Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.

Sebastian Beier; Axel Himmelbach; Christian Colmsee; Xiao-Qi Zhang; Roberto A. Barrero; Qisen Zhang; Lin Li; Micha Bayer; Daniel Bolser; Stefan Taudien; Marco Groth; Marius Felder; Alex Hastie; Hana Šimková; Helena Staňková; Jan Vrána; Saki Chan; María Muñoz-Amatriaín; Rachid Ounit; Steve Wanamaker; Thomas Schmutzer; Lala Aliyeva-Schnorr; Stefano Grasso; Jaakko Tanskanen; Dharanya Sampath; Darren Heavens; Sujie Cao; Brett Chapman; Fei Dai; Yong Han; Hua Li; Xuan Li; Chongyun Lin; John K. McCooke; Cong Tan; Songbo Wang; Shuya Yin; Gaofeng Zhou; Jesse A. Poland; Matthew I. Bellgard; Andreas Houben; Jaroslav Doležel; Sarah Ayling; Stefano Lonardi; Peter Langridge; Gary J. Muehlbauer; Paul Kersey; Matthew D. Clark; Mario Caccamo; Alan H. Schulman; Matthias Platzer; Timothy J. Close; Mats Hansson; Guoping Zhang; Ilka Braumann; Chengdao Li; Robbie Waugh; Uwe Scholz; Nils Stein; Martin Mascher

doi:10.1038/sdata.2017.44

Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.

Sebastian Beier, Axel Himmelbach, Christian Colmsee, Xiao-Qi Zhang, Roberto A. Barrero, Qisen Zhang, Lin Li, Micha Bayer, Daniel Bolser, Stefan Taudien, Marco Groth, Marius Felder, Alex Hastie, Hana Šimková, Helena Staňková, Jan Vrána, Saki Chan, María Muñoz-Amatriaín, Rachid Ounit, Steve WanamakerThomas Schmutzer, Lala Aliyeva-Schnorr, Stefano Grasso, Jaakko Tanskanen, Dharanya Sampath, Darren Heavens, Sujie Cao, Brett Chapman, Fei Dai, Yong Han, Hua Li, Xuan Li, Chongyun Lin, John K. McCooke, Cong Tan, Songbo Wang, Shuya Yin, Gaofeng Zhou, Jesse A. Poland, Matthew I. Bellgard, Andreas Houben, Jaroslav Doležel, Sarah Ayling, Stefano Lonardi, Peter Langridge, Gary J. Muehlbauer, Paul Kersey, Matthew D. Clark, Mario Caccamo, Alan H. Schulman, Matthias Platzer, Timothy J. Close, Mats Hansson, Guoping Zhang, Ilka Braumann, Chengdao Li, Robbie Waugh, Uwe Scholz, Nils Stein, Martin Mascher (Lead Author)

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Abstract

Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. ‘Morex’ was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).

Original language	English
Article number	170044
Journal	Scientific Data
Volume	4
DOIs	https://doi.org/10.1038/sdata.2017.44
Publication status	Published - 27 Apr 2017

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Cite this

Beier, S., Himmelbach, A., Colmsee, C., Zhang, X.-Q., Barrero, R. A., Zhang, Q., Li, L., Bayer, M., Bolser, D., Taudien, S., Groth, M., Felder, M., Hastie, A., Šimková, H., Staňková, H., Vrána, J., Chan, S., Muñoz-Amatriaín, M., Ounit, R., ... Mascher, M. (2017). Construction of a map-based reference genome sequence for barley, Hordeum vulgare L. Scientific Data, 4, Article 170044. https://doi.org/10.1038/sdata.2017.44

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title = "Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.",

abstract = "Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. {\textquoteleft}Morex{\textquoteright} was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).",

author = "Sebastian Beier and Axel Himmelbach and Christian Colmsee and Xiao-Qi Zhang and Barrero, {Roberto A.} and Qisen Zhang and Lin Li and Micha Bayer and Daniel Bolser and Stefan Taudien and Marco Groth and Marius Felder and Alex Hastie and Hana {\v S}imkov{\'a} and Helena Sta{\v n}kov{\'a} and Jan Vr{\'a}na and Saki Chan and Mar{\'i}a Mu{\~n}oz-Amatria{\'i}n and Rachid Ounit and Steve Wanamaker and Thomas Schmutzer and Lala Aliyeva-Schnorr and Stefano Grasso and Jaakko Tanskanen and Dharanya Sampath and Darren Heavens 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 Songbo Wang and Shuya Yin and Gaofeng Zhou and Poland, {Jesse A.} and Bellgard, {Matthew I.} and Andreas Houben and Jaroslav Dole{\v z}el and Sarah Ayling and Stefano Lonardi and Peter Langridge and Muehlbauer, {Gary J.} and Paul Kersey and Clark, {Matthew D.} and Mario Caccamo and Schulman, {Alan H.} and Matthias Platzer and Close, {Timothy J.} and Mats Hansson and Guoping Zhang and Ilka Braumann and Chengdao Li and Robbie Waugh and Uwe Scholz and Nils Stein and Martin Mascher",

year = "2017",

month = apr,

day = "27",

doi = "10.1038/sdata.2017.44",

language = "English",

volume = "4",

journal = "Scientific Data",

issn = "2052-4463",

publisher = "Nature Publishing Group",

}

Beier, S, Himmelbach, A, Colmsee, C, Zhang, X-Q, Barrero, RA, Zhang, Q, Li, L, Bayer, M, Bolser, D, Taudien, S, Groth, M, Felder, M, Hastie, A, Šimková, H, Staňková, H, Vrána, J, Chan, S, Muñoz-Amatriaín, M, Ounit, R, Wanamaker, S, Schmutzer, T, Aliyeva-Schnorr, L, Grasso, S, Tanskanen, J, Sampath, D, Heavens, D, Cao, S, Chapman, B, Dai, F, Han, Y, Li, H, Li, X, Lin, C, McCooke, JK, Tan, C, Wang, S, Yin, S, Zhou, G, Poland, JA, Bellgard, MI, Houben, A, Doležel, J, Ayling, S, Lonardi, S, Langridge, P, Muehlbauer, GJ, Kersey, P, Clark, MD, Caccamo, M, Schulman, AH, Platzer, M, Close, TJ, Hansson, M, Zhang, G, Braumann, I, Li, C, Waugh, R, Scholz, U, Stein, N & Mascher, M 2017, 'Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.', Scientific Data, vol. 4, 170044. https://doi.org/10.1038/sdata.2017.44

TY - JOUR

T1 - Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.

AU - Beier, Sebastian

AU - Himmelbach, Axel

AU - Colmsee, Christian

AU - Zhang, Xiao-Qi

AU - Barrero, Roberto A.

AU - Zhang, Qisen

AU - Li, Lin

AU - Bayer, Micha

AU - Bolser, Daniel

AU - Taudien, Stefan

AU - Groth, Marco

AU - Felder, Marius

AU - Hastie, Alex

AU - Šimková, Hana

AU - Staňková, Helena

AU - Vrána, Jan

AU - Chan, Saki

AU - Muñoz-Amatriaín, María

AU - Ounit, Rachid

AU - Wanamaker, Steve

AU - Schmutzer, Thomas

AU - Aliyeva-Schnorr, Lala

AU - Grasso, Stefano

AU - Tanskanen, Jaakko

AU - Sampath, Dharanya

AU - Heavens, Darren

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, Songbo

AU - Yin, Shuya

AU - Zhou, Gaofeng

AU - Poland, Jesse A.

AU - Bellgard, Matthew I.

AU - Houben, Andreas

AU - Doležel, Jaroslav

AU - Ayling, Sarah

AU - Lonardi, Stefano

AU - Langridge, Peter

AU - Muehlbauer, Gary J.

AU - Kersey, Paul

AU - Clark, Matthew D.

AU - Caccamo, Mario

AU - Schulman, Alan H.

AU - Platzer, Matthias

AU - Close, Timothy J.

AU - Hansson, Mats

AU - Zhang, Guoping

AU - Braumann, Ilka

AU - Li, Chengdao

AU - Waugh, Robbie

AU - Scholz, Uwe

AU - Stein, Nils

AU - Mascher, Martin

PY - 2017/4/27

Y1 - 2017/4/27

N2 - Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. ‘Morex’ was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).

AB - Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. ‘Morex’ was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).

U2 - 10.1038/sdata.2017.44

DO - 10.1038/sdata.2017.44

M3 - Article

SN - 2052-4463

VL - 4

JO - Scientific Data

JF - Scientific Data

M1 - 170044

ER -