Cited by 225Genomics and Phylogenetic StudiesPlant Molecular Biology ResearchPlant Micronutrient Interactions and Effects

A comparison of the Thlaspi caerulescens and Thlaspi arvense shoot transcriptomes

Hammond, John P., Bowen, Helen C., White, Philip J., Mills, Victoria, Pyke, Kevin A., Baker, Alan J. M., Whiting, Steven N., May, Sean T. +1 more·2006·New Phytologist

Abstract

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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Crossref · 10.1111/j.1469-8137.2006.01662.x

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Authors
Hammond, J. P., Bowen, H. C., White, P. J., Mills, V., Pyke, K. A., Baker, A. J. M., Whiting, S. N., May, S. T., & Broadley, M. R.
Affiliations
  • University of Nottingham (GB)
  • University of Warwick (GB)
  • The University of Melbourne (AU)
  • Golder Associates (United Kingdom) (GB)
Corresponding author
Broadley, Martin R.
Venue
New Phytologist
Publisher
Wiley
Published
2006-02-16
Volume
170
Issue
2
Pages
239-260
ISSN
  • 0028-646X (ISSN-L)
  • 1469-8137
OpenAlex
W2134066223
Cited by
223
References
73
Citations by year
2026: 1 · 2025: 4 · 2024: 3 · 2023: 3 · 2022: 7 · 2021: 7 · 2020: 13 · 2019: 9 · 2018: 9 · 2017: 5 · 2016: 16 · 2015: 3 · 2014: 15 · 2013: 13 · 2012: 20
FWCI
6.94
Type
journal article
Language
en
Open access
closed
Locations
  • New Phytologist (publishedVersion)
  • PubMed (publishedVersion)
Funders
  • Nuffield Foundation
  • Research Councils UK
  • Biotechnology and Biological Sciences Research Council (G17764, G18881, BBS/B/1356X)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Micronutrient Interactions and Effects
Keywords
Thlaspi caerulescens, Thlaspi arvense, zinc hyperaccumulation, shoot transcriptome, differential gene expression, zinc transport, probe selection, gene expression profiling
MeSH terms
Alleles, Base Sequence, Biological Transport, Homeostasis, Nucleic Acid Hybridization, Plant Proteins, RNA, Messenger, Genetic Variation, Zinc, DNA Probes, Polymerase Chain Reaction, Sequence Alignment, Plant Shoots, Genome, Plant, Gene Expression Profiling, Thlaspi

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