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

Agronomy and Plant Genetics

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

1186 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.

Original language	English (US)
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 - Nov 29 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.

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

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

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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.",

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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

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AU - Pfeifer, Matthias

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AU - Bayer, Micha

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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.

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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.

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

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