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A comparison of the Thlaspi caerulescens and Thlaspi arvense shoot transcriptomes

  1. John P. Hammond1,2,
  2. Helen C. Bowen1,
  3. Philip J. White1,
  4. Victoria Mills2,
  5. Kevin A. Pyke2,
  6. Alan J. M. Baker3,
  7. Steven N. Whiting4,
  8. Sean T. May5,
  9. Martin R. Broadley2

Article first published online: 16 FEB 2006

DOI: 10.1111/j.1469-8137.2006.01662.x

Issue

New Phytologist

New Phytologist

Volume 170, Issue 2, pages 239–260, April 2006

Additional Information

How to Cite

Hammond, J. P., Bowen, H. C., White, P. J., Mills, V., Pyke, K. A., Baker, A. J. M., Whiting, S. N., May, S. T. and Broadley, M. R. (2006), A comparison of the Thlaspi caerulescens and Thlaspi arvense shoot transcriptomes. New Phytologist, 170: 239–260. doi: 10.1111/j.1469-8137.2006.01662.x

Author Information

  1. 1

    Warwick HRI, University of Warwick, Wellesbourne, Warwick CV35 9EF, UK;

  2. 2

    Plant Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington, Loughborough LE12 5RD, UK;

  3. 3

    School of Botany, University of Melbourne, Melbourne, Victoria 3010, Australia;

  4. 4

    Golder Associates (UK) Ltd, Browns Lane Business Park, Stanton-on-the-Wolds, Nottingham NG12 5BL, UK;

  5. 5

    Nottingham Arabidopsis Stock Centre, Plant Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington, Loughborough LE12 5RD, UK

*Author for correspondence: Martin R. Broadley Tel: +44 (0) 115 9516382 Fax: +44 (0) 115 9516334 Email: martin.broadley@nottingham.ac.uk

Publication History

  1. Issue published online: 16 FEB 2006
  2. Article first published online: 16 FEB 2006
  3. Received: 7 September 2005 Accepted: 1 December 2005

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Keywords:

  • Brassicaceae;
  • cadmium;
  • cross-species;
  • hyperaccumulation;
  • microarray;
  • oligonucleotide;
  • probe masking;
  • transcriptomics;
  • zinc

Summary

  • • 
    Whole-genome transcriptome profiling is revealing how biological systems are regulated at the transcriptional level. This study reports the development of a robust method to profile and compare the transcriptomes of two nonmodel plant species, Thlaspi caerulescens, a zinc (Zn) hyperaccumulator, and Thlaspi arvense, a nonhyperaccumulator, using Affymetrix Arabidopsis thaliana ATH1-121501 GeneChip® arrays (Affymetrix, Santa Clara, CA, USA).
  • • 
    Transcript abundance was quantified in the shoots of agar- and compost-grown plants of both species. Analyses were optimized using a genomic DNA (gDNA)-based probe-selection strategy based on the hybridization efficiency of Thlaspi gDNA with corresponding A. thaliana probes. In silico alignments of GeneChip® probes with Thlaspi gene sequences, and quantitative real-time PCR, confirmed the validity of this approach.
  • • 
    Approximately 5000 genes were differentially expressed in the shoots of T. caerulescens compared with T. arvense, including genes involved in Zn transport and compartmentalization.
  • • 
    Future functional analyses of genes identified as differentially expressed in the shoots of these closely related species will improve our understanding of the molecular mechanisms of Zn hyperaccumulation.
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