A physical, genetic and functional sequence assembly of the barley genome
Open accessAbstract
Barley (Hordeum vulgare L.) is among the world’s earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complementary DNA and deep RNA sequence data onto this framework supports 79,379 transcript clusters, including 26,159 ‘high-confidence’ genes with homology support from other plant genomes. Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Our data provide a platform for both genome-assisted research and enabling contemporary crop improvement. An integrated high-resolution genetic, physical and shotgun sequence assembly of the barley genome, one of the earliest domesticated and most important crops, is described; it will provide a platform for genome-assisted research and future crop improvement. Two groups in this issue report the compilation and analysis of the genome sequences of major cereal crops — bread wheat and barley — providing important resources for future crop improvement. Bread wheat accounts for one-fifth of the calories consumed by humankind. It has a very large and complex hexaploid genome of 17 Gigabases. Michael Bevan and colleagues have analysed the genome using 454 pyrosequencing and compared it with diploid ancestral and progenitor genomes. The authors discovered significant loss of gene family members upon polyploidization and domestication, and expansion of gene classes that may be associated with crop productivity. Barley is one of the earliest domesticated plant crops. Although diploid, it has a very large genome of 5.1 Gigabases. Nils Stein and colleagues describe a physical map anchored to a high-resolution genetic map, on top of which they have overlaid a deep whole-genome shotgun assembly, cDNA and RNA-seq data to provide the first in-depth genome-wide survey of the barley genome.
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For barley, the International Barley Genome Sequencing Consortium (2012) published the first reference genome of 'Morex'.
“For barley, the International Barley Genome Sequencing Consortium (2012) published the first reference genome of 'Morex'.”
From Genetic resources and precise gene editing for targeted improvement of barley abiotic stress tolerance (2023) · cites this paper as International Barley Genome Sequencing Consortium, 2012
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- Authors
- The International Barley Genome Sequencing Consortium
- Venue
- Nature
- Published
- 2012-10-17
- Volume
- 491
- Issue
- 7426
- Pages
- 711-716
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W2118140755
- Cited by
- 1,456
- References
- 63
- Citations by year
- 2026: 29 · 2025: 23 · 2024: 35 · 2023: 62 · 2022: 84 · 2021: 121 · 2020: 78 · 2019: 117 · 2018: 122 · 2017: 124 · 2016: 171 · 2015: 171 · 2014: 167 · 2013: 141 · 2012: 10
- FWCI
- 178.67
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Nature (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- Institutional Research Information System University of Turin (University of Turin) (submittedVersion, other-oa)
- HAL (submittedVersion)
- Institutional Research Information System (University of Udine) (submittedVersion)
- Adelaide Research & Scholarship (AR&S) (University of Adelaide) (submittedVersion, cc-by-nc-sa)
- Discovery Research Portal (University of Dundee) (submittedVersion)
- Jukuri (Natural Resources Institute Finland (Luke)) (submittedVersion)
- Site cant be reached (submittedVersion)
- CINECA IRIS Institutional Research Information System (Sant'Anna School of Advanced Studies) (submittedVersion)
- Funders
- National Science Foundation (1062301, 0321756)
- U.S. Department of Agriculture (2006-55606-16722)
- Bundesministerium für Bildung und Forschung
- Austrian Science Fund (SFB F3705, F3705)
- Ministry of Agriculture, Forestry and Fisheries
- National Institute of Food and Agriculture
- Cooperative State Research, Education, and Extension Service
- Biotechnology and Biological Sciences Research Council (BB/I00663X/1, BB/I008357/1, BB/100663X/1, BBS/E/T/000PR6193)
- Leibniz-Gemeinschaft
- Japan Society for the Promotion of Science (23380007)
- 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 › Agricultural and Biological Sciences › Plant Science › Genetic and Environmental Crop Studies
- Keywords
- barley, genome assembly, physical map, genetic linkage map, transcriptome, genome annotation, alternative splicing, single nucleotide polymorphisms, domestication, crop improvement, cereal genomes
- MeSH terms
- Hordeum, Repetitive Sequences, Nucleic Acid, Genes, Plant, Alternative Splicing, Sequence Analysis, DNA, Codon, Nonsense, Gene Expression Regulation, Plant, Crops, Agricultural, Genome, Plant, Evolution, Molecular, Physical Chromosome Mapping, Polymorphism, Single Nucleotide, Genomics, Molecular Sequence Annotation, Transcriptome
About these checks
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.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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