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

Klaus F. X. Mayer; Robbie Waugh; John W. S. Brown; Alan Schulman; Peter Langridge; Matthias Platzer; Geoffrey B. Fincher; Gary J. Muehlbauer; Kazuhiro Sato; Timothy J. Close; Roger P. Wise; Nils Stein; International Barley Genome Sequencing Consortium

doi:10.1038/nature11543

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

Klaus F. X. Mayer (Lead / Corresponding author), Robbie Waugh (Lead / Corresponding author), John W. S. Brown, Alan Schulman, Peter Langridge, Matthias Platzer, Geoffrey B. Fincher, Gary J. Muehlbauer, Kazuhiro Sato, Timothy J. Close, Roger P. Wise, Nils Stein (Lead / Corresponding author), International Barley Genome Sequencing Consortium

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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.

Original language	English
Pages (from-to)	711-716
Number of pages	6
Journal	Nature
Volume	491
Issue number	7426
DOIs	https://doi.org/10.1038/nature11543
Publication status	Published - 29 Nov 2012

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

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.",

author = "Mayer, {Klaus F. X.} and Robbie Waugh and Brown, {John W. S.} and Alan Schulman and Peter Langridge and Matthias Platzer and Fincher, {Geoffrey B.} and Muehlbauer, {Gary J.} and Kazuhiro Sato and Close, {Timothy J.} and Wise, {Roger P.} and Nils Stein and {International Barley Genome Sequencing Consortium}",

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T1 - A physical, genetic and functional sequence assembly of the barley genome

AU - Mayer, Klaus F. X.

AU - Waugh, Robbie

AU - Brown, John W. S.

AU - Schulman, Alan

AU - Langridge, Peter

AU - Platzer, Matthias

AU - Fincher, Geoffrey B.

AU - Muehlbauer, Gary J.

AU - Sato, Kazuhiro

AU - Close, Timothy J.

AU - Wise, Roger P.

AU - Stein, Nils

AU - International Barley Genome Sequencing Consortium

PY - 2012/11/29

Y1 - 2012/11/29

N2 - 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.

AB - 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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SP - 711

EP - 716

JO - Nature

JF - Nature

IS - 7426

ER -

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

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