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; 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

doi:10.1038/nature22043

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 GrothMarius 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

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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.

Original language	English
Pages (from-to)	427-433
Number of pages	7
Journal	Nature
Volume	544
Issue number	7651
DOIs	https://doi.org/10.1038/nature22043
Publication status	Published - 26 Apr 2017

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Mascher, M., Gundlach, H., Himmelbach, A., Beier, S., Twardziok, S. O., Wicker, T., Radchuk, V., Dockter, C., Hedley, P. E., Russell, J., Bayer, M., Ramsay, L., Liu, H., Haberer, G., Zhang, X. Q., Zhang, Q., Barrero, R. A., Li, L., Taudien, S., ... Stein, N. (2017). A chromosome conformation capture ordered sequence of the barley genome. Nature, 544(7651), 427-433. https://doi.org/10.1038/nature22043

@article{e9dec356f6ec49d3a2585b46f47142a4,

title = "A chromosome conformation capture ordered sequence of the barley genome",

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 {\v S}imkov{\'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",

year = "2017",

month = apr,

day = "26",

doi = "10.1038/nature22043",

language = "English",

volume = "544",

pages = "427--433",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Publishing Group - Macmillan Publishers",

number = "7651",

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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

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

Y1 - 2017/4/26

N2 - 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.

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.

UR - http://www.scopus.com/inward/record.url?scp=85018282934&partnerID=8YFLogxK

U2 - 10.1038/nature22043

DO - 10.1038/nature22043

M3 - Article

C2 - 28447635

AN - SCOPUS:85018282934

SN - 0028-0836

VL - 544

SP - 427

EP - 433

JO - Nature

JF - Nature

IS - 7651

ER -

A chromosome conformation capture ordered sequence of the barley genome

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