Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2018-08-17

AUTHORS

Gabriel Keeble-Gagnère, Philippe Rigault, Josquin Tibbits, Raj Pasam, Matthew Hayden, Kerrie Forrest, Zeev Frenkel, Abraham Korol, B. Emma Huang, Colin Cavanagh, Jen Taylor, Michael Abrouk, Andrew Sharpe, David Konkin, Pierre Sourdille, Benoît Darrier, Frédéric Choulet, Aurélien Bernard, Simone Rochfort, Adam Dimech, Nathan Watson-Haigh, Ute Baumann, Paul Eckermann, Delphine Fleury, Angela Juhasz, Sébastien Boisvert, Marc-Alexandre Nolin, Jaroslav Doležel, Hana Šimková, Helena Toegelová, Jan Šafář, Ming-Cheng Luo, Francisco Câmara, Matthias Pfeifer, Don Isdale, Johan Nyström-Persson, IWGSC, Dal-Hoe Koo, Matthew Tinning, Dangqun Cui, Zhengang Ru, Rudi Appels

ABSTRACT

BackgroundNumerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome.ResultsUsing chromosome 7A of wheat as a model, sequence-finished megabase-scale sections of this chromosome were established by combining a new independent assembly using a bacterial artificial chromosome (BAC)-based physical map, BAC pool paired-end sequencing, chromosome-arm-specific mate-pair sequencing and Bionano optical mapping with the International Wheat Genome Sequencing Consortium RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region.ConclusionsSufficient genome sequence information is shown to now be available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and that yield attributes are affected by five F-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere. More... »

PAGES

112

References to SciGraph publications

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  • Journal

    TITLE

    Genome Biology

    ISSUE

    1

    VOLUME

    19

    Author Affiliations

  • Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, 3083, Bundoora, VIC, Australia
  • Center for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany
  • Institute of Evolution, University of Haifa, Haifa, Israel
  • CSIRO-Plant Industry, Black Mountain, 2601, Canberra, ACT, Australia
  • Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Slechtitelu 31, CZ-78371, Olomouc, Czech Republic
  • Global Institute of Food Security, University of Saskatchewan, 110 Gymnasium Place, Saskatoon, SK, Canada
  • National Research Council of Canada, University of Saskatchewan, 110 Gymnasium Place, Saskatoon, SK, Canada
  • INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039, Clermont-Ferrand, France
  • School of Agriculture, Food and Wine, University of Adelaide, 5064, Urrbrae, South Australia, Australia
  • Veterinary and Agriculture, Murdoch University, 90 South St, 6150, Murdoch, Western Australia, Australia
  • GYDLE, 1135 Grande Allée Ouest, Suite 220, G1S 1E7, Québec, QC, Canada
  • UC Davis Plant Sciences, Plant Genetics and Bioinformatics, 258A Hunt Hall, 95616, Davis, CA, USA
  • Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG) and Universitat Pompeu Fabra (UPF), 88 Dr. Aiguader, 08003, Barcelona, Spain
  • Plant Genome and Systems Biology, Helmholtz Center, Munich, 85764, Neuherberg, Germany
  • Level Five Co. Ltd. GYB Akihabara, Kanda-Sudacho 2-25, Chiyoda-ku, 101-0041, Tokyo, Japan
  • International Wheat Genome Sequencing Consortium, 2841 NE Marywood Ct, 64086, Lee’s Summit, MO, USA
  • Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, 66506, Manhattan, KS, USA
  • Australian Genome Research Facility, Suite 219, 55 Flemington Road, 3051, North Melbourne, VIC, Australia
  • Henan Agricultural University, Zhengzhou, China
  • Henan Institute of Science and Technology, Zhengzhou, China
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/s13059-018-1475-4

    DOI

    http://dx.doi.org/10.1186/s13059-018-1475-4

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1106153772

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/30115128


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        "description": "BackgroundNumerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome.ResultsUsing chromosome 7A of wheat as a model, sequence-finished megabase-scale sections of this chromosome were established by combining a new independent assembly using a bacterial artificial chromosome (BAC)-based physical map, BAC pool paired-end sequencing, chromosome-arm-specific mate-pair sequencing and Bionano optical mapping with the International Wheat Genome Sequencing Consortium RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region.ConclusionsSufficient genome sequence information is shown to now be available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and that yield attributes are affected by five F-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere.", 
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    34 schema:description BackgroundNumerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome.ResultsUsing chromosome 7A of wheat as a model, sequence-finished megabase-scale sections of this chromosome were established by combining a new independent assembly using a bacterial artificial chromosome (BAC)-based physical map, BAC pool paired-end sequencing, chromosome-arm-specific mate-pair sequencing and Bionano optical mapping with the International Wheat Genome Sequencing Consortium RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region.ConclusionsSufficient genome sequence information is shown to now be available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and that yield attributes are affected by five F-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere.
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