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.
294
datasets available to search
ShareScore release 0.9.0
Dataset results
294 results for “Lemna”
Lemna gibba L. (BR0000011394372)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Lemna gibba L. (BR0000012215942)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Lemna gibba L. (BR0000012260898)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Lemna gibba L. (BR0000009535152)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Lemna gibba L. (BR0000011394327)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Lemna gibba L. (BR0000011394624)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Lemna gibba L. (BR0000011394792)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Lemna gibba L. (BR0000010760994)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Fig. 3 in A taxonomic revision of Lemna sect. Uninerves (Lemnaceae)
Fig. 3. Maximum clade credibility tree based on the concatenated cpDNA psbK-psbI + atpF-atpH dataset as inferred by the programme BEAST v.1.8. Numbers on the branches are posterior probability (PP) from the Bayesian inference and bootstrap support (BS) values from the maximum likelihood analysis (PP/BS). A dash means that the node is absent from the respective analysis. Lemna aequinoctialis 6746 and L. tenera 9020 were used as outgroups.
Fig. 1 in A taxonomic revision of Lemna sect. Uninerves (Lemnaceae)
Fig. 1. Ventral view of the investigated duckweed species. A, Lemna minuta clone 9581; B, L. yungensis clone 9208; C, L. valdiviana clone 8685; D, Overview of the measured characters for the morphological analysis. Fronds were prepared using a methanolic carmin staining method. L = length from base to apex, W = width at the widest part of the fronds, LN = length of nerve from node onwards, A = distance between node and end of aerenchyma, N-A = distance from node to apex. Scale bar represents 1 mm.
High tolerance to zinc but no evidence for local adaptation in the aquatic plant Lemna minor
<p>Duckweeds are a widely distributed and economically important aquatic plant family that have high potential for phytoremediation of polluted water bodies. We collected four ecotypes of the common duckweed (<em>Lemna</em> <em>minor</em>) from the four corners of Switzerland and assessed how their home vs. away environments influenced their growth. Additionally, we investigated their response to a metal pollutant (Zn) in both their home and away environments. Zn is found in freshwater systems and can become harmful to plants at elevated concentrations. We hypothesized that growing in their home environment would help the plants buffer the negative effect of the metal pollutant. To test this, we measured <em>Lemna</em> growth in a common garden experiment in a glasshouse where the four ecotypes were grown in each of the water environments, as well as in three different concentrations of Zn. To investigate whether interactions between <em>Lemna</em> and their microbial community can enhance or reduce tolerance to heavy metal pollution, we sampled chlorophyll-a as a proxy for algal biomass. Finally, we measured total nitrogen and total organic carbon to describe the abiotic environment in more detail. The four <em>Lemna</em> ecotypes exhibited significantly different growth rates across the water treatments. This difference in fitness was matched with DNA sequencing revealing genetic differentiation between the four ecotypes. However, the effect of the water and zinc treatment on <em>Lemna</em> growth was the same for all ecotypes. We did not find evidence for local adaptation; instead, we observed strong plastic responses. <em>Lemna</em> growth rates were higher under higher Zn concentrations. This positive effect of Zn on <em>Lemna</em> growth could be in part due to reduced competition with algae. We conclude that <em>L. minor</em> ecotypes may exhibit large differences in growth rate, but that the species overall have a high Zn tolerance and strong plastic adaptive potential in novel environments.</p>
High tolerance to zinc but no evidence for local adaptation in the aquatic plant Lemna minor
Open the record for dataset details and reuse information.
Data from: A demographic assessment of the Lansing Effect in duckweed (Lemna turionifera Landolt)
Open the record for dataset details and reuse information.
Data from: Caloric restriction-mediated reproductive lifespan extension across multiple strains of the clonal aquatic plant <em>Lemna turionifera</em>
Open the record for dataset details and reuse information.
Minimal assay detects population-level senescence in the aquatic plant Lemna minor
Open the record for dataset details and reuse information.
Effect of the growth medium composition on nitrate accumulation in the novel protein crop Lemna minor
<p>Duckweed is a potential alternative protein source for food and feed. However, little is known about the nitrate accumulation in this plant. A high nitrate level in vegetables can indirectly lead to an elevated intake of nitrites and N-nitroso compounds, increasing the risk of diseases for humans and animals. This research hypothesizes that the nitrate accumulation of <em>Lemna minor</em> differs between growing media. Additionally, it evaluates whether legal safety levels of nitrate for human and animal intake are exceeded. The duckweed was grown on (i) rainwater, and (ii) three synthetic media containing different nutrient levels. Furthermore, (iii) biological effluent of swine manure treatment and (iv) aquaculture effluent from pikeperch production were used, as these are potential media for closing nutrient loops in the agriculture sector. It was found that nitrate levels increased with the increasing availability of macronutrients in the water, and pH showed a particularly strong negative correlation with the nitrate levels in the plant. Nevertheless, nitrate content never exceeded 530 mg NO<sub>3</sub> kg<sup>−1</sup> fresh weight. To conclude, <em>Lemna minor</em>'s nitrate content was below safety limits for human consumption in all tested growing media; however, a potential risk for ruminants was observed as these are more sensitive to nitrate conversions in their gastro-intestinal track.</p>
Lemna minor annotation R package (org.Lminor.eg.db) and corresponding files behind the custom built
<p>This public repository containing the following files:</p> <ol> <li>Custom built annotation R package for the <em>Lemna minor </em>reference genome [<a href="https://zenodo.org/api/files/33f1633e-9232-4a1c-af07-5bcf19db9304/org.Lminor.eg.db.7z?versionId=c0a06176-0e46-4732-87ae-c6d9f9c68d0c">org.Lminor.eg.db.7z</a>]. The package was built via AnnotationForge using sequence homology of protein coding genes for functional characterisation (Description, PFAMs, GO terms). A combined approach using <a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download">blastx </a>and <a href="http://eggnog5.embl.de/#/app/home">EMBL's eggNOG mapper</a> was used for this task. This package is compatible with <a href="https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html">clusterProfiler</a> for downstream functional enrichment analysis (ORA / GSEA) of <em>L. minor</em> transcriptomic / proteomic data.<br> <br> For <strong>how to install and use this package</strong> in your R session,<strong> check the R code example below</strong>.<br> </li> <li>Reference genome, genome annotation (gtf), gene coding sequences (cds) and cds translated peptide sequences (cds.pep) of the duckweed <em>Lemna minor </em>[<a href="https://zenodo.org/api/files/33f1633e-9232-4a1c-af07-5bcf19db9304/Lminor_refGenome_GTF_CDS.7z?versionId=c25b53a8-1fc3-4bfb-b559-718ab8b230a9">Lminor_refGenome_GTF_CDS.7z</a>].<br> The reference genome assembly fasta was downloaded from <a href="http://www.lemna.org">www.lemna.org</a>. Matching GTF annotation file was generated via '<em>gffread</em>', from the GFF<em> </em>annotation file available <a href="https://genomevolution.org/coge/LoadGenome.pl?wid=47218">here</a>.<br> </li> <li>With the cds translated peptide file, a blastp search was performed against a custom plant protein sequence database [<a href="https://zenodo.org/api/files/33f1633e-9232-4a1c-af07-5bcf19db9304/Lminor_ref.org.Db4blastp.7z?versionId=d1e69820-edfc-494d-9d44-f6624b190841">Lminor_ref.org.Db4blastp.7z</a>]. The custom database was built from the proteomes of well annotated reference plant species. (For details refer to the readme file within the compressed folder)</li> </ol> <p>For more details please refer to our publication in <a href="https://doi.org/10.1021/acs.est.2c01777">Environmental Science & Technology</a>:<br> Loll, Alexandra, Hannes Reinwald, Steve U. Ayobahan, Bernd Göckener, Gabriela Salinas, Christoph Schäfers, Karsten Schlich, Gerd Hamscher, and Sebastian Eilebrecht. <em><strong>“Short-Term Test for Toxicogenomic Analysis of Ecotoxic Modes of Action in Lemna Minor.”</strong></em> Environmental Science & Technology 56, no. 16 (August 16, 2022): 11504–15.<br> DOI: <a href="https://doi.org/10.1021/acs.est.2c01777">https://doi.org/10.1021/acs.est.2c01777</a></p> <pre><code class="language-bash"># 1. Download and unzip (7zip format) the org.Lminor.eg.db package. # 2. Install the package via: orgDb = "path/to/org.Lminor.eg.db/" install.packages(orgDb, type="source", repos=NULL) # 3. Restart R session then load package require(org.Lminor.eg.db) require(AnnotationDbi) # to check for columns and keytypes: columns(org.Lminor.eg.db) keytypes(org.Lminor.eg.db) # query the org.Lminor.eg.db for particular Lemna gene IDs (GID) gid = keys(org.Lminor.eg.db, keytype="GID") col = columns(org.Lminor.eg.db)[c(5,17,9,15,1,8,14)] df = select(org.Lminor.eg.db, keys=gid[1000:1100], columns=col, keytype="GID") View(df) ### Running overrepresenation analysis in clusterProfiler using the Lminor annotation package ### # ORA for multiple gene sets via compareCluster() require(clusterProfiler) genLs = list(setA = gid[1:40], setB = gid[100:140], setC = gid[1000:1040]) res = compareCluster(genLs, fun = "enrichGO", OrgDb = "org.Lminor.eg.db", keyType = "GID", ont = "BP", universe = gid) # Compute semantic similiarities among GO terms: d = GOSemSim::godata('org.Lminor.eg.db', ont="BP", computeIC=FALSE, keytype = "GID") res = enrichplot::pairwise_termsim(res, method = "Wang", semData = d) # Rmv GO terms with redudant biological information resS = simplify(res, .8) # resort results after pvalues resS@compareClusterResult = resS@compareClusterResult[order(resS@compareClusterResult$pvalue),] View(res@compareClusterResult) # Network plot emapplot(resS, showCategory = 30)</code></pre>
Data from "Population genomic structure of Lemna minor and the cryptic species L. japonica in Switzerland"
<p>SNP data and sample annotation:</p> <ul> <li>sampleTab.csv contains the sample annotation (species and population)</li> <li>L.minor.reference.bcftools.snps.vcf.gz(.tbi) contains SNPs from all samples using the L. minor reference genome (Lm7210)</li> <li>L.japonica.reference.bcftools.snps.vcf.gz(.tbi) contains SNPs from all samples using the L. japonica reference genome (Lj9421)</li> </ul>
Data from: Offspring of older parents are smaller—but no less bilaterally symmetrical—than offspring of younger parents in the aquatic plant Lemna turionifera
Open the record for dataset details and reuse information.
Data from: Demographic senescence in the aquatic plant Lemna gibba L. (Araceae)
Senescence is progressive, age-related bodily deterioration, accompanied at the population level by declines in average survival and fecundity (i.e., 'demographic senescence'). Demographic senescence of plants has been investigated in only a few species, including small, floating macrophytes in the genus Lemna (family Araceae, subfamily Lemnoideae – the 'duckweeds'). Unlike most plant species, Lemna ramets exhibit determinate growth, potentially rendering them more likely to experience demographic senescence. Here, our objective was to investigate senescence in a Lemna species not previously studied in this context, L. gibba L., toward the long-term goal of conducting cross-species comparative analyses. In a longitudinal lab study, we investigated a cohort of 334 individual L. gibba fronds, whose survival and reproduction we followed daily from birth (defined by the date a focal frond detached from its parent) to death (defined by the date a focal frond's last daughter detached). We fit survival data to exponential, Weibull, Gompertz, and logistic models, the first of which represents 'no senescence'. The logistic model was found to have the greatest support (AICC weight >0.99), indicating strong age-related declines in survival. We fit reproduction data using a generalized estimating equation approach, which showed a significant age-related decline in the predicted probability of daily reproduction – from 0.61 at age 3 days to 0.23 at age 52 days (i.e., after excluding the first two days of reproduction data to account for the initial, pre-reproductive phase of the L. gibba lifecycle). These age-related declines provide strong evidence that L. gibba does exhibit demographic senescence, consistent with evidence from congeneric species.
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.