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

Daniel Blande*, Pauliina Halimaa, Arja I. Tervahauta, Mark G.M. Aarts, Sirpa O. Kärenlampi

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

13 Citations (Scopus)

Abstract

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.

Original languageEnglish
Article number160131
JournalScientific Data
Volume4
DOIs
Publication statusPublished - 2017

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tolerance
Metals
Protein Sequence
nutrition
Tolerance
Mineral nutrition
candidacy
Proteins
ability
Nutrition
Soil
Minerals
Group
Roots
Tissue
Soils
Accessions
Protein
Model

Cite this

Blande, Daniel ; Halimaa, Pauliina ; Tervahauta, Arja I. ; Aarts, Mark G.M. ; Kärenlampi, Sirpa O. / De novo transcriptome assemblies of four accessions of the metal hyperaccumulator plant Noccaea caerulescens. In: Scientific Data. 2017 ; Vol. 4.
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abstract = "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.",
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De novo transcriptome assemblies of four accessions of the metal hyperaccumulator plant Noccaea caerulescens. / Blande, Daniel; Halimaa, Pauliina; Tervahauta, Arja I.; Aarts, Mark G.M.; Kärenlampi, Sirpa O.

In: Scientific Data, Vol. 4, 160131, 2017.

Research output: Contribution to journalArticleAcademicpeer-review

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AB - 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.

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