The DOI matches its Crossref record; 63 of the 63 references it cites were found in a registry or an index.
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“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
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1621 · Cited by 15,556
Trapnell, C., Roberts, A., Goff, L. A., Pertea, G. M., Kim, D., Kelley, D. R., Pimentel, H., Salzberg, S. L., Rinn, J. L., & Pachter, L. S. (2012) · Nature Protocols · doi:10.1038/nprot.2012.016 · Cited by 12,145
Velvet: Algorithms for de novo short read assembly using de Bruijn graphsPreprint
Zerbino, D. R., & Birney, E. (2008) · Genome Research · doi:10.1101/gr.074492.107 · Cited by 9,587
A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species
Elshire, R. J., Glaubitz, J. C., Sun, Q., Poland, J., Kawamoto, K., Buckler, E. S., & Mitchell, S. E. (2011) · PLoS ONE · doi:10.1371/journal.pone.0019379 · Cited by 6,461
The B73 Maize Genome: Complexity, Diversity, and Dynamics
Schnable, P. S., Ware, D., Fulton, R. S., Stein, J. C., Wei, F., Pasternak, S., Liang, C., Zhang, J., Fulton, L., Graves, T., et al. (2009) · Science · doi:10.1126/science.1178534 · Cited by 4,096
The map-based sequence of the rice genome
International Rice Genome Sequencing Project, & Sasaki, T. (2005) · Nature · doi:10.1038/nature03895 · Cited by 3,843
The Sorghum bicolor genome and the diversification of grasses
Paterson, A. H., Bowers, J., Bruggmann, R., Dubchak, I. L., Grimwood, J., Gundlach, H., Haberer, G., Hellsten, U., Mitros, T., Poliakov, A., et al. (2009) · Nature · doi:10.1038/nature07723 · Cited by 3,150
Modular regulatory principles of large non-coding RNAs
Guttman, M., & Rinn, J. L. (2012) · Nature · doi:10.1038/nature10887 · Cited by 2,298
Poland, J., Brown, P. J., Sorrells, M. E., & Jannink, J. (2012) · PLoS ONE · doi:10.1371/journal.pone.0032253 · Cited by 1,881
Research works printed but not linked: 3
- Grando, S. & Macpherson, H. G. in Proceedings of the International Workshop on Food Barley Improvement, 14–17 January 2002, Hammamet, Tunisia 156 (ICARDA, Aleppo, Syria, 2005)
- Bockelman, H. E. & Valkoun, J. in Barley: Production, Improvement, and Uses (ed. S. E. Ullrich ) 144–159 (Wiley-Blackwell, 2011)
- Comadran, J. et al. A homologue of Antirrhinum CENTRORADIALIS is a component of the quantitative photoperiod and vernalization independent EARLINESS PER SE 2 locus in cultivated barley. Nature Genet. (in the press).
Cited by
Sorted by citations
Shifting the limits in wheat research and breeding using a fully annotated reference genome
Appels, R., Eversole, K., Stein, N., Feuillet, C., Keller, B., Rogers, J., Pozniak, C. J., Choulet, F., Distelfeld, A., Poland, J., et al. (2018) · Science · doi:10.1126/science.aar7191 · Cited by 3,183
A chromosome-based draft sequence of the hexaploid bread wheat ( Triticum aestivum ) genome
The International Wheat Genome Sequencing Consortium (IWGSC), Mayer, K. F. X., Rogers, J., Doležel, J., Pozniak, C., Eversole, K., Feuillet, C., Gill, B., Friebe, B., Lukaszewski, A. J., et al. (2014) · Science · doi:10.1126/science.1251788 · Cited by 1,583
A chromosome conformation capture ordered sequence of the barley genome
Mascher, M., Gundlach, H., Himmelbach, A., Beier, S., Twardziok, S. O., Wicker, T., Radchuk, V., Dockter, C., Hedley, P. E., Russell, J., et al. (2017) · Nature · doi:10.1038/nature22043 · Cited by 1,450
Gene duplication and evolution in recurring polyploidization–diploidization cycles in plants
Qiao, X., Li, Q., Yin, H., Qi, K., Li, L., Wang, R., Zhang, S., & Paterson, A. H. (2019) · Genome biology · doi:10.1186/s13059-019-1650-2 · Cited by 1,180
Analysis of the bread wheat genome using whole-genome shotgun sequencing
Brenchley, R., Spannagl, M., Pfeifer, M., Barker, G., D'Amore, R., Allen, A. M., McKenzie, N., Kramer, M., Kerhornou, A., Bolser, D. M., et al. (2012) · Nature · doi:10.1038/nature11650 · Cited by 1,113
Metadata
- 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 › Biochemistry, Genetics and Molecular Biology › Genetics › 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 ›
Are you an author, or do you see a problem with this page? Request a review
