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

Klaus F.X. Mayer; Robbie Waugh; Peter Langridge; Timothy J. Close; Roger P. Wise; Andreas Graner; Takashi Matsumoto; Kazuhiro Sato; Alan Schulman; Ruvini Ariyadasa; Daniela Schulte; Naser Poursarebani; Ruonan Zhou; Burkhard Steuernagel; Martin Mascher; Uwe Scholz; Bujun Shi; Kavitha Madishetty; Jan T. Svensson; Prasanna Bhat; Matthew Moscou; Josh Resnik; Gary J. Muehlbauer; Pete Hedley; Hui Liu; Jenny Morris; Zeev Frenkel; Avraham Korol; Hélène Bergès; Stefan Taudien; Marius Felder; Marco Groth; Matthias Platzer; Axel Himmelbach; Stefano Lonardi; Denisa Duma; Matthew Alpert; Francesa Cordero; Marco Beccuti; Gianfranco Ciardo; Yaqin Ma; Steve Wanamaker; Federica Cattonaro; Vera Vendramin; Simone Scalabrin; Slobodanka Radovic; Rod Wing; Michele Morgante; Thomas Nussbaumer; Heidrun Gundlach; Mihaela Martis; Jesse Poland; Matthias Pfeifer; Cédric Moisy; Jaakko Tanskanen; Andrea Zuccolo; Manuel Spannagl; Joanne Russell; Arnis Druka; David Marshall; Micha Bayer; David Swarbreck; Dharanya Sampath; Sarah Ayling; Melanie Febrer; Mario Caccamo; Tsuyoshi Tanaka; Steve Wannamaker; Thomas Schmutzer; John W.S. Brown; Geoffrey B. Fincher; Nils Stein

doi:10.1038/nature11543

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

Klaus F.X. Mayer, Robbie Waugh, Peter Langridge, Timothy J. Close, Roger P. Wise, Andreas Graner, Takashi Matsumoto, Kazuhiro Sato, Alan Schulman, Ruvini Ariyadasa, Daniela Schulte, Naser Poursarebani, Ruonan Zhou, Burkhard Steuernagel, Martin Mascher, Uwe Scholz, Bujun Shi, Kavitha Madishetty, Jan T. Svensson, Prasanna BhatMatthew Moscou, Josh Resnik, Gary J. Muehlbauer, Pete Hedley, Hui Liu, Jenny Morris, Zeev Frenkel, Avraham Korol, Hélène Bergès, Stefan Taudien, Marius Felder, Marco Groth, Matthias Platzer, Axel Himmelbach, Stefano Lonardi, Denisa Duma, Matthew Alpert, Francesa Cordero, Marco Beccuti, Gianfranco Ciardo, Yaqin Ma, Steve Wanamaker, Federica Cattonaro, Vera Vendramin, Simone Scalabrin, Slobodanka Radovic, Rod Wing, Michele Morgante, Thomas Nussbaumer, Heidrun Gundlach, Mihaela Martis, Jesse Poland, Matthias Pfeifer, Cédric Moisy, Jaakko Tanskanen, Andrea Zuccolo, Manuel Spannagl, Joanne Russell, Arnis Druka, David Marshall, Micha Bayer, David Swarbreck, Dharanya Sampath, Sarah Ayling, Melanie Febrer, Mario Caccamo, Tsuyoshi Tanaka, Steve Wannamaker, Thomas Schmutzer, John W.S. Brown, Geoffrey B. Fincher, Nils Stein

Research output: Contribution to journal › Article › peer-review

1209 Scopus citations

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. © 2012 Macmillan Publishers Limited. All rights reserved.

Original language	English (US)
Journal	Nature
Volume	491
Issue number	7426
DOIs	https://doi.org/10.1038/nature11543
State	Published - Nov 29 2012
Externally published	Yes

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Mayer, K. F. X., Waugh, R., Langridge, P., Close, T. J., Wise, R. P., Graner, A., Matsumoto, T., Sato, K., Schulman, A., Ariyadasa, R., Schulte, D., Poursarebani, N., Zhou, R., Steuernagel, B., Mascher, M., Scholz, U., Shi, B., Madishetty, K., Svensson, J. T., ... Stein, N. (2012). A physical, genetic and functional sequence assembly of the barley genome. Nature, 491(7426). https://doi.org/10.1038/nature11543

@article{2f3dfc7690af4d01a1e9c89c78e57230,

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. {\textcopyright} 2012 Macmillan Publishers Limited. All rights reserved.",

author = "Mayer, {Klaus F.X.} and Robbie Waugh and Peter Langridge and Close, {Timothy J.} and Wise, {Roger P.} and Andreas Graner and Takashi Matsumoto and Kazuhiro Sato and Alan Schulman and Ruvini Ariyadasa and Daniela Schulte and Naser Poursarebani and Ruonan Zhou and Burkhard Steuernagel and Martin Mascher and Uwe Scholz and Bujun Shi and Kavitha Madishetty and Svensson, {Jan T.} and Prasanna Bhat and Matthew Moscou and Josh Resnik and Muehlbauer, {Gary J.} and Pete Hedley and Hui Liu and Jenny Morris and Zeev Frenkel and Avraham Korol and H{\'e}l{\`e}ne Berg{\`e}s and Stefan Taudien and Marius Felder and Marco Groth and Matthias Platzer and Axel Himmelbach and Stefano Lonardi and Denisa Duma and Matthew Alpert and Francesa Cordero and Marco Beccuti and Gianfranco Ciardo and Yaqin Ma and Steve Wanamaker and Federica Cattonaro and Vera Vendramin and Simone Scalabrin and Slobodanka Radovic and Rod Wing and Michele Morgante and Thomas Nussbaumer and Heidrun Gundlach and Mihaela Martis and Jesse Poland and Matthias Pfeifer and C{\'e}dric Moisy and Jaakko Tanskanen and Andrea Zuccolo and Manuel Spannagl and Joanne Russell and Arnis Druka and David Marshall and Micha Bayer and David Swarbreck and Dharanya Sampath and Sarah Ayling and Melanie Febrer and Mario Caccamo and Tsuyoshi Tanaka and Steve Wannamaker and Thomas Schmutzer and Brown, {John W.S.} and Fincher, {Geoffrey B.} and Nils Stein",

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Mayer, KFX, Waugh, R, Langridge, P, Close, TJ, Wise, RP, Graner, A, Matsumoto, T, Sato, K, Schulman, A, Ariyadasa, R, Schulte, D, Poursarebani, N, Zhou, R, Steuernagel, B, Mascher, M, Scholz, U, Shi, B, Madishetty, K, Svensson, JT, Bhat, P, Moscou, M, Resnik, J, Muehlbauer, GJ, Hedley, P, Liu, H, Morris, J, Frenkel, Z, Korol, A, Bergès, H, Taudien, S, Felder, M, Groth, M, Platzer, M, Himmelbach, A, Lonardi, S, Duma, D, Alpert, M, Cordero, F, Beccuti, M, Ciardo, G, Ma, Y, Wanamaker, S, Cattonaro, F, Vendramin, V, Scalabrin, S, Radovic, S, Wing, R, Morgante, M, Nussbaumer, T, Gundlach, H, Martis, M, Poland, J, Pfeifer, M, Moisy, C, Tanskanen, J, Zuccolo, A, Spannagl, M, Russell, J, Druka, A, Marshall, D, Bayer, M, Swarbreck, D, Sampath, D, Ayling, S, Febrer, M, Caccamo, M, Tanaka, T, Wannamaker, S, Schmutzer, T, Brown, JWS, Fincher, GB & Stein, N 2012, 'A physical, genetic and functional sequence assembly of the barley genome', Nature, vol. 491, no. 7426. https://doi.org/10.1038/nature11543

TY - JOUR

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

AU - Mayer, Klaus F.X.

AU - Waugh, Robbie

AU - Langridge, Peter

AU - Close, Timothy J.

AU - Wise, Roger P.

AU - Graner, Andreas

AU - Matsumoto, Takashi

AU - Sato, Kazuhiro

AU - Schulman, Alan

AU - Ariyadasa, Ruvini

AU - Schulte, Daniela

AU - Poursarebani, Naser

AU - Zhou, Ruonan

AU - Steuernagel, Burkhard

AU - Mascher, Martin

AU - Scholz, Uwe

AU - Shi, Bujun

AU - Madishetty, Kavitha

AU - Svensson, Jan T.

AU - Bhat, Prasanna

AU - Moscou, Matthew

AU - Resnik, Josh

AU - Muehlbauer, Gary J.

AU - Hedley, Pete

AU - Liu, Hui

AU - Morris, Jenny

AU - Frenkel, Zeev

AU - Korol, Avraham

AU - Bergès, Hélène

AU - Taudien, Stefan

AU - Felder, Marius

AU - Groth, Marco

AU - Platzer, Matthias

AU - Himmelbach, Axel

AU - Lonardi, Stefano

AU - Duma, Denisa

AU - Alpert, Matthew

AU - Cordero, Francesa

AU - Beccuti, Marco

AU - Ciardo, Gianfranco

AU - Ma, Yaqin

AU - Wanamaker, Steve

AU - Cattonaro, Federica

AU - Vendramin, Vera

AU - Scalabrin, Simone

AU - Radovic, Slobodanka

AU - Wing, Rod

AU - Morgante, Michele

AU - Nussbaumer, Thomas

AU - Gundlach, Heidrun

AU - Martis, Mihaela

AU - Poland, Jesse

AU - Pfeifer, Matthias

AU - Moisy, Cédric

AU - Tanskanen, Jaakko

AU - Zuccolo, Andrea

AU - Spannagl, Manuel

AU - Russell, Joanne

AU - Druka, Arnis

AU - Marshall, David

AU - Bayer, Micha

AU - Swarbreck, David

AU - Sampath, Dharanya

AU - Ayling, Sarah

AU - Febrer, Melanie

AU - Caccamo, Mario

AU - Tanaka, Tsuyoshi

AU - Wannamaker, Steve

AU - Schmutzer, Thomas

AU - Brown, John W.S.

AU - Fincher, Geoffrey B.

AU - Stein, Nils

N1 - Generated from Scopus record by KAUST IRTS on 2019-11-20

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. © 2012 Macmillan Publishers Limited. All rights reserved.

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. © 2012 Macmillan Publishers Limited. All rights reserved.

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U2 - 10.1038/nature11543

DO - 10.1038/nature11543

M3 - Article

SN - 0028-0836

VL - 491

JO - Nature

JF - Nature

IS - 7426

ER -

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

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