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ZENODO
Dataset . 2017
License: CC 0
Data sources: ZENODO
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Research@WUR
Dataset . 2017
Data sources: Research@WUR
DRYAD
Dataset . 2017
License: CC 0
Data sources: Datacite
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Data from: De novo transcriptome assemblies of four accessions of the metal hyperaccumulator plant Noccaea caerulescens

Authors: Blande, D.; Halimaa, Pauliina; Tervahauta, Arja I.; Aarts, M.G.M.; Kärenlampi, Sirpa O.;

Data from: De novo transcriptome assemblies of four accessions of the metal hyperaccumulator plant Noccaea caerulescens

Abstract

GAk32 transcriptome annotationAnnotation of the GAK32 (Ganges 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.GAk32_annotation_final.xlsxLCk32 transcriptome annotationAnnotation 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.LCk32_annotation_final.xlsxLEk32 transcriptome annotationAnnotation 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.LEk32_annotation_final.xlsxMPk32 transcriptome annotationAnnotation 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.MPk32_annotation_final.xlsxFasta files of ortholog groupsA zip archive containing the fasta files of the protein sequences clustered into ortholog groups by OrthoFinder.fasta.zipPython code - taxonomic groupPython code to extract the taxonomic group after blast search.python_tax_code.py

Noccaea caerulescens of the Brassicaceae family has become the key model plant among the metal hyperaccumulator plants. Populations/accessions of N. caerulescens from geographic locations with different soil metal concentrations differ in their ability to hyperaccumulate and hypertolerate metals. Comparison of transcriptomes in several accessions provides candidates for detailed exploration of the mechanisms of metal accumulation and tolerance and local adaptation. This can have implications in the development of plants for phytoremediation and improved mineral nutrition. Transcriptomes from root and shoot tissues of four N. caerulescens accessions with contrasting Zn, Cd and Ni hyperaccumulation and tolerance traits were sequenced with Illumina Hiseq2000. Transcriptomes were assembled using the Trinity de novo assembler and were annotated and the protein sequences predicted. The comparison against the BUSCO plant early release dataset indicated high-quality assemblies.The predicted protein sequences have been clustered into ortholog groups with closely related species. The data serve as important reference sequences in whole transcriptome studies, in analyses of genetic differences between the accessions and other species, and for primer design.

Country
Netherlands
Keywords

assembly, Assembly, Noccaea caerulescens, transcriptome, Metal Hyperaccumulation

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
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