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A comparison of the Thlaspi caerulescens and Thlaspi arvense shoot transcriptomes

Hammond, J. P. ORCID:, 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 (2). pp. 239-260. ISSN 0028-646X

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To link to this item DOI: 10.1111/j.1469-8137.2006.01662.x


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 (R) 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 (R) 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.

Item Type:Article
Divisions:Life Sciences > School of Biological Sciences > Department of Bio-Engineering
Interdisciplinary centres and themes > Centre for Food Security
Life Sciences > School of Agriculture, Policy and Development > Department of Crop Science
ID Code:33858
Uncontrolled Keywords:Brassicaceae cadmium cross-species hyperaccumulation microarray oligonucleotide probe masking transcriptomics zinc Thlaspi caerulescens arvense noccaea

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