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, David A Kudrna, Prasanna R. Bhat, Shiaoman Chao, Pascal Condamine, Shane Heinen, Josh ResnikRod A 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

Research output: Contribution to journalArticle

21 Citations (Scopus)

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 languageEnglish (US)
Pages (from-to)216-227
Number of pages12
JournalPlant Journal
Volume84
Issue number1
DOIs
StatePublished - Oct 1 2015

Fingerprint

Bacterial Artificial Chromosomes
bacterial artificial chromosomes
Hordeum
barley
Genome
genome
Genes
genes
Aegilops tauschii
Genetic Recombination
Synteny
genomics
physical chromosome mapping
Firearms
Hordeum vulgare
Genomics
molecular cloning
Triticum
ancestry
Organism Cloning

Keywords

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

ASJC Scopus subject areas

  • Plant Science
  • Cell Biology
  • Genetics

Cite this

Muñoz-Amatriaín, M., Lonardi, S., Luo, M., Madishetty, K., Svensson, J. T., Moscou, M. J., ... 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

Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. / Muñoz-Amatriaín, María; Lonardi, Stefano; Luo, Mingcheng; Madishetty, Kavitha; Svensson, Jan T.; Moscou, Matthew J.; Wanamaker, Steve; Jiang, Tao; Kleinhofs, Andris; Muehlbauer, Gary J.; Wise, Roger P.; Stein, Nils; Ma, Yaqin; Rodriguez, Edmundo; Kudrna, David A; Bhat, Prasanna R.; Chao, Shiaoman; Condamine, Pascal; Heinen, Shane; Resnik, Josh; Wing, Rod A; Witt, Heather N.; Alpert, Matthew; Beccuti, Marco; Bozdag, Serdar; Cordero, Francesca; Mirebrahim, Hamid; Ounit, Rachid; Wu, Yonghui; You, Frank; Zheng, Jie; Simková, Hana; Dolezel, Jaroslav; Grimwood, Jane; Schmutz, Jeremy; Duma, Denisa; Altschmied, Lothar; Blake, Tom; Bregitzer, Phil; Cooper, Laurel; Dilbirligi, Muharrem; Falk, Anders; Feiz, Leila; Graner, Andreas; Gustafson, Perry; Hayes, Patrick M.; Lemaux, Peggy; Mammadov, Jafar; Close, Timothy J.

In: Plant Journal, Vol. 84, No. 1, 01.10.2015, p. 216-227.

Research output: Contribution to journalArticle

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, DA, Bhat, PR, Chao, S, Condamine, P, Heinen, S, Resnik, J, Wing, RA, 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
Muñoz-Amatriaín M, Lonardi S, Luo M, Madishetty K, Svensson JT, Moscou MJ et al. Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. Plant Journal. 2015 Oct 1;84(1):216-227. https://doi.org/10.1111/tpj.12959
Muñoz-Amatriaín, María ; Lonardi, Stefano ; Luo, Mingcheng ; Madishetty, Kavitha ; Svensson, Jan T. ; Moscou, Matthew J. ; Wanamaker, Steve ; Jiang, Tao ; Kleinhofs, Andris ; Muehlbauer, Gary J. ; Wise, Roger P. ; Stein, Nils ; Ma, Yaqin ; Rodriguez, Edmundo ; Kudrna, David A ; Bhat, Prasanna R. ; Chao, Shiaoman ; Condamine, Pascal ; Heinen, Shane ; Resnik, Josh ; Wing, Rod A ; Witt, Heather N. ; Alpert, Matthew ; Beccuti, Marco ; Bozdag, Serdar ; Cordero, Francesca ; Mirebrahim, Hamid ; Ounit, Rachid ; Wu, Yonghui ; You, Frank ; Zheng, Jie ; Simková, Hana ; Dolezel, Jaroslav ; Grimwood, Jane ; Schmutz, Jeremy ; Duma, Denisa ; Altschmied, Lothar ; Blake, Tom ; Bregitzer, Phil ; Cooper, Laurel ; Dilbirligi, Muharrem ; Falk, Anders ; Feiz, Leila ; Graner, Andreas ; Gustafson, Perry ; Hayes, Patrick M. ; Lemaux, Peggy ; Mammadov, Jafar ; Close, Timothy J. / Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. In: Plant Journal. 2015 ; Vol. 84, No. 1. pp. 216-227.
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AU - Beccuti, Marco

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AU - Mirebrahim, Hamid

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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

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