A chromosome conformation capture ordered sequence of the barley genome

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 Ramsay; Hui Liu; Georg Haberer; Xiao-Qi Zhang; Qisen Zhang; Roberto A. Barrero; Lin Li; Stefan Taudien; Marco Groth; Marius Felder; Alex Hastie; Hana Simkova; Helena Stankova; Jan Vrana; Saki Chan; Mara Munoz-Amatrian; Rachid Ounit; Steve Wanamaker; Daniel Bolser; Christian Colmsee; Thomas Schmutzer; Lala Aliyeva-Schnorr; Stefano Grasso; Jaakko Tanskanen; Anna Chailyan; Dharanya Sampath; Darren Heavens; Leah Clissold; Sujie Cao; Brett Chapman; Fei Dai; Yong Han; Hua Li; Xuan Li; Chongyun Lin; John K. McCooke; Cong Tan; Penghao Wang; Songbo Wang; Shuya Yin; Gaofeng Zhou; Jesse A. Poland; Matthew I. Bellgard; Ljudmilla Borisjuk; Andreas Houben; Jaroslav Dolezel; Sarah Ayling; Stefano Lonardi; Paul Kersey; Peter Lagridge; Gary J. Muehlbauer; Matthew D. Clark; Mario Caccamo; Alan H. Schulman; Klaus F. X. Mayer; Matthias Platzer; Timothy J. Close; Uwe Scholz; Mats Hansson; Guoping Zhang; Ilka Braumann; Manuel Spannagl; Chengdao Li; Robbie Waugh; Nils Stein

doi:10.1038/nature22043

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A chromosome conformation capture ordered sequence of the barley genome

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A chromosome conformation capture ordered sequence of the barley genome

Martin Mascher, Heidrun Gundlach, Axel Himmelbach, Sebastian Beier, Sven O. Twardziok, Thomas Wicker, Volodymyr Radchuk, Christoph Dockter, Pete E. Hedley, Joanne Russell, …

Nature (London), Vol.544(7651), pp.426-433

27/04/2017

DOI: https://doi.org/10.1038/nature22043

PMID: 28447635

Abstract

Multidisciplinary Sciences

Science & Technology

Science & Technology - Other Topics

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.

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Title: A chromosome conformation capture ordered sequence of the barley genome
Creators - without role: Martin Mascher - Leibniz Institute of Plant Genetics and Crop Plant Research
Heidrun Gundlach - Helmholtz Zentrum München
Axel Himmelbach - Leibniz Institute of Plant Genetics and Crop Plant Research
Sebastian Beier - Leibniz Institute of Plant Genetics and Crop Plant Research
Sven O. Twardziok - Helmholtz Zentrum München
Thomas Wicker - University of Zurich
Volodymyr Radchuk - Leibniz Institute of Plant Genetics and Crop Plant Research
Christoph Dockter - Carlsberg Laboratory
Pete E. Hedley - James Hutton Institute
Joanne Russell - James Hutton Institute
Micha Bayer - James Hutton Institute
Luke Ramsay - James Hutton Institute
Hui Liu - James Hutton Institute
Georg Haberer - Helmholtz Zentrum München
Xiao-Qi Zhang - Murdoch University
Qisen Zhang - Australian Export Grains Innovation Centre
Roberto A. Barrero - Murdoch University
Lin Li - University of Minnesota
Stefan Taudien - Leibniz Institute on Aging – Fritz Lipmann Institute
Marco Groth - Leibniz Institute on Aging – Fritz Lipmann Institute
Marius Felder - Leibniz Institute on Aging – Fritz Lipmann Institute
Alex Hastie - BioNano Genomics
Hana Simkova - Czech Academy of Sciences, Institute of Experimental Botany
Helena Stankova - Czech Academy of Sciences, Institute of Experimental Botany
Jan Vrana - Czech Academy of Sciences, Institute of Experimental Botany
Saki Chan - BioNano Genomics
Mara Munoz-Amatrian - Plant
Rachid Ounit - University of California, Riverside
Steve Wanamaker - University of California, Riverside
Daniel Bolser - European Bioinformat Inst, European Mol Biol Lab, Hinxton CB10 1SD, England
Christian Colmsee - Leibniz Institute of Plant Genetics and Crop Plant Research
Thomas Schmutzer - Leibniz Institute of Plant Genetics and Crop Plant Research
Lala Aliyeva-Schnorr - Leibniz Institute of Plant Genetics and Crop Plant Research
Stefano Grasso - University of Udine
Jaakko Tanskanen - University of Helsinki
Anna Chailyan - Carlsberg Laboratory
Dharanya Sampath - Earlham Institute
Darren Heavens - Earlham Institute
Leah Clissold - Earlham Institute
Sujie Cao - BGI Group
Brett Chapman - Murdoch University
Fei Dai - Zhejiang University
Yong Han - Zhejiang University
Hua Li - BGI Group
Xuan Li - BGI Group
Chongyun Lin - BGI Group
John K. McCooke - Murdoch University
Cong Tan - Murdoch University
Penghao Wang - Murdoch University
Songbo Wang - BGI Group
Shuya Yin - Zhejiang University
Gaofeng Zhou - Murdoch University
Jesse A. Poland - Kansas State University
Matthew I. Bellgard - Murdoch University
Ljudmilla Borisjuk - Leibniz Institute of Plant Genetics and Crop Plant Research
Andreas Houben - Leibniz Institute of Plant Genetics and Crop Plant Research
Jaroslav Dolezel - Czech Academy of Sciences, Institute of Experimental Botany
Sarah Ayling - Earlham Institute
Stefano Lonardi - University of California, Riverside
Paul Kersey - European Bioinformatics Institute
Peter Lagridge - University of Adelaide
Gary J. Muehlbauer - University of Minnesota
Matthew D. Clark - Earlham Institute
Mario Caccamo - National Institute of Agricultural Botany
Alan H. Schulman - Natural Resources Institute Finland
Klaus F. X. Mayer - HLT
Matthias Platzer - Leibniz Institute on Aging – Fritz Lipmann Institute
Timothy J. Close - University of California, Riverside
Uwe Scholz - Leibniz Institute of Plant Genetics and Crop Plant Research
Mats Hansson - Lund University
Guoping Zhang - Zhejiang University
Ilka Braumann - Carlsberg Laboratory
Manuel Spannagl - Helmholtz Zentrum München
Chengdao Li - Murdoch University
Robbie Waugh - James Hutton Institute
Nils Stein - Leibniz Institute of Plant Genetics and Crop Plant Research
Publication Details: Nature (London), Vol.544(7651), pp.426-433
Publisher: NATURE PORTFOLIO
Number of pages: 22
Grant note: LO1204 / Czech Ministry of Education, Youth and Sports grant 2012_01_0461 / Carlsberg Foundation RD-2012-3776 / Agriculture and Horticulture Development Board project IMPROMALT BB/100663X/1 / Scottish Government/UK Biotechnology and Biological Sciences Research Council (BBSRC); UK Research & Innovation (UKRI); Biotechnology and Biological Sciences Research Council (BBSRC) RD-2012-3776 / Agriculture and Horticulture Development Board project AGOUEB BB/J004669/1 / BBSRC Institute Strategic Programme; UK Research & Innovation (UKRI); Biotechnology and Biological Sciences Research Council (BBSRC) Leibniz 'Pakt f. Forschung und Innovation' grant BBS/E/T/000PR6193; BB/I00663X/1; BB/L026317/1; BBS/E/T/000PR5885; BB/H531519/1 / BBSRC; UK Research & Innovation (UKRI); Biotechnology and Biological Sciences Research Council (BBSRC) 0314000; 0315954; 031A536 / German Ministry of Education and Research; Federal Ministry of Education & Research (BMBF) 31129005 / National Natural Science Foundation of China (NSFC) DAW00233 / Grains Research and Development Corporation (GRDC); Grains R&D Corp CA-R-BPS-5306-H / University of California; University of California System DBI 0321756 / US National Science Foundation (NSF); National Science Foundation (NSF) 681 / Department of Agricultural and Food, Government of Western Australia 266430 / Finland grant BioNano grant BB/I00663X/1; BB/L026317/1; BB/I008357/1; BB/H531519/1; BB/I008071/1; BBS/E/T/000PR6193; BBS/E/T/000PR5885 / Biotechnology and Biological Sciences Research Council; UK Research & Innovation (UKRI); Biotechnology and Biological Sciences Research Council (BBSRC) BB/J010375/1 / BBSRC National Capability in Genomics; UK Research & Innovation (UKRI); Biotechnology and Biological Sciences Research Council (BBSRC) DBI 0321756 / NSF; National Science Foundation (NSF) BB/I008357/1; BB/I008071/1 / BBSRC; UK Research & Innovation (UKRI); Biotechnology and Biological Sciences Research Council (BBSRC) 2009-65300-05645; 2011-68002-30029 / US Department of Agriculture-Cooperative State Research, Education, and Extension Service-National Institute of Food and Agriculture (USDA-CSREES-NIFA) 31330055 / NSFC; National Natural Science Foundation of China (NSFC)
Identifiers: 9943033108331
Academic Unit: King Abdullah University of Science & Technology
Language: English
Resource Type: Journal article