Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
35
datasets available to search
ShareScore release 0.9.0
Dataset results
35 results for “Hyperaccumulator”
De novo transcriptome assembly of hyperaccumulating Noccaea praecox
<p>Trinity de novo assembly for hyperaccumulating plant species Noccaea praecox (syn. Thlaspi praecox), Brassicaceae. The dataset includes annotations from SwissProt, Pfam, Rfam databases and information on transmembrane regions and signal peptide cleavage sites (annotated using BLAST, HMMER, infernal, tmHMM and signalP through Trinotate). Detailed information on the preprocessing, assembly, post-processing and annotations are described in the ReadMe file.</p> <p>Supplementary material for Bočaj, V., Pongrac, P., Fischer, S. <em>et al.</em> <em>De novo</em> transcriptome assembly of hyperaccumulating <em>Noccaea praecox</em> for gene discovery. <em>Sci Data</em> <strong>10</strong>, 856 (2023). <a href="https://doi.org/10.1038/s41597-023-02776-x">https://doi.org/10.1038/s41597-023-02776-x</a></p>
Dataset for the manuscript entitled "Can vermicomposting be used to process hyperaccumulator biomass in nickel agromining?"
<p>Data generated during an experiment of decomposition of biomass of the nickel hyperaccumulator <i>Bornmuellera emarginata </i>by the earthworm <i>Eisenia andrei</i> and associated microoganisms.</p><p>Five files are included:</p><p>"<strong>readme.txt</strong>" is a file where we explain the meaning of each column (and in which units is expressed) in each of the other four files.</p><p>"<strong>biomass.csv</strong>" is a table with biomass of different fractions and the number of <i>Eisenia andrei</i> individuals in each experimental unit.</p><p><strong>"FTIR.csv" </strong>is a file with the raw spectral data we obtained from the litter by Fourier Transform Infrared spectroscopy combined with Attenuated Total Reflectance (FTIR-ATR). First column indicate the wavenumber (cm-1) and the other columns indicate the absorbance values of each biomass sample for each wavenumber.</p><p><strong>"composition.csv"</strong> is a file with the pH, electrical conductivity, basal respiration and concentrations of different chemical elements measured in different fractions of each experimental unit</p><p><strong>"nickel.csv"</strong> contains the pseudototal and DTPA-extractable concentrations of Ni in different compartments of each experimental unit, as well as the total amount of this element (mg of Ni) in each compartment of each experimental unit.</p>
Interactive effects of rhizospheric soil microbes and litter on the growth of the invasive hyperaccumulator Bidens pilosa in cadmium-contaminated soil
Open the record for dataset details and reuse information.
Data from: Evolutionary dynamics of quantitative variation in an adaptive trait at the regional scale: the case of zinc hyperaccumulation in Arabidopsis halleri
Metal hyperaccumulation in plants is an ecological trait whose biological significance remains debated, in particular because the selective pressures that govern its evolutionary dynamics are complex. One of the possible causes of quantitative variation in hyperaccumulation may be local adaptation to metalliferous soils. Here we explored the population genetic structure of Arabidopsis halleri at fourteen metalliferous and non-metalliferous sampling sites in Southern Poland. The results were integrated with a quantitative assessment of variation in zinc hyperaccumulation to trace local adaptation. We identified a clear hierarchical structure with two distinct genetic groups at the upper level of clustering. Interestingly, these groups corresponded to different geographic sub-regions, rather than to ecological types (i.e. metallicolous vs non-metallicolous). Also, approximate Bayesian computation analyses suggested that the current distribution of A. halleri in Southern Poland could be relictual as a result of habitat fragmentation caused by climatic shifts during the Holocene, rather than due to recent colonization of industrially polluted sites. In addition, we find evidence that some non-metallicolous lowland populations may have actually derived from metallicolous populations. Meanwhile, the distribution of quantitative variation in zinc hyperaccumulation did separate metallicolous and non-metallicolous accessions, indicating more recent adaptive evolution and diversifying selection between metalliferous and non-metalliferous habitats. This suggests that zinc hyperaccumulation evolves both ways – towards higher levels at non-metalliferous sites and lower levels at metalliferous sites. Our results open a new perspective on possible evolutionary relationships between A. halleri edaphic types that may inspire future genetic studies of quantitative variation in metal hyperaccumulation.
Data from: Genome assembly and annotation of Arabidopsis halleri, a model for heavy metal hyperaccumulation and evolutionary ecology
The self-incompatible species Arabidopsis halleri is a close relative of the self-compatible model plant Arabidopsis thaliana. The broad European and Asian distribution and heavy metal hyperaccumulation ability make A. halleri a useful model for ecological genomics studies. We used long-insert mate-pair libraries to improve the genome assembly of the A. halleri ssp. gemmifera Tada mine genotype (W302) collected from a site with high contamination by heavy metals in Japan. After five rounds of forced selfing, heterozygosity was reduced to 0.04%, which facilitated subsequent genome assembly. Our assembly now covers 196 Mb or 78% of the estimated genome size and achieved scaffold N50 length of 712 kb. To validate assembly and annotation, we used synteny of A. halleri Tada mine with a previously published high-quality reference assembly of a closely related species, Arabidopsis lyrata. Further validation of the assembly quality comes from synteny and phylogenetic analysis of the HEAVY METAL ATPASE4 (HMA4) and METAL TOLERANCE PROTEIN1 (MTP1) regions using published sequences from European A. halleri for comparison. Three tandemly duplicated copies of HMA4, key gene involved in cadmium and zinc hyperaccumulation, were assembled on a single scaffold. The assembly will enhance the genomewide studies of A. halleri as well as the allopolyploid Arabidopsis kamchatica derived from A. lyrata and A. halleri.
The role of biotic interactions in determining metal hyperaccumulation in plants
<p>• Heavy metal hyperaccumulation (MH) is a rare trait found in plant species that inhabit metal contaminated soils. Two main hypotheses proposed to explain the selective advantage of MH are the elemental defense hypothesis and elemental allelopathy hypothesis. The elemental defence hypothesis suggests that MH functions as defence against herbivores while the elemental allelopathy hypothesis suggests that MH acts to inhibit the growth of neighbours. Nevertheless, these hypotheses are not likely to be mutually exclusive. Here, we present the first study to test both hypotheses simultaneously. We examined these hypotheses with the Cd hyperaccumulator Arabidopsis halleri, which inhabits both metalliferous and non-metalliferous soils, thus providing an opportunity to test the hypotheses both habitats.</p> <p>• A. halleri plants originating from several populations in both metalliferous and non-metalliferous soils were grown in a greenhouse in soils with or without cadmium (Cd), Their leaves were used in a feeding experiment with a specialist herbivore and in a set of leaf-leachate experiments that tested their effect on seed germination and seedling establishment of species co-occurring with A. halleri. Finally, a field survey in several A. halleri populations was conducted to compare herbivore load between A. halleri and neighbours from metalliferous vs. non-metalliferous soils.</p> <p>• Results of the feeding experiment and field-survey suggest that Cd accumulation in A. halleri leaves could provide it with defence against herbivores. Results of the leaf-leachate experiments reveal that Cd accumulation has no effect on seed germination of neighbouring species but inhibits seedling establishment, particularly of plant species originating from non-metalliferous soils.</p> <p>• Our results suggest that both herbivores and competing neighbours may jointly select for MH in plants. Moreover, MH could provide a selective advantage particularly in non-metalliferous soils, where neighbouring plants lack metal tolerance. These results highlight the importance of including different origins and populations of both the target species and its neighbouring plant species when studying the ecological role of metal hyperaccumulation.</p>
Data from: Evolutionary dynamics of quantitative variation in an adaptive trait at the regional scale: the case of zinc hyperaccumulation in Arabidopsis halleri
Open the record for dataset details and reuse information.
Data from: Evolution of nickel hyperaccumulation and serpentine adaptation in the Alyssum serpyllifolium species complex
Open the record for dataset details and reuse information.
Data from: Genome assembly and annotation of Arabidopsis halleri, a model for heavy metal hyperaccumulation and evolutionary ecology
Open the record for dataset details and reuse information.
The role of biotic interactions in determining metal hyperaccumulation in plants
Open the record for dataset details and reuse information.
Data from: Conserved but attenuated parental gene expression in allopolyploids: constitutive zinc hyperaccumulation in the allotetraploid Arabidopsis kamchatica
Open the record for dataset details and reuse information.
Data from: Demographic history of the trace metal hyperaccumulator Noccaea caerulescens (J. Presl and C. Presl) F. K. Mey. in Western Europe
Open the record for dataset details and reuse information.
Data from: Variation in defence strategies in the metal hyperaccumulator Noccaea caerulescens is indicative of synergies and trade-offs between forms of defence
The metal hyperaccumulator, N. caerulescens, uses metals as a defence against pathogens. Earlier work has suggested both trade-offs and synergies between metals and inducible defences. Different populations of N. caerulescens vary in metal accumulation. Here, we test the hypothesis that this produces different outcomes in trade-offs between defences. We compare zinc concentrations, glucosinolate concentrations, and inducible stress responses, including ROS and cell death, in four N. caerulescens populations, and relate these to the growth of the plant pathogen Pseudomonas syringae, its zinc tolerance mutants, and Pseudomonas pathogens isolated from a natural population of N. caerulescens. The populations display strikingly different defences. Where defences are successful, pathogens are limited primarily by metals, cell death, or organic defences, with evidence of both trade-offs and synergies between these, depending upon population. In addition, we find evidence that Pseudomonas pathogens may evolve to overcome any of these strategies, indicating that the arms race continues. These data indicate that defensive enhancement, joint effects and trade-offs between forms of defence are all plausible explanations for the evolution of metal-based defences, with factors including metal availability and pressures from metal-tolerant pathogens likely shaping the current strategy of each ecotype.
Data from: De novo transcriptome assemblies of four accessions of the metal hyperaccumulator plant Noccaea caerulescens
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.
Data from: Local adaptation is associated with zinc tolerance in Pseudomonas endophytes of the metal-hyperaccumulator plant Noccaea caerulescens
Metal hyperaccumulating plants, which are hypothesised to use metals for defence against pests and pathogens, provide a unique context in which to study plant–pathogen co-evolution. Previously, we demonstrated that the high concentrations of zinc found in leaves of the hyperaccumulator Noccaea caerulescens provide protection against bacterial pathogens, with a potential trade-off between metal-based and pathogen-induced defences. We speculated that an evolutionary arms race between zinc-based defences in N. caerulescens and zinc tolerance in pathogens might have driven the development of the hyperaccumulation phenotype. Here, we investigate the possibility of local adaptation by bacteria to the zinc-rich environment of N. caerulescens leaves and show that leaves sampled from the contaminated surroundings of a former mine site harboured endophytes with greater zinc tolerance than those within plants of an artificially created hyperaccumulating population. Experimental manipulation of zinc concentrations in plants of this artificial population influenced the zinc tolerance of recovered endophytes. In laboratory experiments, only endophytic bacteria isolated from plants of the natural population were able to grow to high population densities in any N. caerulescens plants. These findings suggest that long-term co-existence with zinc hyperaccumulating plants leads to local adaptation by endophytic bacteria to the environment within their leaves.
Figure 3 from: Fernando E, Quimado M, Doronila A (2014) Rinorea niccolifera (Violaceae), a new, nickel-hyperaccumulating species from Luzon Island, Philippines. PhytoKeys 37: 1-13. https://doi.org/10.3897/phytokeys.37.7136
Figure 3 - Rinorea niccolifera Fernando, shown as a nickel hyperaccumulator by a field test using filter paper impregnated with 1% dimethylglyoxime dissolved in 95% ethanol. Scale bar = 10 mm. Fernando 2421 (LBC). Photograph by Edwino S. Fernando.
Figure 2 from: Fernando E, Quimado M, Doronila A (2014) Rinorea niccolifera (Violaceae), a new, nickel-hyperaccumulating species from Luzon Island, Philippines. PhytoKeys 37: 1-13. https://doi.org/10.3897/phytokeys.37.7136
Figure 2 - Rinorea niccolifera Fernando. A Immature fruit showing depressed globose or obscurely 3-angular shape with prominent stylar remains B Mature, dehisced fruit showing three locules and seeds C Seedling showing foliaceus cotyledons and first three eophylls. Scale bars: A, B = 5 mm; C = 10 mm. A from Fernando 3016 (LBC), B from Fernando 3042 (LBC), C from Fernando 3042A (LBC), from seed of Fernando 3042 germinated in nursery. All photographs by Edwino S. Fernando.
Figure 1 from: Fernando E, Quimado M, Doronila A (2014) Rinorea niccolifera (Violaceae), a new, nickel-hyperaccumulating species from Luzon Island, Philippines. PhytoKeys 37: 1-13. https://doi.org/10.3897/phytokeys.37.7136
Figure 1 - Rinorea niccolifera Fernando. A Growth habit at type locality B Twig with flower buds and leaves showing distinct domatia on abaxial surface C Twig with flowers in axillary sessile clusters or fascicles, some on young, leafless portions of the twig; note prominent stipular scars D Close-up of flower, showing recurved tips of petals E Twig with young fruit subtended by the persistent sepals and petals; note the caducous stipules. Scale bars: A = 20 cm; B, E = 10 mm; C = 5 mm; D = 1 mm A–E from Fernando 3016 (LBC). All photographs by Edwino S. Fernando.
Data from: De novo transcriptome assemblies of four accessions of the metal hyperaccumulator plant Noccaea caerulescens
Open the record for dataset details and reuse information.
Data from: Variation in defence strategies in the metal hyperaccumulator Noccaea caerulescens is indicative of synergies and trade-offs between forms of defence
Open the record for dataset details and reuse information.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.