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Sci Data. 2017 Apr 27;4:170044. doi: 10.1038/sdata.2017.44.

Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.

Author information

1
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany.
2
School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia.
3
Centre for Comparative Genomics, Murdoch University, Murdoch, Western Australia 6150, Australia.
4
Australian Export Grains Innovation Centre, South Perth, Western Australia 6151, Australia.
5
Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, Minnesota 55108, USA.
6
The James Hutton Institute, Dundee DD2 5DA, UK.
7
European Molecular Biology Laboratory-The European Bioinformatics Institute, Hinxton CB10 1SD, UK.
8
Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), 07745 Jena, Germany.
9
BioNano Genomics Inc., San Diego, California 92121, USA.
10
Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, 78371 Olomouc, Czech Republic.
11
Department of Botany &Plant Sciences, University of California, Riverside, Riverside, California 92521, USA.
12
Department of Computer Science and Engineering, University of California, Riverside, Riverside, California 92521, USA.
13
Department of Agricultural and Environmental Sciences, University of Udine, 33100 Udine, Italy.
14
Green Technology, Natural Resources Institute (Luke), Viikki Plant Science Centre, and Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland.
15
Earlham Institute, Norwich NR4 7UH, UK.
16
BGI-Shenzhen, Shenzhen 518083, China.
17
College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.
18
Kansas State University, Wheat Genetics Resource Center, Department of Plant Pathology and Department of Agronomy, Manhattan, Kansas 66506, USA.
19
School of Agriculture, University of Adelaide, Urrbrae, South Australia 5064, Australia.
20
Department of Plant and Microbial Biology, University of Minnesota, St Paul, Minnesota 55108, USA.
21
School of Environmental Sciences, University of East Anglia, Norwich NR4 7UH, UK.
22
National Institute of Agricultural Botany, Cambridge CB3 0LE, UK.
23
Department of Biology, Lund University, 22362 Lund, Sweden.
24
Carlsberg Research Laboratory, 1799 Copenhagen, Denmark.
25
Department of Agriculture and Food, Government of Western Australia, South Perth, Western Australia 6150, Australia.
26
Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, Hubei 434025, China.
27
School of Life Sciences, University of Dundee, Dundee DD2 5DA, UK.
28
School of Plant Biology, University of Western Australia, Crawley 6009, Australia.
29
German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany.

Abstract

Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. 'Morex' was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).

PMID:
28448065
PMCID:
PMC5407242
DOI:
10.1038/sdata.2017.44
[Indexed for MEDLINE]
Free PMC Article

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