A chromosome conformation capture ordered sequence of the barley genome
Open accessAbstract
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. The International Barley Genome Sequencing Consortium reports sequencing and assembly of a reference genome for barley, Hordeum vulgare. Triticeae grasses, which include barley, wheat and rye, are widely cultivated plants with particularly complex genomes and evolutionary histories. Sequencing of the barley genome has been particularly challenging owing to its large size and particular genomic features, such as an abundance of repetitive elements. Nils Stein and colleagues of the International Barley Genome Sequencing Consortium report sequencing and assembly of a reference genome for barley (Hordeumvulgare L). They use a combined approach of hierarchical shotgun sequencing of bacterial artificial chromosomes, genome mapping on nanochannel arrays and chromosome-scale scaffolding with Hi-C sequencing. This brings the first comprehensive, completely ordered assembly of the pericentromeric regions of a Triticeae genome. The authors also sequenced and examined genetic diversity in the exomes of 96 European elite barley lines with a spring or winter growth habit, and highlight the utility of this resource for cereal genomics and breeding programs.
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Genome annotation and assembly were subsequently improved.
“Genome annotation and assembly were subsequently improved (Mascher et al., 2017;Monat et al., 2019).”
From Genetic resources and precise gene editing for targeted improvement of barley abiotic stress tolerance (2023) · cites this paper as Mascher et al., 2017
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Preparation of HMW DNA from Plant Nuclei and Chromosomes Isolated from Root Tips
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Caspase-Like Activities Accompany Programmed Cell Death Events in Developing Barley Grains
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Self-citationSequencing of BAC pools by different next generation sequencing platforms and strategies
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Self-citationZimin, A. V., Puiu, D., Luo, M., et al. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/066100 · Cited by 11 · see citing works
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The barley pan-genome reveals the hidden legacy of mutation breeding
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Self-citationA Genome Assembly of the Barley ‘Transformation Reference’ Cultivar Golden Promise
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Self-citationHighly efficient and genotype-independent barley gene editing based on anther culture
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Karunarathne, S., Walker, E., Sharma, D., Li, C., & Han, Y. (2023) · Journal of Zhejiang University-SCIENCE B · doi:10.1631/jzus.b2200552 · Cited by 18 · see citing works
“Genome annotation and assembly were sub‐ sequently improved (Mascher et al., 2017; Monat et al., 2019).”
Self-citation
- Authors
- Mascher, M., Gundlach, H., Himmelbach, A., Beier, S., Twardziok, S. O., Wicker, T., Radchuk, V., Dockter, C., Hedley, P. E., Russell, J., Bayer, M., Ramsay, L., Liu, H., Haberer, G., Zhang, X.-Q., Zhang, Q., Barrero, R. A., Li, L., Taudien, S., Groth, M., Felder, M., Hastie, A., Šimková, H., Staňková, H., Vrána, J., Chan, S., Muñoz-Amatriaín, M., Ounit, R., Wanamaker, S., Bolser, D., Colmsee, C., Schmutzer, T., Aliyeva-Schnorr, L., Grasso, S., Tanskanen, J., Chailyan, A., Sampath, D., Heavens, D., Clissold, L., Cao, S., Chapman, B., Dai, F., Han, Y., Li, H., Li, X., Lin, C., McCooke, J. K., Tan, C., Wang, P., Wang, S., Yin, S., Zhou, G., Poland, J. A., Bellgard, M. I., Borisjuk, L., Houben, A., Doležel, J., Ayling, S., Lonardi, S., Kersey, P., Langridge, P., Muehlbauer, G. J., Clark, M. D., Caccamo, M., Schulman, A. H., Mayer, K. F. X., Platzer, M., Close, T. J., Scholz, U., Hansson, M., Zhang, G., Braumann, I., Spannagl, M., Li, C., Waugh, R., & Stein, N.
- Affiliations
- German Centre for Integrative Biodiversity Research (DE)
- Helmholtz Munich (DE)
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) (DE)
- University of Zurich (CH)
- Carlsberg Laboratory (DK)
- James Hutton Institute (GB)
- Murdoch University (AU)
- Australian Export Grains Innovation Centre (AU)
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) (DE)
- BioNano Genomics (United States) (US)
- Centre of the Region Haná for Biotechnical and Agricultural Research (CZ)
- University of California, Riverside (US)
- University of Udine (IT)
- University of Helsinki (FI)
- Earlham Institute (GB)
- BGI Group (China) (CN)
- Zhejiang University (CN)
- Kansas State University (US)
- European Bioinformatics Institute (GB)
- The University of Adelaide (AU)
- University of Minnesota (US)
- University of East Anglia (GB)
- Lund University (SE)
- The University of Western Australia (AU)
- Corresponding author
- Zhang, Guoping
- Braumann, Ilka
- Spannagl, Manuel
- Li, Chengdao
- Waugh, Robbie
- Stein, Nils
- ORCID
- Mascher, Martin
- Gundlach, Heidrun
- Himmelbach, Axel
- Beier, Sebastian
- Twardziok, Sven O.
- Wicker, Thomas
- Radchuk, Volodymyr
- Dockter, Christoph
- Hedley, Pete E.
- Russell, Joanne
- Bayer, Micha
- Ramsay, Luke
- Liu, Hui
- Haberer, Georg
- Zhang, Xiao-Qi
- Barrero, Roberto A.
- Groth, Marco
- Hastie, Alex
- Šimková, Hana
- Vrána, Jan
- Chan, Saki
- Ounit, Rachid
- Colmsee, Christian
- Schmutzer, Thomas
- Grasso, Stefano
- Tanskanen, Jaakko
- Chailyan, Anna
- Sampath, Dharanya
- Heavens, Darren
- Chapman, Brett
- Dai, Fei
- Han, Yong
- Li, Hua
- Li, Xuan
- Tan, Cong
- Wang, Penghao
- Wang, Songbo
- Yin, Shuya
- Zhou, Gaofeng
- Poland, Jesse A.
- Bellgard, Matthew I.
- Borisjuk, Ljudmilla
- Houben, Andreas
- Doležel, Jaroslav
- Lonardi, Stefano
- Kersey, Paul
- Langridge, Peter
- Muehlbauer, Gary J.
- Clark, Matthew D.
- Schulman, Alan H.
- Mayer, Klaus F. X.
- Platzer, Matthias
- Close, Timothy J.
- Scholz, Uwe
- Hansson, Mats
- Zhang, Guoping
- Braumann, Ilka
- Spannagl, Manuel
- Li, Chengdao
- Waugh, Robbie
- Stein, Nils
- Venue
- Nature
- Published
- 2017-04
- Volume
- 544
- Issue
- 7651
- Pages
- 427-433
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W2610080502
- Cited by
- 1,450
- References
- 103
- Citations by year
- 2026: 81 · 2025: 92 · 2024: 105 · 2023: 119 · 2022: 174 · 2021: 231 · 2020: 217 · 2019: 202 · 2018: 169 · 2017: 53 · 2016: 2
- FWCI
- 173.74
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Nature (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Discovery Research Portal (University of Dundee) (publishedVersion, cc-by)
- Zurich Open Repository and Archive (University of Zurich) (acceptedVersion, other-oa)
- QUT ePrints (Queensland University of Technology) (submittedVersion, cc-by)
- UWA Profiles and Research Repository (UWA) (submittedVersion, other-oa)
- Murdoch University Research Portal (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- ASEP (submittedVersion, public-domain)
- Buleria (Universidad de León) (submittedVersion, cc-by)
- Adelaide Research & Scholarship (AR&S) (University of Adelaide) (submittedVersion, cc-by)
- eScholarship (California Digital Library) (submittedVersion)
- Informationszentrum Lebenswissenschaften (ZB MED) (submittedVersion, cc-by)
- Jukuri (Natural Resources Institute Finland (Luke)) (submittedVersion, cc-by)
- Lund University Publications (Lund University) (submittedVersion)
- Site cant be reached (submittedVersion, cc-by)
- Zurich Open Repository and Archive (University of Zurich) (submittedVersion, other-oa)
- Zurich Open Repository and Archive (University of Zurich)
- Funders
- National Science Foundation (0315954, 1062301, 0321756)
- U.S. Department of Agriculture (2011‐68002‐30029)
- Grains Research and Development Corporation (DAW00233)
- National Natural Science Foundation of China (31330055, 31129005)
- Government of Western Australia
- Directorate for Biological Sciences
- National Institute of Food and Agriculture (2011–68002–30029)
- Cooperative State Research, Education, and Extension Service
- Biotechnology and Biological Sciences Research Council (BB/I00663X/1, BB/I008357/1, BB/I008071/1, BB/J004669/1, BBS/E/T/000PR5885, BB/J010375/1, BBS/E/T/000PR6193, BB/H531519/1, BB/L026317/1)
- Leibniz-Gemeinschaft
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Wheat and Barley Genetics and Pathology
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- barley, reference genome, chromosome conformation capture, pericentromeric regions, chromatin spatial organization, repetitive elements, genetic diversity, genetic erosion, Triticeae, cereal genomics, breeding
- MeSH terms
- Hordeum, Cell Nucleus, Centromere, Chromatin, Chromosome Mapping, Haplotypes, Meiosis, Repetitive Sequences, Nucleic Acid, Seeds, Genetic Variation, Genome, Plant, Chromosomes, Artificial, Bacterial, Genomics, Chromosomes, Plant
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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