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A comparison of the Thlaspi caerulescens and Thlaspi arvense shoot transcriptomes
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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“The overexpression of ZNT1 was further confirmed by microarray analysis (Hammond et al., 2006; van de Mortel et al., 2006).”
From Plant hyperaccumulators: a state-of-the-art review on mechanism of heavy metal transport and sequestration (2025) · cites this paper as Hammond et al., 2006
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Metadata
- 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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