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

by Scholz, Uwe , The James Hutton Institute , Wise, Roger P , Zuccolo, Andrea , Scalabrin, Simone , Swarbreck, David , Natl Inst Agrobiol Sci ; Partenaires INRAE , Svensson, Jan T , Liu, Hui , Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben) , Close, Timothy J , University of Minnesota [Twin Cities] (UMN) ; University of Minnesota System (UMN) , Sato, Kazuhiro , Graner, Andreas , Bhat, Prasanna , Hedley, Pete , Inst Evolut ; Ǧāmiʿat͏̈ Hayfā = University of Haifa , Felder, Marius , Moscou, Matthew , Frenkel, Zeev , Muehlbauer, Gary J , Fincher, Geoffrey B , Matsumoto, Takashi , Ariyadasa, Ruvini , Korol, Avraham , Langridge, Peter , Poursarebani, Naser , Stein, Nils , Schulte, Daniela , Schulman, Alan , Vendramin, Vera , Mayer, Klaus F. X , Taudien, Stefan , Shi, Bujun , Madishetty, Kavitha , Berges, Hélène , Platzer, Matthias , Iowa State University (ISU) , Steuernagel, Burkhard , Zhou, Ruonan , Morgante, Michele , Resnik, Josh , German Ministry of Education and Research (BMBF) ; Leibniz Association; European project of the 7th framework programme "TriticeaeGenome"; Aus

in 631/208/191 / 631/449/2491 / Agricultural productivity / Agronomy. Soil science and plant productions / Alternative Splicing - genetics / Artificial chromosomes / Barley / Biological and medical sciences / Cloning / Codon, Nonsense - genetics / Crop improvement / Crops, Agricultural - genetics / Evolution, Molecular / Food / Fundamental and applied biological sciences. Psychology / Gene expression / Gene Expression Regulation, Plant / Generalities. Genetics. Plant material / Genes, Plant - genetics / Genetic aspects / Genetic research / Genetics and breeding of economic plants / Genome, Plant - genetics / Genomes / Genomics / Hordeum - classification / Hordeum - genetics / Hordeum vulgare / Humanities and Social Sciences / Life Sciences / Molecular Sequence Annotation / multidisciplinary / Natural history / Nucleotide sequence / Origin, evolution, domestication / Physical Chromosome Mapping / Physiological aspects / Plant genetics / Plant material / Polymorphism, Single Nucleotide - genetics / Repetitive Sequences, Nucleic Acid - genetics / Science / Sequence Analysis, DNA / Transcriptome - genetics

2012

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

2012

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2012

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Journal Article

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

Scholz, Uwe,

The James Hutton Institute,

Wise, Roger P,

Zuccolo, Andrea,

Scalabrin, Simone,

Swarbreck, David,

Natl Inst Agrobiol Sci ; Partenaires INRAE,

Svensson, Jan T,

Liu, Hui,

Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben),

Close, Timothy J,

University of Minnesota [Twin Cities] (UMN) ; University of Minnesota System (UMN),

Sato, Kazuhiro,

Graner, Andreas,

Bhat, Prasanna,

Hedley, Pete,

Inst Evolut ; Ǧāmiʿat͏̈ Hayfā = University of Haifa,

Felder, Marius,

Moscou, Matthew,

Frenkel, Zeev,

Muehlbauer, Gary J,

Fincher, Geoffrey B,

Matsumoto, Takashi,

Ariyadasa, Ruvini,

Korol, Avraham,

Langridge, Peter,

Poursarebani, Naser,

Stein, Nils,

Schulte, Daniela,

Schulman, Alan,

Vendramin, Vera,

Mayer, Klaus F. X,

Taudien, Stefan,

Shi, Bujun,

Madishetty, Kavitha,

Berges, Hélène,

Platzer, Matthias,

Iowa State University (ISU),

Steuernagel, Burkhard,

Zhou, Ruonan,

Morgante, Michele,

Resnik, Josh,

German Ministry of Education and Research (BMBF) ; Leibniz Association; European project of the 7th framework programme "TriticeaeGenome"; Aus

2012

Overview

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.

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Publisher

Nature Publishing Group,CCSD,Nature Publishing Group UK

Subject

631/208/191

/ 631/449/2491

/ Agricultural productivity

/ Agronomy. Soil science and plant productions

/ Alternative Splicing - genetics

/ Artificial chromosomes

/ Barley