phenomics

Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data

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Most cited references 21

The generic genome browser: a building block for a model organism system database.

Structural and functional partitioning of bread wheat chromosome 3B.

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

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