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

Agronomy and Plant Genetics

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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. â € 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 (US)
Article number	170044
Journal	Scientific Data
Volume	4
DOIs	https://doi.org/10.1038/sdata.2017.44
State	Published - Apr 27 2017

Bibliographical note

Funding Information:
This work was carried out under the auspices of the International Barley Genome Sequencing Consortium and supported from the following funding sources: German Ministry of Education and Research (BMBF) grant 0314000 'BARLEX' and 0315954 'TRITEX' to M.P., U.S. and N.S and 031A536 'de.NBI' to U.S. Leibniz Association grant ('Pakt f. Forschung und Innovation') 'sequencing barley chromosome 3H' to N.S. and U.S.; Scottish Government/UK Biotechnology and Biological Sciences Research Council (BBSRC) grant BB/100663X/1 to R.W, P.E.H., J.R.; BBSRC grants BB/I008357/1 to M. D.C., M.C. and BB/I008071/1 to P.K.; of Finland grant 266430 and a BioNano grant to A.H.S.; Carlsberg Foundation grant nr. 2012-01-0461 to the Carlsberg Research Laboratory; Grain Research and Development Corporation (GRDC) grant DAW00233 to C.L. and P.L.; Department of Agricultural and Food, Government of Western Australia grant 681 to C.L.; National Natural Science Foundation of China (NSFC) grant 31129005 to C.L. and G.Zhang; NSFC grant 31330055 to G.Zhang.; Czech Ministry of Education, Youth and Sports grant LO1204 to J.D.; National Science Foundation grant DBI 0321756 'Coupling EST and Bacterial Artificial Chromosome Resources to Access the Barley Genome' to T.J.C. and S.L.; United States Department of Agriculture (USDA), Agriculture and Food Research Initiative Plant Genome, Genetics and Breeding Program of USDA-CSREES-NIFA grant 2009-65300-05645 'Advancing the Barley Genome' and 2011-68002-30029 'TriticeaeCAP' to T.J.C., S.L. and G.J.M.; United States National Science Foundation (NSF)-ABI grant DBI-1062301 to T.J.C. and S.L.; University of California grant CA-R-BPS-5306-H to T.J.C and S.L.;National Science Foundation grant DBI 0321756 'Algorithms for Genome Assembly of Ultra-deep Sequencing Data' to S.L. Next-generation sequencing and library construction was delivered via the BBSRC National Capability in Genomics (BB/J010375/1) at Earlham Institute (formerly The Genome Analysis Centre) by members of the Platforms and Pipelines group and BBSRC Institute Strategic Programme funding for Bioinformatics (BB/J004669/1) to M.D.C., S.A. and M.C.

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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

Beier, S, Himmelbach, A, Colmsee, C, Zhang, XQ, 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

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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. {\^a} € 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).",

author = "Sebastian Beier and Axel Himmelbach and Christian Colmsee and Zhang, {Xiao Qi} 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",

note = "Funding Information: This work was carried out under the auspices of the International Barley Genome Sequencing Consortium and supported from the following funding sources: German Ministry of Education and Research (BMBF) grant 0314000 'BARLEX' and 0315954 'TRITEX' to M.P., U.S. and N.S and 031A536 'de.NBI' to U.S. Leibniz Association grant ('Pakt f. Forschung und Innovation') 'sequencing barley chromosome 3H' to N.S. and U.S.; Scottish Government/UK Biotechnology and Biological Sciences Research Council (BBSRC) grant BB/100663X/1 to R.W, P.E.H., J.R.; BBSRC grants BB/I008357/1 to M. D.C., M.C. and BB/I008071/1 to P.K.; of Finland grant 266430 and a BioNano grant to A.H.S.; Carlsberg Foundation grant nr. 2012-01-0461 to the Carlsberg Research Laboratory; Grain Research and Development Corporation (GRDC) grant DAW00233 to C.L. and P.L.; Department of Agricultural and Food, Government of Western Australia grant 681 to C.L.; National Natural Science Foundation of China (NSFC) grant 31129005 to C.L. and G.Zhang; NSFC grant 31330055 to G.Zhang.; Czech Ministry of Education, Youth and Sports grant LO1204 to J.D.; National Science Foundation grant DBI 0321756 'Coupling EST and Bacterial Artificial Chromosome Resources to Access the Barley Genome' to T.J.C. and S.L.; United States Department of Agriculture (USDA), Agriculture and Food Research Initiative Plant Genome, Genetics and Breeding Program of USDA-CSREES-NIFA grant 2009-65300-05645 'Advancing the Barley Genome' and 2011-68002-30029 'TriticeaeCAP' to T.J.C., S.L. and G.J.M.; United States National Science Foundation (NSF)-ABI grant DBI-1062301 to T.J.C. and S.L.; University of California grant CA-R-BPS-5306-H to T.J.C and S.L.;National Science Foundation grant DBI 0321756 'Algorithms for Genome Assembly of Ultra-deep Sequencing Data' to S.L. Next-generation sequencing and library construction was delivered via the BBSRC National Capability in Genomics (BB/J010375/1) at Earlham Institute (formerly The Genome Analysis Centre) by members of the Platforms and Pipelines group and BBSRC Institute Strategic Programme funding for Bioinformatics (BB/J004669/1) to M.D.C., S.A. and M.C.",

year = "2017",

month = apr,

day = "27",

doi = "10.1038/sdata.2017.44",

language = "English (US)",

volume = "4",

journal = "Scientific Data",

issn = "2052-4463",

publisher = "Nature Publishing Group",

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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

N1 - Funding Information: This work was carried out under the auspices of the International Barley Genome Sequencing Consortium and supported from the following funding sources: German Ministry of Education and Research (BMBF) grant 0314000 'BARLEX' and 0315954 'TRITEX' to M.P., U.S. and N.S and 031A536 'de.NBI' to U.S. Leibniz Association grant ('Pakt f. Forschung und Innovation') 'sequencing barley chromosome 3H' to N.S. and U.S.; Scottish Government/UK Biotechnology and Biological Sciences Research Council (BBSRC) grant BB/100663X/1 to R.W, P.E.H., J.R.; BBSRC grants BB/I008357/1 to M. D.C., M.C. and BB/I008071/1 to P.K.; of Finland grant 266430 and a BioNano grant to A.H.S.; Carlsberg Foundation grant nr. 2012-01-0461 to the Carlsberg Research Laboratory; Grain Research and Development Corporation (GRDC) grant DAW00233 to C.L. and P.L.; Department of Agricultural and Food, Government of Western Australia grant 681 to C.L.; National Natural Science Foundation of China (NSFC) grant 31129005 to C.L. and G.Zhang; NSFC grant 31330055 to G.Zhang.; Czech Ministry of Education, Youth and Sports grant LO1204 to J.D.; National Science Foundation grant DBI 0321756 'Coupling EST and Bacterial Artificial Chromosome Resources to Access the Barley Genome' to T.J.C. and S.L.; United States Department of Agriculture (USDA), Agriculture and Food Research Initiative Plant Genome, Genetics and Breeding Program of USDA-CSREES-NIFA grant 2009-65300-05645 'Advancing the Barley Genome' and 2011-68002-30029 'TriticeaeCAP' to T.J.C., S.L. and G.J.M.; United States National Science Foundation (NSF)-ABI grant DBI-1062301 to T.J.C. and S.L.; University of California grant CA-R-BPS-5306-H to T.J.C and S.L.;National Science Foundation grant DBI 0321756 'Algorithms for Genome Assembly of Ultra-deep Sequencing Data' to S.L. Next-generation sequencing and library construction was delivered via the BBSRC National Capability in Genomics (BB/J010375/1) at Earlham Institute (formerly The Genome Analysis Centre) by members of the Platforms and Pipelines group and BBSRC Institute Strategic Programme funding for Bioinformatics (BB/J004669/1) to M.D.C., S.A. and M.C.

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. â € 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. â € 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).

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DO - 10.1038/sdata.2017.44

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SN - 2052-4463

VL - 4

JO - Scientific Data

JF - Scientific Data

M1 - 170044

ER -

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

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