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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., Broadley, Martin R.·2006·New Phytologist

DOI 10.1111/j.1469-8137.2006.01662.x

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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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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.
ORCID: Hammond, John P.
White, Philip J.
Pyke, Kevin A.
Baker, Alan J. M.
May, Sean T.
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
DOI: 10.1111/j.1469-8137.2006.01662.x
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
Licence: onlinelibrary.wiley.com/termsAndConditions#vor (vor)
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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A comparison of the Thlaspi caerulescens and Thlaspi arvense shoot transcriptomes

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