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

Department of Evolutionary and Environmental Biology

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

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
State	Published - 29 Nov 2012

Bibliographical note

Funding Information:
Acknowledgements This work has been supported from the following funding sources: German Ministry of Education and Research (BMBF) grant 0314000 ‘‘BARLEX’’ to K.F.X.M., M.P., U.S. and N.S.; Leibniz Association grant (Pakt f. Forschung und Innovation) to N.S.; European project of the 7th framework programme ‘‘TriticeaeGenome’’ to R.W., A.S., K.F.X.M., M.M. and N.S.; SFB F3705, of the Austrian Wissenschaftsfond (FWF) to K.F.X.M.; ERA-NET PG project ‘‘BARCODE’’ grant to M.M., N.S. and R.W.; Scottish Government/BBSRC grant BB/100663X/1 to R.W., D.M., P.H., J.R., M.C. and P.K.; National Science Foundation grant DBI 0321756 ‘‘Coupling EST and Bacterial Artificial Chromosome Resources to Access the Barley Genome’’ and DBI-1062301 "Barcoding-Free Multiplexing: Leveraging Combinatorial Pooling for High-Throughput Sequencing" to T.J.C. and S.L.; USDA-CSREES-NRI grant 2006-55606-16722 ‘‘Barley Coordinated Agricultural Project: Leveraging Genomics, Genetics, and Breeding for Gene Discovery and Barley Improvement’’ to G.J.M., R.P.W., T.J.C.and S.L.;the Agriculture and FoodResearchInitiativePlantGenome,Genetics and Breeding Program of USDA-CSREES-NIFA grant 2009-65300-05645 ‘‘Advancing the Barley Genome’’ to T.J.C., S.L. and G.J.M.; BRAIN and NBRP-Japan grants to K.S., Japanese MAFF Grant (TRG1008) to T.M. A full list of acknowledgements is in the Supplementary Information.

ASJC Scopus subject areas

General

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1038/nature11543

Cite this

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), 711-716. https://doi.org/10.1038/nature11543

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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 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",

note = "Funding Information: Acknowledgements This work has been supported from the following funding sources: German Ministry of Education and Research (BMBF) grant 0314000 {\textquoteleft}{\textquoteleft}BARLEX{\textquoteright}{\textquoteright} to K.F.X.M., M.P., U.S. and N.S.; Leibniz Association grant (Pakt f. Forschung und Innovation) to N.S.; European project of the 7th framework programme {\textquoteleft}{\textquoteleft}TriticeaeGenome{\textquoteright}{\textquoteright} to R.W., A.S., K.F.X.M., M.M. and N.S.; SFB F3705, of the Austrian Wissenschaftsfond (FWF) to K.F.X.M.; ERA-NET PG project {\textquoteleft}{\textquoteleft}BARCODE{\textquoteright}{\textquoteright} grant to M.M., N.S. and R.W.; Scottish Government/BBSRC grant BB/100663X/1 to R.W., D.M., P.H., J.R., M.C. and P.K.; National Science Foundation grant DBI 0321756 {\textquoteleft}{\textquoteleft}Coupling EST and Bacterial Artificial Chromosome Resources to Access the Barley Genome{\textquoteright}{\textquoteright} and DBI-1062301 {"}Barcoding-Free Multiplexing: Leveraging Combinatorial Pooling for High-Throughput Sequencing{"} to T.J.C. and S.L.; USDA-CSREES-NRI grant 2006-55606-16722 {\textquoteleft}{\textquoteleft}Barley Coordinated Agricultural Project: Leveraging Genomics, Genetics, and Breeding for Gene Discovery and Barley Improvement{\textquoteright}{\textquoteright} to G.J.M., R.P.W., T.J.C.and S.L.;the Agriculture and FoodResearchInitiativePlantGenome,Genetics and Breeding Program of USDA-CSREES-NIFA grant 2009-65300-05645 {\textquoteleft}{\textquoteleft}Advancing the Barley Genome{\textquoteright}{\textquoteright} to T.J.C., S.L. and G.J.M.; BRAIN and NBRP-Japan grants to K.S., Japanese MAFF Grant (TRG1008) to T.M. A full list of acknowledgements is in the Supplementary Information.",

year = "2012",

month = nov,

day = "29",

doi = "10.1038/nature11543",

language = "English",

volume = "491",

pages = "711--716",

journal = "Nature",

issn = "0028-0836",

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number = "7426",

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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, pp. 711-716. 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 - Funding Information: Acknowledgements This work has been supported from the following funding sources: German Ministry of Education and Research (BMBF) grant 0314000 ‘‘BARLEX’’ to K.F.X.M., M.P., U.S. and N.S.; Leibniz Association grant (Pakt f. Forschung und Innovation) to N.S.; European project of the 7th framework programme ‘‘TriticeaeGenome’’ to R.W., A.S., K.F.X.M., M.M. and N.S.; SFB F3705, of the Austrian Wissenschaftsfond (FWF) to K.F.X.M.; ERA-NET PG project ‘‘BARCODE’’ grant to M.M., N.S. and R.W.; Scottish Government/BBSRC grant BB/100663X/1 to R.W., D.M., P.H., J.R., M.C. and P.K.; National Science Foundation grant DBI 0321756 ‘‘Coupling EST and Bacterial Artificial Chromosome Resources to Access the Barley Genome’’ and DBI-1062301 "Barcoding-Free Multiplexing: Leveraging Combinatorial Pooling for High-Throughput Sequencing" to T.J.C. and S.L.; USDA-CSREES-NRI grant 2006-55606-16722 ‘‘Barley Coordinated Agricultural Project: Leveraging Genomics, Genetics, and Breeding for Gene Discovery and Barley Improvement’’ to G.J.M., R.P.W., T.J.C.and S.L.;the Agriculture and FoodResearchInitiativePlantGenome,Genetics and Breeding Program of USDA-CSREES-NIFA grant 2009-65300-05645 ‘‘Advancing the Barley Genome’’ to T.J.C., S.L. and G.J.M.; BRAIN and NBRP-Japan grants to K.S., Japanese MAFF Grant (TRG1008) to T.M. A full list of acknowledgements is in the Supplementary Information.

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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U2 - 10.1038/nature11543

DO - 10.1038/nature11543

M3 - Article

C2 - 23075845

AN - SCOPUS:84870265846

SN - 0028-0836

VL - 491

SP - 711

EP - 716

JO - Nature

JF - Nature

IS - 7426

ER -

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

Abstract

Bibliographical note

ASJC Scopus subject areas

UN SDGs

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