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.

Australian Export Grains Innovation Centre South Perth WA6151 Australia

BGI Shenzhen Shenzhen 518083 China

BioNano Genomics Inc San Diego CA 92121 California USA

Carlsberg Research Laboratory 1799 Copenhagen Denmark

Centre for Comparative Genomics Murdoch University WA6150 Murdoch Australia

College of Agriculture and Biotechnology Zhejiang University Hangzhou 310058 China

Department of Agricultural and Environmental Sciences University of Udine 33100 Udine Italy

Department of Agriculture and Food Government of Western Australia South Perth WA 6151 Australia

Department of Agronomy and Plant Genetics University of Minnesota St Paul MN 55108 Minnesota USA

Department of Biology Lund University 22362 Lund Sweden

Department of Botany and Plant Sciences University of California Riverside Riverside CA 92521 California USA

Department of Computer Science and Engineering University of California Riverside Riverside CA 92521 California USA

Department of Plant and Microbial Biology University of Minnesota St Paul MN 55108 Minnesota USA

Department of Plant and Microbial Biology University of Zurich 8008 Zurich Switzerland

Earlham Institute Norwich NR4 7UH UK

European Molecular Biology Laboratory The European Bioinformatics Institute Hinxton CB10 1SD UK

German Centre for Integrative Biodiversity Research Halle Jena Leipzig 04103 Leipzig Germany

Green Technology Natural Resources Institute Viikki Plant Science Centre and Institute of Biotechnology University of Helsinki 00014 Helsinki Finland

Hubei Collaborative Innovation Centre for Grain Industry Yangtze University Jingzhou Hubei 434023 China

Institute of Experimental Botany Centre of the Region Haná for Biotechnological and Agricultural Research 78371 Olomouc Czech Republic

Kansas State University Wheat Genetics Resource Center Department of Plant Pathology and Department of Agronomy Manhattan KS 66506 Kansas USA

Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben 06466 Seeland Germany

Leibniz Institute on Aging Fritz Lipmann Institute 07745 Jena Germany

National Institute of Agricultural Botany Cambridge CB3 0LE UK

PGSB Plant Genome and Systems Biology Helmholtz Center Munich German Research Center for Environmental Health 85764 Neuherberg Germany

School of Agriculture University of Adelaide Urrbrae SA5064 Australia

School of Environmental Sciences University of East Anglia Norwich NR4 7TJ UK

School of Life Sciences University of Dundee Dundee DD2 5DA UK

School of Plant Biology University of Western Australia Crawley WA6009 Australia

School of Veterinary and Life Sciences Murdoch University Murdoch WA6150 Australia

The James Hutton Institute Dundee DD2 5DA UK

Wissenschaftszentrum Weihenstephan Technical University Munich 85354 Freising Germany

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Nature. 2017 Apr 26;544(7651):424-425. doi: 10.1038/544424a. PubMed

Zobrazit více v PubMed

Bioinformatics. 2010 Feb 1;26(3):401-2 PubMed

Nature. 2012 Nov 29;491(7426):711-6 PubMed

Plant J. 2015 Oct;84(2):385-94 PubMed

Gigascience. 2012 Dec 27;1(1):18 PubMed

Chromosoma. 1996;104(5):315-20 PubMed

Plant J. 2003 Mar;33(6):967-73 PubMed

Cell. 2014 Dec 18;159(7):1665-80 PubMed

Plant Physiol. 2014 Jan;164(1):412-23 PubMed

Bioinformatics. 2010 Dec 15;26(24):3133-4 PubMed

IEEE/ACM Trans Comput Biol Bioinform. 2013 May-Jun;10(3):645-56 PubMed

Cell. 2015 Jul 30;162(3):527-39 PubMed

Chromosome Res. 1999;7(6):431-44 PubMed

Bioinformatics. 2011 Nov 1;27(21):2987-93 PubMed

Biochem Genet. 1974 Oct;12(4):257-69 PubMed

Nat Genet. 1998 Sep;20(1):43-5 PubMed

BMC Genomics. 2009 Nov 20;10:547 PubMed

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D258-61 PubMed

Plant J. 2015 Oct;84(1):216-27 PubMed

Mol Cell. 2014 Sep 4;55(5):678-93 PubMed

Proc Natl Acad Sci U S A. 1994 Feb 15;91(4):1411-5 PubMed

Bioinformatics. 2015 Oct 1;31(19):3210-2 PubMed

J Comput Biol. 2000 Feb-Apr;7(1-2):203-14 PubMed

Genome Res. 2003 Sep;13(9):2178-89 PubMed

Proc Natl Acad Sci U S A. 2014 Feb 11;111(6):2104-9 PubMed

Nucleic Acids Res. 2016 Jan 4;44(D1):D1141-7 PubMed

Nucleic Acids Res. 2001 Dec 15;29(24):5029-35 PubMed

Science. 2009 Nov 20;326(5956):1112-5 PubMed

Plant J. 2013 Nov;76(3):494-505 PubMed

Bioinformatics. 2012 Oct 1;28(19):2537-9 PubMed

Nature. 2010 May 20;465(7296):363-7 PubMed

J Biol Chem. 1984 Nov 25;259(22):13637-9 PubMed

Nat Methods. 2011 Sep 29;8(10):785-6 PubMed

Nat Genet. 2016 Sep;48(9):1024-30 PubMed

Plant Cell. 2016 Nov;28(11):2700-2714 PubMed

Bioinformatics. 2012 Dec 1;28(23):3131-3 PubMed

Genome Biol. 2004;5(10):R80 PubMed

Methods. 2012 Nov;58(3):268-76 PubMed

BMC Bioinformatics. 2008 Jan 14;9:18 PubMed

Nature. 2009 Jan 29;457(7229):551-6 PubMed

BMC Genomics. 2015 Mar 25;16:236 PubMed

Nature. 2005 Aug 11;436(7052):793-800 PubMed

Genome Res. 2009 Jun;19(6):1117-23 PubMed

Bioinformatics. 2005 Jan 15;21(2):263-5 PubMed

Genetics. 2000 Jan;154(1):397-412 PubMed

Theor Appl Genet. 2009 Feb;118(3):483-97 PubMed

Bioinformatics. 2010 Mar 15;26(6):841-2 PubMed

Science. 2014 Jul 18;345(6194):1251788 PubMed

Science. 2012 Jan 13;335(6065):207-11 PubMed

J Mol Biol. 1990 Oct 5;215(3):403-10 PubMed

Science. 2014 Jul 18;345(6194):1249721 PubMed

Nat Genet. 2011 May;43(5):491-8 PubMed

Gigascience. 2014 Dec 30;3(1):34 PubMed

Mol Plant. 2015 Jun;8(6):964-6 PubMed

Nature. 2010 Feb 11;463(7282):763-8 PubMed

Plant Cell. 1994 Jun;6(6):907-16 PubMed

PLoS Comput Biol. 2011 Oct;7(10):e1002195 PubMed

Proc Natl Acad Sci U S A. 2016 Jun 7;113(23 ):6444-8 PubMed

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D138-41 PubMed

Plant Physiol. 2011 May;156(1):20-8 PubMed

Plant Biotechnol J. 2011 Dec;9(9):1022-37 PubMed

PLoS One. 2014 Oct 06;9(10):e109426 PubMed

J Biol Chem. 1988 Dec 15;263(35):18953-60 PubMed

Nat Biotechnol. 2013 Dec;31(12):1119-25 PubMed

Nat Protoc. 2012 Mar 01;7(3):562-78 PubMed

Science. 1996 Nov 1;274(5288):765-8 PubMed

Nat Genet. 2012 Dec;44(12):1388-92 PubMed

J Exp Bot. 2011 Jan;62(3):1217-27 PubMed

Nature. 2000 Dec 14;408(6814):796-815 PubMed

Bioinformatics. 2009 Jul 15;25(14):1754-60 PubMed

Plant Mol Biol. 1990 May;14(5):655-68 PubMed

Science. 2009 Oct 9;326(5950):289-93 PubMed

Plant J. 2013 Nov;76(4):718-27 PubMed

Genome Res. 2017 May;27(5):787-792 PubMed

Plant Biotechnol J. 2016 Jul;14 (7):1523-31 PubMed

Bioinformatics. 2011 Feb 15;27(4):578-9 PubMed

Nat Biotechnol. 2012 Aug;30(8):771-6 PubMed

Science. 2013 Jul 5;341(6141):65-7 PubMed

Plant Physiol. 2012 Jan;158(1):26-34 PubMed

J Virol. 1999 Jun;73(6):5186-90 PubMed

Nat Methods. 2015 Aug;12(8):780-6 PubMed

Sci Data. 2017 Apr 27;4:170044 PubMed

Methods Mol Biol. 2016;1374:115-40 PubMed

PLoS One. 2011;6(7):e21800 PubMed

BMC Res Notes. 2011 Oct 14;4:411 PubMed

Plant Biotechnol J. 2016 Jul;14 (7):1511-22 PubMed

Science. 1991 May 24;252(5009):1162-4 PubMed

Nat Biotechnol. 2011 Dec 25;30(1):90-8 PubMed

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