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Nature. 2017 Apr 26;544(7651):427-433. doi: 10.1038/nature22043.

A chromosome conformation capture ordered sequence of the barley genome.

Author information

1
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany.
2
German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany.
3
PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, 85764 Neuherberg, Germany.
4
Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland.
5
Carlsberg Research Laboratory, 1799 Copenhagen, Denmark.
6
The James Hutton Institute, Dundee DD2 5DA, UK.
7
School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA6150, Australia.
8
Australian Export Grains Innovation Centre, South Perth, WA6151, Australia.
9
Centre for Comparative Genomics, Murdoch University, WA6150, Murdoch, Australia.
10
Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, Minnesota, USA.
11
Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany.
12
BioNano Genomics Inc., San Diego, CA 92121, California, USA.
13
Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, 78371 Olomouc, Czech Republic.
14
Department of Botany &Plant Sciences, University of California, Riverside, Riverside, CA 92521, California, USA.
15
Department of Computer Science and Engineering, University of California, Riverside, Riverside, CA 92521 California, USA.
16
European Molecular Biology Laboratory - The European Bioinformatics Institute, Hinxton CB10 1SD, UK.
17
Department of Agricultural and Environmental Sciences, University of Udine, 33100 Udine, Italy.
18
Green Technology, Natural Resources Institute (Luke), Viikki Plant Science Centre, and Institute of Biotechnology, University of Helsinki, 00014, Helsinki, Finland.
19
Earlham Institute, Norwich NR4 7UH, UK.
20
BGI-Shenzhen, Shenzhen, 518083, China.
21
College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
22
Kansas State University, Wheat Genetics Resource Center, Department of Plant Pathology and Department of Agronomy, Manhattan, KS 66506, Kansas, USA.
23
School of Agriculture, University of Adelaide, Urrbrae, SA5064, Australia.
24
Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, Minnesota, USA.
25
School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
26
National Institute of Agricultural Botany, Cambridge CB3 0LE, UK.
27
Wissenschaftszentrum Weihenstephan (WZW), Technical University Munich, 85354 Freising, Germany.
28
Department of Biology, Lund University, 22362 Lund, Sweden.
29
Department of Agriculture and Food, Government of Western Australia, South Perth WA 6151, Australia.
30
Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, Hubei, 434023, China.
31
School of Life Sciences, University of Dundee, Dundee DD2 5DA, UK.
32
School of Plant Biology, University of Western Australia, Crawley, WA6009, 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.

PMID:
28447635
DOI:
10.1038/nature22043
[Indexed for MEDLINE]
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