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A comparison of the Thlaspi caerulescens and Thlaspi arvense shoot transcriptomes
Author(s) -
Hammond John P.,
Bowen Helen C.,
White Philip J.,
Mills Victoria,
Pyke Kevin A.,
Baker Alan J. M.,
Whiting Steven N.,
May Sean T.,
Broadley Martin R.
Publication year - 2006
Publication title -
new phytologist
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.742
H-Index - 244
eISSN - 1469-8137
pISSN - 0028-646X
DOI - 10.1111/j.1469-8137.2006.01662.x
Subject(s) - biology , arabidopsis thaliana , hyperaccumulator , transcriptome , botany , arabidopsis , gene , genetics , gene expression , phytoremediation , ecology , contamination , mutant
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.