Comparative transcriptome analysis of the metal hyperaccumulator Noccaea caerulescens

Abstract

The metal hyperaccumulator Noccaea caerulescens is an established model to study the adaptation of plants to metalliferous soils. Various comparators have been used in these studies. The choice of suitable comparators is important and depends on the hypothesis to be tested and methods to be used. In high-throughput analyses such as microarray, N. caerulescens has been compared to non-tolerant, non-accumulator plants like Arabidopsis thaliana or Thlaspi arvense rather than to the related hypertolerant or hyperaccumulator plants. An underutilized source is N. caerulescens populations with considerable variation in their capacity to accumulate and tolerate metals. Whole transcriptome sequencing (RNA-Seq) is revealing interesting variation in their gene expression profiles. Combining physiological characteristics of N. caerulescens accessions with their RNA-Seq has a great potential to provide detailed insight into the underlying molecular mechanisms, including entirely new gene products. In this review we will critically consider comparative transcriptome analyses carried out to explore metal hyperaccumulation and hypertolerance of N. caerulescens, and demonstrate the potential of RNA-Seq analysis as a tool in evolutionary genomics.

Inhibition of DNA demethylation enhances plant tolerance to cadmium toxicity by improving iron nutrition

“…Although various abiotic stresses have been shown to alter DNA methylation in plants (Zhang et al, ), little information is available on whether alteration in DNA methylation in turn affects the tolerance of plants against the corresponding abiotic stresses. Previously, several authors have proposed that epigenetic modification in metal hyperaccumulators might be involved in determining their high‐tolerance phenotype against heavy metal stress (Gullì, Marchi, Fragni, Buschini, & Visioli, ; Halimaa et al, ). Nevertheless, to the best of our knowledge, the genetic evidence supporting this assumption is lacking.…”

Unveiling the transcriptome complexity of the High- and Low- Zinc & Iron accumulating Indian wheat (Triticum aestivum L.) cultivars

“…To determine the genes involved in minerals updates, numerous comparative transcriptomic studies have been performed in hyperaccumulating as well as in non-hyperaccumulating plant species [Gao et al 2013; Di et al, 2011; Halimaa et al, 2014; Yang et al 2017]. Current study also deals with comparative transcriptome analysis of 7 genotypes of low- and high- Zn & Fe accumulating wheat, contrasting the reason for grain mineral concentration by recognizing various DEGs associated in the uptakes of minerals ( Figure 1 ).…”

Comparative RNA‐seq analysis of nickel hyperaccumulating and non‐accumulating populations of Senecio coronatus (Asteraceae)

“…(Merlot et al, 2014;Sobczyk et al, 2017). RNA-Seq provides the means by which to analyse gene expression in these species, but the choice of plant system is critical to extraction of the most biologically meaningful information (Halimaa et al, 2014a). Expression profiling of a plant species that exhibits variation in Ni accumulation will minimise any variation due to evolutionary divergence or adaptation to other environmental factors, and is therefore an attractive strategy by which to identify the patterns of gene expression that underpin the Ni hyperaccumulation phenotype (Sobczyk et al, 2017).…”