A comparison of the Thlaspi caerulescens and Thlaspi arvense shoot transcriptomes

Abstract

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.

Transition metal transport

“…In A. halleri and T. caerulescens, NRAMP3 is highly expressed in roots. AhNRAMP3 is also highly expressed in shoots, whereas NRAMP1 and NRAMP5 are highly expressed in shoots of T. caerulescens [44,[46][47][48][49]. The primary biological function of A. thaliana NRAMP transporters appears to be in Fe homeostasis.…”

Moving micronutrients from the soil to the seeds: Genes and physiological processes from a biofortification perspective

“…Studies in hyperaccumulator species have highlighted the involvement of ZIP genes in shoot Zn distribution. In Thlaspi caerulescens, the ZIP genes Znt1 and Znt5 are highly expressed compared to the nonaccumulator, T. arvense [79,112,113]. T. caerulescens accumulates Zn in epidermal storage cells of leaves to several-fold higher than in mesophyll cells [114].…”

Isolation of Zn-responsive genes from two accessions of the hyperaccumulator plant Thlaspi caerulescens

“…With cross-species microarray (Weber et al 2004;Becher et al 2004;Hammond et al 2006) there is a risk that important genes with low sequence identity will not be detected. Although a T. caerulescens speciWc cDNA array has been made (Plessl et al 2005), the number of cDNA sequences is still far from that needed to make a "whole-genome" cDNA array (Rigola et al 2006).…”