A chromosome conformation capture ordered sequence of the barley genome

Martin Mascher, Heidrun Gundlach, Axel Himmelbach, Sebastian Beier, Sven O. Twardziok, Thomas Wicker, Volodymyr Radchuk, Christoph Dockter, Pete E. Hedley, Joanne Russell, Micha Bayer, Luke Ramsay, Hui Liu, Georg Haberer, Xiao Qi Zhang, Qisen Zhang, Roberto A. Barrero, Lin Li, Stefan Taudien, Marco Groth & 56 others Marius Felder, Alex Hastie, Hana Šimková, Helena Stanková, Jan Vrána, Saki Chan, Mariá Munõz-Amatriaín, Rachid Ounit, Steve Wanamaker, Daniel Bolser, Christian Colmsee, Thomas Schmutzer, Lala Aliyeva-Schnorr, Stefano Grasso, Jaakko Tanskanen, Anna Chailyan, Dharanya Sampath, Darren Heavens, Leah Clissold, Sujie Cao, Brett Chapman, Fei Dai, Yong Han, Hua Li, Xuan Li, Chongyun Lin, John K. McCooke, Cong Tan, Penghao Wang, Songbo Wang, Shuya Yin, Gaofeng Zhou, Jesse A. Poland, Matthew I. Bellgard, Ljudmilla Borisjuk, Andreas Houben, Jaroslav Doleael, Sarah Ayling, Stefano Lonardi, Paul J. Kersey, Peter Langridge, Gary J. Muehlbauer, Matthew D. Clark, Mario Caccamo, Alan H. Schulman, Klaus F.X. Mayer, Matthias Platzer, Timothy J. Close, Uwe Scholz, Mats Hansson, Guoping Zhang, Ilka Braumann, Manuel Spannagl, Chengdao Li, Robbie Waugh, Nils Stein

    Research output: Contribution to journalArticle

    331 Citations (Scopus)

    Abstract

    Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion. 

    Original languageEnglish
    Pages (from-to)427-433
    Number of pages7
    JournalNature
    Volume544
    Issue number7651
    DOIs
    Publication statusPublished - 26 Apr 2017

    Fingerprint

    Hordeum
    Chromosomes
    Conformations
    Genes
    Genome
    Food
    Gene Duplication
    Poaceae
    Agriculture
    Genetic Recombination
    Chromatin
    Breeding
    Seeds
    Carbohydrates
    Nutrients
    Seed
    Erosion
    Chemical analysis

    Cite this

    Mascher, M., Gundlach, H., Himmelbach, A., Beier, S., Twardziok, S. O., Wicker, T., ... Stein, N. (2017). A chromosome conformation capture ordered sequence of the barley genome. Nature, 544(7651), 427-433. https://doi.org/10.1038/nature22043
    Mascher, Martin ; Gundlach, Heidrun ; Himmelbach, Axel ; Beier, Sebastian ; Twardziok, Sven O. ; Wicker, Thomas ; Radchuk, Volodymyr ; Dockter, Christoph ; Hedley, Pete E. ; Russell, Joanne ; Bayer, Micha ; Ramsay, Luke ; Liu, Hui ; Haberer, Georg ; Zhang, Xiao Qi ; Zhang, Qisen ; Barrero, Roberto A. ; Li, Lin ; Taudien, Stefan ; Groth, Marco ; Felder, Marius ; Hastie, Alex ; Šimková, Hana ; Stanková, Helena ; Vrána, Jan ; Chan, Saki ; Munõz-Amatriaín, Mariá ; Ounit, Rachid ; Wanamaker, Steve ; Bolser, Daniel ; Colmsee, Christian ; Schmutzer, Thomas ; Aliyeva-Schnorr, Lala ; Grasso, Stefano ; Tanskanen, Jaakko ; Chailyan, Anna ; Sampath, Dharanya ; Heavens, Darren ; Clissold, Leah ; Cao, Sujie ; Chapman, Brett ; Dai, Fei ; Han, Yong ; Li, Hua ; Li, Xuan ; Lin, Chongyun ; McCooke, John K. ; Tan, Cong ; Wang, Penghao ; Wang, Songbo ; Yin, Shuya ; Zhou, Gaofeng ; Poland, Jesse A. ; Bellgard, Matthew I. ; Borisjuk, Ljudmilla ; Houben, Andreas ; Doleael, Jaroslav ; Ayling, Sarah ; Lonardi, Stefano ; Kersey, Paul J. ; Langridge, Peter ; Muehlbauer, Gary J. ; Clark, Matthew D. ; Caccamo, Mario ; Schulman, Alan H. ; Mayer, Klaus F.X. ; Platzer, Matthias ; Close, Timothy J. ; Scholz, Uwe ; Hansson, Mats ; Zhang, Guoping ; Braumann, Ilka ; Spannagl, Manuel ; Li, Chengdao ; Waugh, Robbie ; Stein, Nils. / A chromosome conformation capture ordered sequence of the barley genome. In: Nature. 2017 ; Vol. 544, No. 7651. pp. 427-433.
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    abstract = "Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion. ",
    author = "Martin Mascher and Heidrun Gundlach and Axel Himmelbach and Sebastian Beier and Twardziok, {Sven O.} and Thomas Wicker and Volodymyr Radchuk and Christoph Dockter and Hedley, {Pete E.} and Joanne Russell and Micha Bayer and Luke Ramsay and Hui Liu and Georg Haberer and Zhang, {Xiao Qi} and Qisen Zhang and Barrero, {Roberto A.} and Lin Li and Stefan Taudien and Marco Groth and Marius Felder and Alex Hastie and Hana Šimkov{\'a} and Helena Stankov{\'a} and Jan Vr{\'a}na and Saki Chan and Mari{\'a} Mun{\~o}z-Amatria{\'i}n and Rachid Ounit and Steve Wanamaker and Daniel Bolser and Christian Colmsee and Thomas Schmutzer and Lala Aliyeva-Schnorr and Stefano Grasso and Jaakko Tanskanen and Anna Chailyan and Dharanya Sampath and Darren Heavens and Leah Clissold and Sujie Cao and Brett Chapman and Fei Dai and Yong Han and Hua Li and Xuan Li and Chongyun Lin and McCooke, {John K.} and Cong Tan and Penghao Wang and Songbo Wang and Shuya Yin and Gaofeng Zhou and Poland, {Jesse A.} and Bellgard, {Matthew I.} and Ljudmilla Borisjuk and Andreas Houben and Jaroslav Doleael and Sarah Ayling and Stefano Lonardi and Kersey, {Paul J.} and Peter Langridge and Muehlbauer, {Gary J.} and Clark, {Matthew D.} and Mario Caccamo and Schulman, {Alan H.} and Mayer, {Klaus F.X.} and Matthias Platzer and Close, {Timothy J.} and Uwe Scholz and Mats Hansson and Guoping Zhang and Ilka Braumann and Manuel Spannagl and Chengdao Li and Robbie Waugh and Nils Stein",
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    Mascher, M, Gundlach, H, Himmelbach, A, Beier, S, Twardziok, SO, Wicker, T, Radchuk, V, Dockter, C, Hedley, PE, Russell, J, Bayer, M, Ramsay, L, Liu, H, Haberer, G, Zhang, XQ, Zhang, Q, Barrero, RA, Li, L, Taudien, S, Groth, M, Felder, M, Hastie, A, Šimková, H, Stanková, H, Vrána, J, Chan, S, Munõz-Amatriaín, M, Ounit, R, Wanamaker, S, Bolser, D, Colmsee, C, Schmutzer, T, Aliyeva-Schnorr, L, Grasso, S, Tanskanen, J, Chailyan, A, Sampath, D, Heavens, D, Clissold, L, Cao, S, Chapman, B, Dai, F, Han, Y, Li, H, Li, X, Lin, C, McCooke, JK, Tan, C, Wang, P, Wang, S, Yin, S, Zhou, G, Poland, JA, Bellgard, MI, Borisjuk, L, Houben, A, Doleael, J, Ayling, S, Lonardi, S, Kersey, PJ, Langridge, P, Muehlbauer, GJ, Clark, MD, Caccamo, M, Schulman, AH, Mayer, KFX, Platzer, M, Close, TJ, Scholz, U, Hansson, M, Zhang, G, Braumann, I, Spannagl, M, Li, C, Waugh, R & Stein, N 2017, 'A chromosome conformation capture ordered sequence of the barley genome' Nature, vol. 544, no. 7651, pp. 427-433. https://doi.org/10.1038/nature22043

    A chromosome conformation capture ordered sequence of the barley genome. / Mascher, Martin; Gundlach, Heidrun; Himmelbach, Axel; Beier, Sebastian; Twardziok, Sven O.; Wicker, Thomas; Radchuk, Volodymyr; Dockter, Christoph; Hedley, Pete E.; Russell, Joanne; Bayer, Micha; Ramsay, Luke; Liu, Hui; Haberer, Georg; Zhang, Xiao Qi; Zhang, Qisen; Barrero, Roberto A.; Li, Lin; Taudien, Stefan; Groth, Marco; Felder, Marius; Hastie, Alex; Šimková, Hana; Stanková, Helena; Vrána, Jan; Chan, Saki; Munõz-Amatriaín, Mariá; Ounit, Rachid; Wanamaker, Steve; Bolser, Daniel; Colmsee, Christian; Schmutzer, Thomas; Aliyeva-Schnorr, Lala; Grasso, Stefano; Tanskanen, Jaakko; Chailyan, Anna; Sampath, Dharanya; Heavens, Darren; Clissold, Leah; Cao, Sujie; Chapman, Brett; Dai, Fei; Han, Yong; Li, Hua; Li, Xuan; Lin, Chongyun; McCooke, John K.; Tan, Cong; Wang, Penghao; Wang, Songbo; Yin, Shuya; Zhou, Gaofeng; Poland, Jesse A.; Bellgard, Matthew I.; Borisjuk, Ljudmilla; Houben, Andreas; Doleael, Jaroslav; Ayling, Sarah; Lonardi, Stefano; Kersey, Paul J.; Langridge, Peter; Muehlbauer, Gary J.; Clark, Matthew D.; Caccamo, Mario; Schulman, Alan H.; Mayer, Klaus F.X.; Platzer, Matthias; Close, Timothy J.; Scholz, Uwe; Hansson, Mats; Zhang, Guoping; Braumann, Ilka; Spannagl, Manuel; Li, Chengdao; Waugh, Robbie; Stein, Nils.

    In: Nature, Vol. 544, No. 7651, 26.04.2017, p. 427-433.

    Research output: Contribution to journalArticle

    TY - JOUR

    T1 - A chromosome conformation capture ordered sequence of the barley genome

    AU - Mascher, Martin

    AU - Gundlach, Heidrun

    AU - Himmelbach, Axel

    AU - Beier, Sebastian

    AU - Twardziok, Sven O.

    AU - Wicker, Thomas

    AU - Radchuk, Volodymyr

    AU - Dockter, Christoph

    AU - Hedley, Pete E.

    AU - Russell, Joanne

    AU - Bayer, Micha

    AU - Ramsay, Luke

    AU - Liu, Hui

    AU - Haberer, Georg

    AU - Zhang, Xiao Qi

    AU - Zhang, Qisen

    AU - Barrero, Roberto A.

    AU - Li, Lin

    AU - Taudien, Stefan

    AU - Groth, Marco

    AU - Felder, Marius

    AU - Hastie, Alex

    AU - Šimková, Hana

    AU - Stanková, Helena

    AU - Vrána, Jan

    AU - Chan, Saki

    AU - Munõz-Amatriaín, Mariá

    AU - Ounit, Rachid

    AU - Wanamaker, Steve

    AU - Bolser, Daniel

    AU - Colmsee, Christian

    AU - Schmutzer, Thomas

    AU - Aliyeva-Schnorr, Lala

    AU - Grasso, Stefano

    AU - Tanskanen, Jaakko

    AU - Chailyan, Anna

    AU - Sampath, Dharanya

    AU - Heavens, Darren

    AU - Clissold, Leah

    AU - Cao, Sujie

    AU - Chapman, Brett

    AU - Dai, Fei

    AU - Han, Yong

    AU - Li, Hua

    AU - Li, Xuan

    AU - Lin, Chongyun

    AU - McCooke, John K.

    AU - Tan, Cong

    AU - Wang, Penghao

    AU - Wang, Songbo

    AU - Yin, Shuya

    AU - Zhou, Gaofeng

    AU - Poland, Jesse A.

    AU - Bellgard, Matthew I.

    AU - Borisjuk, Ljudmilla

    AU - Houben, Andreas

    AU - Doleael, Jaroslav

    AU - Ayling, Sarah

    AU - Lonardi, Stefano

    AU - Kersey, Paul J.

    AU - Langridge, Peter

    AU - Muehlbauer, Gary J.

    AU - Clark, Matthew D.

    AU - Caccamo, Mario

    AU - Schulman, Alan H.

    AU - Mayer, Klaus F.X.

    AU - Platzer, Matthias

    AU - Close, Timothy J.

    AU - Scholz, Uwe

    AU - Hansson, Mats

    AU - Zhang, Guoping

    AU - Braumann, Ilka

    AU - Spannagl, Manuel

    AU - Li, Chengdao

    AU - Waugh, Robbie

    AU - Stein, Nils

    PY - 2017/4/26

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    AB - Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion. 

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    Mascher M, Gundlach H, Himmelbach A, Beier S, Twardziok SO, Wicker T et al. A chromosome conformation capture ordered sequence of the barley genome. Nature. 2017 Apr 26;544(7651):427-433. https://doi.org/10.1038/nature22043