Journal Article

comparison of the Thlaspi caerulescens and Thlaspi arvense shoot transcriptomes

Broadley, Martin R, Pyke, Kevin A, Baker, Alan J.M, Hammond, John P, Mills, Victoria, Whiting, Steven N, Bowen, Helen C, White, Philip J, May, Sean T

2006

Overview

• 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 siIico 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.

• Publisher: Oxford, UK : Blackwell Publishing Ltd,Blackwell Science,Blackwell Publishing Ltd
• Subject: Alleles / Arabidopsis thaliana / Base Sequence / Biological Transport / Brassicaceae / cadmium / Compost / cross‐species / DNA Probes / Gene Expression Profiling / Gene Expression Profiling - methods / gene expression regulation / Genes / Genetic hybridization / Genetic Variation / genetics / genome / Genome, Plant / heavy metals / Homeostasis / hyperaccumulation / Hyperaccumulators / metabolism / methods / microarray / Noccaea caerulescens / nucleic acid hybridization / Nucleic Acid Hybridization - methods / oligonucleotide / plant genetics / Plant Proteins / Plant Proteins - genetics / Plant Proteins - metabolism / Plant Shoots / Plant Shoots - genetics / Plant Shoots - metabolism / Plants / Polymerase Chain Reaction / probe masking / RNA / RNA probes / RNA, Messenger / RNA, Messenger - metabolism / Sequence Alignment / Thlaspi / Thlaspi - genetics / Thlaspi - metabolism / Thlaspi arvense / Thlaspi caerulescens / transcription (genetics) / transcriptome / Transcriptomes / transcriptomics / Zinc / Zinc - metabolism