LCk32 transcriptome annotation

Annotation of the LCK32 (La Calamine accession) de novo assembly. Annotation was performed using the Trinotate pipeline. Ortholog clustering was performed using OrthoFinder. Ortholog groups and the corresponding A thaliana TAIR codes have been combined with the Trinotate annotation

LEk32 transcriptome annotation

Annotation of the LEK32 (Lellingen accession) de novo assembly. Annotation was performed using the Trinotate pipeline. Ortholog clustering was performed using OrthoFinder. Ortholog groups and the corresponding A thaliana TAIR codes have been combined with the Trinotate annotation

MPk32 transcriptome annotation

Annotation of the MPK32 (Monte Prinzera accession) de novo assembly. Annotation was performed using the Trinotate pipeline. Ortholog clustering was performed using OrthoFinder. Ortholog groups and the corresponding A thaliana TAIR codes have been combined with the Trinotate annotation

Python code - taxonomic group

Python code to extract the taxonomic group after blast search

Gene Expression Differences between <i>Noccaea caerulescens</i> Ecotypes Help to Identify Candidate Genes for Metal Phytoremediation

Populations of <i>Noccaea caerulescens</i> show tremendous differences in their capacity to hyperaccumulate and hypertolerate metals. To explore the differences that could contribute to these traits, we undertook SOLiD high-throughput sequencing of the root transcriptomes of three phenotypically well-characterized <i>N. caerulescens</i> accessions, <i>i.e.</i>, Ganges, La Calamine, and Monte Prinzera. Genes with possible contribution to zinc, cadmium, and nickel hyperaccumulation and hypertolerance were predicted. The most significant differences between the accessions were related to metal ion (di-, trivalent inorganic cation) transmembrane transporter activity, iron and calcium ion binding, (inorganic) anion transmembrane transporter activity, and antioxidant activity. Analysis of correlation between the expression profile of each gene and the metal-related characteristics of the accessions disclosed both previously characterized (<i>HMA4</i>, <i>HMA3</i>) and new candidate genes (<i>e.g.</i>, for nickel <i>IRT1</i>, <i>ZIP10</i>, and <i>PDF2.3</i>) as possible contributors to the hyperaccumulation/tolerance phenotype. A number of unknown <i>Noccaea</i>-specific transcripts also showed correlation with Zn²⁺, Cd²⁺, or Ni²⁺ hyperaccumulation/tolerance. This study shows that <i>N. caerulescens</i> populations have evolved great diversity in the expression of metal-related genes, facilitating adaptation to various metalliferous soils. The information will be helpful in the development of improved plants for metal phytoremediation