Cited by 1,456Wheat and Barley Genetics and PathologyChromosomal and Genetic VariationsGenetic and Environmental Crop Studies

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A physical, genetic and functional sequence assembly of the barley genome

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The International Barley Genome Sequencing Consortium·2012·Nature

DOI 10.1038/nature11543

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Abstract

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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Authors: The International Barley Genome Sequencing Consortium
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2012-10-17
Volume: 491
Issue: 7426
Pages: 711-716
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature11543
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: cc-by-nc-sa
creativecommons.org/licenses/by-nc-sa/3.0/ (tdm)
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

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A physical, genetic and functional sequence assembly of the barley genome

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