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Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation

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Abstract

Complex Triticeae genomes pose a challenge to genome sequencing efforts due to their size and repetitive nature. Genome sequencing can reveal details of conservation and rearrangements between related genomes. We have applied Illumina second generation sequencing technology to sequence and assemble the low copy and unique regions of Triticum aestivum chromosome arm 7BS, followed by the construction of a syntenic build based on gene order in Brachypodium. We have delimited the position of a previously reported translocation between 7BS and 4AL with a resolution of one or a few genes and report approximately 13% genes from 7BS having been translocated to 4AL. An additional 13 genes are found on 7BS which appear to have originated from 4AL. The gene content of the 7DS and 7BS syntenic builds indicate a total of ~77,000 genes in wheat. Within wheat syntenic regions, 7BS and 7DS share 740 genes and a common gene conservation rate of ~39% of the genes from the corresponding regions in Brachypodium, as well as a common rate of colinearity with Brachypodium of ~60%. Comparison of wheat homoeologues revealed ~84% of genes previously identified in 7DS have a homoeologue on 7BS or 4AL. The conservation rates we have identified among wheat homoeologues and with Brachypodium provide a benchmark of homoeologous gene conservation levels for future comparative genomic analysis. The syntenic build of 7BS is publicly available at http://www.wheatgenome.info.

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Acknowledgments

The authors would like to acknowledge funding support from the Australian Research Council (Projects LP0882095, LP0883462 and DP0985953), the Czech Republic Ministry of Education, Youth and Sports (grant no. LC06004), the European Regional Development Fund (Operational Programme Research and Development for Innovations No. CZ.1.05/2.1.00/01.0007) and the Spanish Ministry of Science and Innovation (MICINN grants BIO2009-07443 and AGL2010-17316). We thank Dr. Jarmila Číhalíková, Romana Nováková, Bc. and Ms. Zdeňka Dubská for their assistance with chromosome sorting. Support from the Australian Genome Research Facility (AGRF), the Queensland Cyber Infrastructure Foundation (QCIF), the Australian Partnership for Advanced Computing (APAC) and Queensland Facility for Advanced Bioinformatics (QFAB) is gratefully acknowledged.

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Authors and Affiliations

  1. School of Agriculture and Food Sciences and Australian Centre for Plant Functional Genomics, University of Queensland, Brisbane, QLD, 4072, Australia

    Paul J. Berkman, Adam Skarshewski, Sahana Manoli, Michał T. Lorenc, Jiri Stiller, Lars Smits, Kaitao Lai & David Edwards

  2. Centre for Integrative Legume Research, University of Queensland, School of Agriculture and Food Sciences, Brisbane, QLD, 4072, Australia

    Emma Campbell & Jacqueline Batley

  3. Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovská 6, 77200, Olomouc, Czech Republic

    Marie Kubaláková, Hana Šimková & Jaroslav Doležel

  4. Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Cientificas (IAS, CSIC), Alameda del Obispo s/n, 14080, Cordoba, Spain

    Pilar Hernandez

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  1. Paul J. Berkman
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  2. Adam Skarshewski
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  14. David Edwards
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Correspondence to David Edwards.

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Communicated by T. Close.

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Berkman, P.J., Skarshewski, A., Manoli, S. et al. Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation. Theor Appl Genet 124, 423–432 (2012). https://doi.org/10.1007/s00122-011-1717-2

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