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A chromosome conformation capture ordered sequence of the barley genome

Author

Listed:
  • Martin Mascher

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
    German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig)

  • Heidrun Gundlach

    (PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health)

  • Axel Himmelbach

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben)

  • Sebastian Beier

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben)

  • Sven O. Twardziok

    (PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health)

  • Thomas Wicker

    (University of Zurich)

  • Volodymyr Radchuk

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben)

  • Christoph Dockter

    (Carlsberg Research Laboratory)

  • Pete E. Hedley

    (The James Hutton Institute)

  • Joanne Russell

    (The James Hutton Institute)

  • Micha Bayer

    (The James Hutton Institute)

  • Luke Ramsay

    (The James Hutton Institute)

  • Hui Liu

    (The James Hutton Institute)

  • Georg Haberer

    (PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health)

  • Xiao-Qi Zhang

    (School of Veterinary and Life Sciences, Murdoch University)

  • Qisen Zhang

    (Australian Export Grains Innovation Centre)

  • Roberto A. Barrero

    (Centre for Comparative Genomics, Murdoch University)

  • Lin Li

    (University of Minnesota)

  • Stefan Taudien

    (Leibniz Institute on Aging - Fritz Lipmann Institute (FLI))

  • Marco Groth

    (Leibniz Institute on Aging - Fritz Lipmann Institute (FLI))

  • Marius Felder

    (Leibniz Institute on Aging - Fritz Lipmann Institute (FLI))

  • Alex Hastie

    (BioNano Genomics Inc.)

  • Hana Šimková

    (Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research)

  • Helena Staňková

    (Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research)

  • Jan Vrána

    (Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research)

  • Saki Chan

    (BioNano Genomics Inc.)

  • María Muñoz-Amatriaín

    (University of California, Riverside)

  • Rachid Ounit

    (University of California, Riverside)

  • Steve Wanamaker

    (University of California, Riverside)

  • Daniel Bolser

    (European Molecular Biology Laboratory - The European Bioinformatics Institute)

  • Christian Colmsee

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben)

  • Thomas Schmutzer

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben)

  • Lala Aliyeva-Schnorr

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben)

  • Stefano Grasso

    (University of Udine)

  • Jaakko Tanskanen

    (Green Technology, Natural Resources Institute (Luke), Viikki Plant Science Centre, and Institute of Biotechnology, University of Helsinki)

  • Anna Chailyan

    (Carlsberg Research Laboratory)

  • Dharanya Sampath

    (Earlham Institute)

  • Darren Heavens

    (Earlham Institute)

  • Leah Clissold

    (Earlham Institute)

  • Sujie Cao

    (BGI-Shenzhen)

  • Brett Chapman

    (Centre for Comparative Genomics, Murdoch University)

  • Fei Dai

    (College of Agriculture and Biotechnology, Zhejiang University)

  • Yong Han

    (College of Agriculture and Biotechnology, Zhejiang University)

  • Hua Li

    (BGI-Shenzhen)

  • Xuan Li

    (BGI-Shenzhen)

  • Chongyun Lin

    (BGI-Shenzhen)

  • John K. McCooke

    (Centre for Comparative Genomics, Murdoch University)

  • Cong Tan

    (Centre for Comparative Genomics, Murdoch University)

  • Penghao Wang

    (School of Veterinary and Life Sciences, Murdoch University)

  • Songbo Wang

    (BGI-Shenzhen)

  • Shuya Yin

    (College of Agriculture and Biotechnology, Zhejiang University)

  • Gaofeng Zhou

    (School of Veterinary and Life Sciences, Murdoch University)

  • Jesse A. Poland

    (Kansas State University, Wheat Genetics Resource Center)

  • Matthew I. Bellgard

    (Centre for Comparative Genomics, Murdoch University)

  • Ljudmilla Borisjuk

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben)

  • Andreas Houben

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben)

  • Jaroslav Doležel

    (Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research)

  • Sarah Ayling

    (Earlham Institute)

  • Stefano Lonardi

    (University of California, Riverside)

  • Paul Kersey

    (European Molecular Biology Laboratory - The European Bioinformatics Institute)

  • Peter Langridge

    (School of Agriculture, University of Adelaide)

  • Gary J. Muehlbauer

    (University of Minnesota
    University of Minnesota)

  • Matthew D. Clark

    (Earlham Institute
    School of Environmental Sciences, University of East Anglia)

  • Mario Caccamo

    (Earlham Institute
    National Institute of Agricultural Botany)

  • Alan H. Schulman

    (Green Technology, Natural Resources Institute (Luke), Viikki Plant Science Centre, and Institute of Biotechnology, University of Helsinki)

  • Klaus F. X. Mayer

    (PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health
    Wissenschaftszentrum Weihenstephan (WZW), Technical University Munich)

  • Matthias Platzer

    (Leibniz Institute on Aging - Fritz Lipmann Institute (FLI))

  • Timothy J. Close

    (University of California, Riverside)

  • Uwe Scholz

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben)

  • Mats Hansson

    (Lund University)

  • Guoping Zhang

    (College of Agriculture and Biotechnology, Zhejiang University)

  • Ilka Braumann

    (Carlsberg Research Laboratory)

  • Manuel Spannagl

    (PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health)

  • Chengdao Li

    (School of Veterinary and Life Sciences, Murdoch University
    Government of Western Australia
    Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University)

  • Robbie Waugh

    (The James Hutton Institute
    School of Life Sciences, University of Dundee)

  • Nils Stein

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
    School of Plant Biology, University of Western Australia)

Abstract

Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.

Suggested Citation

  • Martin Mascher & Heidrun Gundlach & Axel Himmelbach & Sebastian Beier & Sven O. Twardziok & Thomas Wicker & Volodymyr Radchuk & Christoph Dockter & Pete E. Hedley & Joanne Russell & Micha Bayer & Luke, 2017. "A chromosome conformation capture ordered sequence of the barley genome," Nature, Nature, vol. 544(7651), pages 427-433, April.
  • Handle: RePEc:nat:nature:v:544:y:2017:i:7651:d:10.1038_nature22043
    DOI: 10.1038/nature22043
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    Cited by:

    1. Guotai Yu & Oadi Matny & Nicolas Champouret & Burkhard Steuernagel & Matthew J. Moscou & Inmaculada Hernández-Pinzón & Phon Green & Sadiye Hayta & Mark Smedley & Wendy Harwood & Ngonidzashe Kangara & , 2022. "Aegilops sharonensis genome-assisted identification of stem rust resistance gene Sr62," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    2. Jessen V. Bredeson & Austin B. Mudd & Sofia Medina-Ruiz & Therese Mitros & Owen Kabnick Smith & Kelly E. Miller & Jessica B. Lyons & Sanjit S. Batra & Joseph Park & Kodiak C. Berkoff & Christopher Plo, 2024. "Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    3. Carmen Escudero-Martinez & Max Coulter & Rodrigo Alegria Terrazas & Alexandre Foito & Rumana Kapadia & Laura Pietrangelo & Mauro Maver & Rajiv Sharma & Alessio Aprile & Jenny Morris & Pete E. Hedley &, 2022. "Identifying plant genes shaping microbiota composition in the barley rhizosphere," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    4. Varvara Lukyanchikova & Miroslav Nuriddinov & Polina Belokopytova & Alena Taskina & Jiangtao Liang & Maarten J. M. F. Reijnders & Livio Ruzzante & Romain Feron & Robert M. Waterhouse & Yang Wu & Chunh, 2022. "Anopheles mosquitoes reveal new principles of 3D genome organization in insects," Nature Communications, Nature, vol. 13(1), pages 1-22, December.
    5. Mariam Amouzoune & Sajid Rehman & Rachid Benkirane & Swati Verma & Sanjaya Gyawali & Muamar Al-Jaboobi & Ramesh Pal Singh Verma & Zakaria Kehel & Ahmed Amri, 2022. "Genome-Wide Association Study of Leaf Rust Resistance at Seedling and Adult Plant Stages in a Global Barley Panel," Agriculture, MDPI, vol. 12(11), pages 1-26, November.
    6. Taikui Zhang & Weichen Huang & Lin Zhang & De-Zhu Li & Ji Qi & Hong Ma, 2024. "Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages," Nature Communications, Nature, vol. 15(1), pages 1-27, December.
    7. Guifang Lin & Hui Chen & Bin Tian & Sunish K. Sehgal & Lovepreet Singh & Jingzhong Xie & Nidhi Rawat & Philomin Juliana & Narinder Singh & Sandesh Shrestha & Duane L. Wilson & Hannah Shult & Hyeonju L, 2022. "Cloning of the broadly effective wheat leaf rust resistance gene Lr42 transferred from Aegilops tauschii," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    8. Jessen V. Bredeson & Jessica B. Lyons & Ibukun O. Oniyinde & Nneka R. Okereke & Olufisayo Kolade & Ikenna Nnabue & Christian O. Nwadili & Eva Hřibová & Matthew Parker & Jeremiah Nwogha & Shengqiang Sh, 2022. "Chromosome evolution and the genetic basis of agronomically important traits in greater yam," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    9. Giorgia Capasso & Giorgia Santini & Mariagioia Petraretti & Sergio Esposito & Simone Landi, 2021. "Wild and Traditional Barley Genomic Resources as a Tool for Abiotic Stress Tolerance and Biotic Relations," Agriculture, MDPI, vol. 11(11), pages 1-15, November.
    10. Habteab Goitom Gebremedhin & Yahui Li & Jinghuang Hu & Dan Qiu & Qiuhong Wu & Hongjun Zhang & Li Yang & Yang Zhou & Yijun Zhou & Zhiyong Liu & Peng Zhang & Hongjie Li, 2022. "Development of KASP and SSR Markers for PmQ , a Recessive Gene Conferring Powdery Mildew Resistance in Wheat Landrace Qingxinmai," Agriculture, MDPI, vol. 12(9), pages 1-10, August.
    11. Yi Liao & Juntao Wang & Zhangsheng Zhu & Yuanlong Liu & Jinfeng Chen & Yongfeng Zhou & Feng Liu & Jianjun Lei & Brandon S. Gaut & Bihao Cao & J. J. Emerson & Changming Chen, 2022. "The 3D architecture of the pepper genome and its relationship to function and evolution," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    12. Olga Afanasenko & Irina Rozanova & Anastasiia Gofman & Nina Lashina & Fluturë Novakazi & Nina Mironenko & Olga Baranova & Alexandr Zubkovich, 2022. "Validation of Molecular Markers of Barley Net Blotch Resistance Loci on Chromosome 3H for Marker-Assisted Selection," Agriculture, MDPI, vol. 12(4), pages 1-20, March.
    13. Simone Scalabrin & Gabriele Magris & Mario Liva & Nicola Vitulo & Michele Vidotto & Davide Scaglione & Lorenzo Terra & Manuela Rosanna Ruosi & Luciano Navarini & Gloria Pellegrino & Jorge Carlos Berny, 2024. "A chromosome-scale assembly reveals chromosomal aberrations and exchanges generating genetic diversity in Coffea arabica germplasm," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

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