A comprehensive set of transcript sequences of the heavy metal hyperaccumulator Noccaea caerulescens

Abstract

Noccaea caerulescens is an extremophile plant species belonging to the Brassicaceae family. It has adapted to grow on soils containing high, normally toxic, concentrations of metals such as nickel, zinc, and cadmium. Next to being extremely tolerant to these metals, it is one of the few species known to hyperaccumulate these metals to extremely high concentrations in their aboveground biomass. In order to provide additional molecular resources for this model metal hyperaccumulator species to study and understand the mechanism of adaptation to heavy metal exposure, we aimed to provide a comprehensive database of transcript sequences for N. caerulescens. In this study, 23,830 transcript sequences (isotigs) with an average length of 1025 bp were determined for roots, shoots and inflorescences of N. caerulescens accession “Ganges” by Roche GS-FLEX 454 pyrosequencing. These isotigs were grouped into 20,378 isogroups, representing potential genes. This is a large expansion of the existing N. caerulescens transcriptome set consisting of 3705 unigenes. When translated and compared to a Brassicaceae proteome set, 22,232 (93.2%) of the N. caerulescens isotigs (corresponding to 19,191 isogroups) had a significant match and could be annotated accordingly. Of the remaining sequences, 98 isotigs resembled non-plant sequences and 1386 had no significant similarity to any sequence in the GenBank database. Among the annotated set there were many isotigs with similarity to metal homeostasis genes or genes for glucosinolate biosynthesis. Only for transcripts similar to Metallothionein3 (MT3), clear evidence for an additional copy was found. This comprehensive set of transcripts is expected to further contribute to the discovery of mechanisms used by N. caerulescens to adapt to heavy metal exposure.

An evolutionary and functional genomics study of Noccaea caerulescens, a heavy metal hyperaccumulating plant species

“…Based on our biomass data, it seemed that NAV did not grow well in multiple experiments under the control conditions in our hydroponic system, thus, the Zn or phloem-specific iron transporter that is essential for systemic iron signalling and redistribution of iron and cadmium in A. thaliana (Zhai et al, 2014). Large variations in the region ( between 500 nucleotides up-and downstream of this gene) were detected between populations, Five of these were found to result in amino acid changes in the conserved region of the protein (Supplement 1).This gene was also found to be differently expressed under metal stress in N. caerulescens (Halimaa et al, 2014a;Lin et al, 2014). In addition, we found also a non-synonymous SNP in the transcription factor WRKY72, which has a role in plant abiotic stresses like Pi deprivation, salt and drought (Yu et al, 2010;Chen et al, 2012b;Niu et al, 2012).…”

“…caerulescens (Halimaa et al, 2014;Lin et al, 2014), and by comparative transcriptomic analysis in A. thaliana and A. halleri (Becher et al, 2004;Weber et al, 2004Weber et al, , 2006 or A. thaliana and N. caerulescens (Rigola et al, 2006;Hammond et al, 2006;van de Mortel et al, 2006;van de Mortel et al, 2008;Plessl et al, 2010). These studies have revealed many genes that are overexpressed in Zn/Cd hyperaccumulator species compared to A. thaliana, which may therefore be related to the variation in Zn/Cd accumulation and tolerance among different species.…”

“…The relevance of such mutations in relation to variations in metal accumulation and tolerance have not yet been tested for these strongly expressed genes because transcriptome analysis does not cover non-exon sequences (Halimaa et al, 2014b;Lin et al, 2014). These mutations can only be accessed by whole-genome sequencing.…”

“…Assuming one mutant/3000 M2 plants, with around 30,000 genes (29,712) being predicted in the N. caerulescens genome (Lin et al, 2014), we expect every M2 plant to carry on average knock-out mutations for 10 genes.…”

“…The mechanisms, underlying this variation are incompletely understood, but attributable to variation in metal uptake, xylem loading, sequestration and detoxification in the shoot (Clemens, 2001;Hall, 2002;DalCorso et al, 2010). The availability of the genome sequence of Arabidopsis thaliana and other Brassicaceae species has greatly facilitated the understanding of these physiological processes and the underlying molecular mechanisms in N. caerulescens (Pence et al, 2000;van de Mortel et al, 2008;Halimaa et al, 2014b;Lin et al, 2014) and Arabidopsis halleri, another Zn/Cd hyperaccumulating Brassicaceae (Clemens et al, 2002;Krämer, 2010;Verbruggen et al, 2013) Progenies of crosses between N. caerulescens accessions with contrasting phenotypes for tolerance and accumulation have yielded more or less continuous phenotype distributions, indicating genetic control by a number of loci (Assunção et al 2006;Deniau et al 2006;Assunção et al 2003b;Zha et al 2004). (Lombi et al, 2001;Zhao et al, 2002).…”