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 Šimková, Helena Staňková, Jan Vrána, Saki Chan, María Muñoz-Amatriaín, 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 Doležel, Sarah Ayling, Stefano Lonardi, Paul Kersey, Peter Langridge, 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 () and Nils Stein ()
Additional contact information
Martin Mascher: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
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
Matthew D. Clark: Earlham Institute
Mario Caccamo: Earlham Institute
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
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
Robbie Waugh: The James Hutton Institute
Nils Stein: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben

Nature, 2017, vol. 544, issue 7651, 427-433

Abstract: 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.

Date: 2017
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DOI: 10.1038/nature22043

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