Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome

María Muñoz-Amatriaín; Stefano Lonardi; Mingcheng Luo; Kavitha Madishetty; Jan T. Svensson; Matthew J. Moscou; Steve Wanamaker; Tao Jiang; Andris Kleinhofs; Gary J. Muehlbauer; Roger P. Wise; Nils Stein; Yaqin Ma; Edmundo Rodriguez; Dave Kudrna; Prasanna R. Bhat; Shiaoman Chao; Pascal Condamine; Shane Heinen; Josh Resnik; Rod Wing; Heather N. Witt; Matthew Alpert; Marco Beccuti; Serdar Bozdag; Francesca Cordero; Hamid Mirebrahim; Rachid Ounit; Yonghui Wu; Frank You; Jie Zheng; Hana Simková; Jaroslav Dolezel; Jane Grimwood; Jeremy Schmutz; Denisa Duma; Lothar Altschmied; Tom Blake; Phil Bregitzer; Laurel Cooper; Muharrem Dilbirligi; Anders Falk; Leila Feiz; Andreas Graner; Perry Gustafson; Patrick M. Hayes; Peggy Lemaux; Jafar Mammadov; Timothy J. Close

doi:10.1111/tpj.12959

Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome

María Muñoz-Amatriaín, Stefano Lonardi, Mingcheng Luo, Kavitha Madishetty, Jan T. Svensson, Matthew J. Moscou, Steve Wanamaker, Tao Jiang, Andris Kleinhofs, Gary J. Muehlbauer, Roger P. Wise, Nils Stein, Yaqin Ma, Edmundo Rodriguez, Dave Kudrna, Prasanna R. Bhat, Shiaoman Chao, Pascal Condamine, Shane Heinen, Josh ResnikRod Wing, Heather N. Witt, Matthew Alpert, Marco Beccuti, Serdar Bozdag, Francesca Cordero, Hamid Mirebrahim, Rachid Ounit, Yonghui Wu, Frank You, Jie Zheng, Hana Simková, Jaroslav Dolezel, Jane Grimwood, Jeremy Schmutz, Denisa Duma, Lothar Altschmied, Tom Blake, Phil Bregitzer, Laurel Cooper, Muharrem Dilbirligi, Anders Falk, Leila Feiz, Andreas Graner, Perry Gustafson, Patrick M. Hayes, Peggy Lemaux, Jafar Mammadov, Timothy J. Close

Agronomy and Plant Genetics

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

27 Scopus citations

Abstract

Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15 622 BACs representing the minimal tiling path of 72 052 physical-mapped gene-bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high recombination rates, there are also gene-dense regions with suppressed recombination. We made use of published map-anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D-genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST:Barley provides facile access to BAC sequences and their annotations, along with the barley-Ae. tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map-based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene-dense but low recombination is particularly relevant.

Original language	English (US)
Pages (from-to)	216-227
Number of pages	12
Journal	Plant Journal
Volume	84
Issue number	1
DOIs	https://doi.org/10.1111/tpj.12959
State	Published - Oct 1 2015

Bibliographical note

Publisher Copyright:
© 2015 The Authors The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.

Keywords

Aegilops tauschii
BAC sequencing
Barley
HarvEST:Barley
Hordeum vulgare L.
centromere BACs
gene distribution
recombination frequency
synteny

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Muñoz-Amatriaín, M., Lonardi, S., Luo, M., Madishetty, K., Svensson, J. T., Moscou, M. J., Wanamaker, S., Jiang, T., Kleinhofs, A., Muehlbauer, G. J., Wise, R. P., Stein, N., Ma, Y., Rodriguez, E., Kudrna, D., Bhat, P. R., Chao, S., Condamine, P., Heinen, S., ... Close, T. J. (2015). Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. Plant Journal, 84(1), 216-227. https://doi.org/10.1111/tpj.12959

Muñoz-Amatriaín, M, Lonardi, S, Luo, M, Madishetty, K, Svensson, JT, Moscou, MJ, Wanamaker, S, Jiang, T, Kleinhofs, A, Muehlbauer, GJ, Wise, RP, Stein, N, Ma, Y, Rodriguez, E, Kudrna, D, Bhat, PR, Chao, S, Condamine, P, Heinen, S, Resnik, J, Wing, R, Witt, HN, Alpert, M, Beccuti, M, Bozdag, S, Cordero, F, Mirebrahim, H, Ounit, R, Wu, Y, You, F, Zheng, J, Simková, H, Dolezel, J, Grimwood, J, Schmutz, J, Duma, D, Altschmied, L, Blake, T, Bregitzer, P, Cooper, L, Dilbirligi, M, Falk, A, Feiz, L, Graner, A, Gustafson, P, Hayes, PM, Lemaux, P, Mammadov, J & Close, TJ 2015, 'Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome', Plant Journal, vol. 84, no. 1, pp. 216-227. https://doi.org/10.1111/tpj.12959

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abstract = "Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15 622 BACs representing the minimal tiling path of 72 052 physical-mapped gene-bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high recombination rates, there are also gene-dense regions with suppressed recombination. We made use of published map-anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D-genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST:Barley provides facile access to BAC sequences and their annotations, along with the barley-Ae. tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map-based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene-dense but low recombination is particularly relevant.",

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author = "Mar{\'i}a Mu{\~n}oz-Amatria{\'i}n and Stefano Lonardi and Mingcheng Luo and Kavitha Madishetty and Svensson, {Jan T.} and Moscou, {Matthew J.} and Steve Wanamaker and Tao Jiang and Andris Kleinhofs and Muehlbauer, {Gary J.} and Wise, {Roger P.} and Nils Stein and Yaqin Ma and Edmundo Rodriguez and Dave Kudrna and Bhat, {Prasanna R.} and Shiaoman Chao and Pascal Condamine and Shane Heinen and Josh Resnik and Rod Wing and Witt, {Heather N.} and Matthew Alpert and Marco Beccuti and Serdar Bozdag and Francesca Cordero and Hamid Mirebrahim and Rachid Ounit and Yonghui Wu and Frank You and Jie Zheng and Hana Simkov{\'a} and Jaroslav Dolezel and Jane Grimwood and Jeremy Schmutz and Denisa Duma and Lothar Altschmied and Tom Blake and Phil Bregitzer and Laurel Cooper and Muharrem Dilbirligi and Anders Falk and Leila Feiz and Andreas Graner and Perry Gustafson and Hayes, {Patrick M.} and Peggy Lemaux and Jafar Mammadov and Close, {Timothy J.}",

note = "Publisher Copyright: {\textcopyright} 2015 The Authors The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.",

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AU - Muñoz-Amatriaín, María

AU - Lonardi, Stefano

AU - Luo, Mingcheng

AU - Madishetty, Kavitha

AU - Svensson, Jan T.

AU - Moscou, Matthew J.

AU - Wanamaker, Steve

AU - Jiang, Tao

AU - Kleinhofs, Andris

AU - Muehlbauer, Gary J.

AU - Wise, Roger P.

AU - Stein, Nils

AU - Ma, Yaqin

AU - Rodriguez, Edmundo

AU - Kudrna, Dave

AU - Bhat, Prasanna R.

AU - Chao, Shiaoman

AU - Condamine, Pascal

AU - Heinen, Shane

AU - Resnik, Josh

AU - Wing, Rod

AU - Witt, Heather N.

AU - Alpert, Matthew

AU - Beccuti, Marco

AU - Bozdag, Serdar

AU - Cordero, Francesca

AU - Mirebrahim, Hamid

AU - Ounit, Rachid

AU - Wu, Yonghui

AU - You, Frank

AU - Zheng, Jie

AU - Simková, Hana

AU - Dolezel, Jaroslav

AU - Grimwood, Jane

AU - Schmutz, Jeremy

AU - Duma, Denisa

AU - Altschmied, Lothar

AU - Blake, Tom

AU - Bregitzer, Phil

AU - Cooper, Laurel

AU - Dilbirligi, Muharrem

AU - Falk, Anders

AU - Feiz, Leila

AU - Graner, Andreas

AU - Gustafson, Perry

AU - Hayes, Patrick M.

AU - Lemaux, Peggy

AU - Mammadov, Jafar

AU - Close, Timothy J.

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KW - HarvEST:Barley

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Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome

Abstract

Bibliographical note

Keywords

Access

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