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.
Highlights
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
Unlike N. caerulescens it is self-incompatible, which complicates genetic analysis, but it is much closer to the general plant model species Arabidopsis thaliana, with which is shares more sequence synteny
It is fortunate that the first plant species for which genomic data became available, A. thaliana, belongs to the Brassicaceae family, as this triggered further interest in generating genome sequence information from several members of this family
Summary
K. Mey., formerly named Thlaspi caerulescens, is an outstanding model plant species to study heavy metal hyperaccumulation (Assunção et al, 2003; Peer et al, 2003; Milner and Kochian, 2008). Mey., formerly named Thlaspi caerulescens, is an outstanding model plant species to study heavy metal hyperaccumulation (Assunção et al, 2003; Peer et al, 2003; Milner and Kochian, 2008) It is one of the few plant species of which genotypes are known that are adapted to grow on soil containing high levels of zinc (Zn), cadmium (Cd), nickel (Ni), and/or lead (Pb) (Mohtadi et al, 2012). For neither A. halleri nor N. caerulescens the genome sequence has been determined, which is why most of the gene expression research on these species so far has relied on heterologous micro-array analysis using the available A. thaliana micro-arrays
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