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4,536 results for “Arabidopsis”
Natural variation across Arabidopsis diversity panel in early responses to salt stress
<p>The data of Arabidopsis thaliana accessions which were grown according to the established protocol for studying salt stress in soil experiment (described in detail here dx.doi.org/10.17504/protocols.io.4xzgxp6), in the PSI facility, Czech Republic. </p>
Spatially corrected dataset for natural variation across Arabidopsis diversity panel in early responses to salt stress
<p>The spatially corrected data of Arabidopsis thaliana accessions, which were grown according to the established protocol for studying salt stress in soil experiment (described in detail here dx.doi.org/10.17504/protocols.io.4xzgxp6), in the PSI facility, Czech Republic.</p> <p>The spatial correction was done using the asreml package. The data was subsequently used for the Genome-Wide Association Study. </p>
Abiotic stress mediated modulation of chromatin landscape in Arabidopsis thaliana
<p>This dataset include figures and supplementary material for the manuscript entitled<strong> </strong>"Abiotic stress mediated modulation of chromatin landscape in <em>Arabidopsis thaliana" </em>to be published in Journal of Experimental Botany special issue focused on Chromatin.</p> <p><strong>Supplementary File 1:</strong> Table describing read count, mapping percentage and genome coverage from each sample in FAIRE-seq and DNase-seq.</p> <p><strong>Supplementary File 2:</strong> List of DHSs obtained from control and stress subjected samples.</p> <p><strong>Supplementary File 3:</strong> List of FIRs obtained from control and stress subjected samples.</p> <p><strong>Supplementary File 4:</strong> List of uniquely merged OCRs with respective chromatin accessibility score in cold, heat, salt and drought stress.</p> <p><strong>Supplementary File 5:</strong> List of GO terms enriched in nrOCRs, SRCRs, and SACRs.</p> <p><strong>Supplementary File 6:</strong> List of GO terms enriched in overlapping nrOCRs, SRCRs, and SACRs.</p> <p><strong>Supplementary File 7:</strong> List of digital footprints (DFPs) obtained from nrOCRs regions of control-cold, control-heat, control-salt and control-drought pairs.</p> <p><strong>Supplementary File 8: </strong>Annotation details of the chromatin regions which were either found to be in state of accessible (CAS > 0.2) or inaccessible (CAS < -0.2) upon exposure to all of the stresses studied (heat, cold, salt and drought stress).</p> <p><strong>Supplementary Fig S1: Overlap of DHSs in control sample of present study with previously published studies.</strong></p> <p>A Venn diagram showing overlap of DNase hypersensitive sites (DHSs) found in control sample of present study and Zhang et al 2010 (<strong>A</strong>) and Sullivan et al 2014 (<strong>B</strong>). The statistical significance of overlap is calculate using hypergeometric Fischer`s exact test.</p> <p><strong>Supplementary Fig S2: Genomic locations of DHSs and FIRs</strong></p> <p>A line diagram representing the genomic location of unique DHSs and FIRs over each chromosome. DHSs/FIRs identified from each sample were merged to generate unique non-redundant subset of DHSs/FIRs before plotting over genome.</p> <p><strong>Supplementary Fig S3: Validation of correlation between OCRs and gene expression using microarray.</strong></p> <p>Box plot representing expression of genes (log10(normalised expression)) whose various structual elements fall in OCRs.</p> <p><strong>Supplementary Fig S4: First exons are highly enriched in both DHSs and FIRs</strong></p> <p> A bar plot showing presence of uFIRs, uDHSs, and ovOCRs in various positions of exon in Arabidopsis genes. The X-axis represent the exon number whereas Y-axis represent the fraction of OCRs found in each exon number.</p> <p><strong>Supplementary Fig S5: Validation of correlation between Ha-SACRs/Ha-SRCRs and gene expression using microarray.</strong></p> <p>Relative expression of genes (log2 fold change) corresponding to Ha-SACRs (Top) and (Ha-SRCRs (bottom) in cold (A), heat (B), salt (C) and drought (D) stress are plotted as box plot (p- value from Mann-Whitney test). To further compare RNA-seq data of salt stress with microarray, RNA-seq data was down-sampled to include genes which were also present in microarray data (E).</p> <p><strong>Supplementary Fig S6: Genomic location of SACRs and SRCRs found in Drought sample.</strong></p> <p>A snapshot of Integrative Genome Viewer (IGV) showing genomic location of stress activated chromatin regions (SACRs) and stress repressed chromatin region (SRCRs) in drought sample. The location of the centromere on each chromosome is shown as green bar IGV track.</p>
16S gene and ASV sequences of bacteria isolated from soil and the phyllosphere of Arabidopsis thaliana
<p>Data from "Induction of antibiotic specialized metabolism by co-culturing in a collection of phyllosphere bacteria" by Qi et al. </p> <p>- 16S gene sequences of bacteria isolated from soil and the phyllosphere of Arabidopsis thaliana in FASTA format. </p> <p>- Filtered OTU (ASV) table across all samples </p> <p>- ASV sequences</p>
Data from: Local adaptation (mostly) remains local: reassessing environmental associations of climate-related candidate SNPs in Arabidopsis halleri
<p>Numerous landscape genomic studies have identified single-nucleotide polymorphisms (SNPs) and genes potentially involved in local adaptation. Rarely, it has been explicitly evaluated whether these environmental associations also hold true beyond the populations studied. We tested whether putatively adaptive SNPs in <em>Arabidopsis</em> <em>halleri</em> (Brassicaceae), characterized in a previous study investigating local adaptation to a highly heterogeneous environment, show the same environmental associations in an independent, geographically enlarged set of 18 populations. We analysed new SNP data of 444 plants with the same methodology (partial Mantel tests, PMTs) as in the original study and additionally with a latent factor mixed model (LFMM) approach. Of the 74 candidate SNPs, 41% (PMTs) and 51% (LFMM) were associated with environmental factors in the independent data set. However, only 5% (PMTs) and 15% (LFMM) of the associations showed the same environment–allele relationships as in the original study. In total, we found 11 genes (31%) containing the same association in the original and independent data set. These can be considered prime candidate genes for environmental adaptation at a broader geographical scale. Our results suggest that selection pressures in highly heterogeneous alpine environments vary locally and signatures of selection are likely to be population-specific. Thus, genotype-by-environment interactions underlying adaptation are more heterogeneous and complex than is often assumed, which might represent a problem when testing for adaptation at specific loci.</p>
Effect of shade and nitrogen content on Arabidopsis Col-0 and cytokinin mutants abcg14 and cypDM mRNA-seq gene expression processed tables.
<p>This dataset is an add-on for Gautrat et al., containing processed files for the mRNAseq data in tab delimited txt format.</p> <p>Here, you can obtain the raw counts file, the normalized CPM values, and the normalized logCPM values</p> <p>The RNA-seq raw data supporting the conclusions of this article have been deposited in ArrayExpress (Kolesnikov et al., 2015) at EMBL-EBI (www.ebi.ac.uk/arrayexpress), under accession numbers E-MTAB-13638.</p> <p>All relevant custom r scripts are available at https://github.com/aromanowski/shade_N_ck</p>
Spatiotemporally distinct responses to mechanical forces shape the developing seed of Arabidopsis
<p><span>Source Data File related to the manuscript:</span></p> <p><a name="_Hlk141697088"></a><span> </span></p> <p><span>Spatiotemporally distinct responses to mechanical forces</span></p> <p><span>shape the developing seed of Arabidopsis</span></p> <p> </p> <p><span>See Description Dataset file for full description</span></p> <p><span> </span></p>
qPCR analysis: Arabidopsis AGO1 N-terminal extension acts as an essential hub for PRMT5 interaction and post-translational modifications
<p>Arabidopsis AGO1 N-terminal extension acts as an essential hub for PRMT5 interaction and post-translational modifications' qPCR data following the MIQE guidelines.</p>
Nitrogen resorption dynamics and slow-fast strategies in 137 Arabidopsis thaliana genotypes
<p>Leaf nitrogen resorption efficiency (R_efficiency, %) and the relative maximum resorption rate of nitrogen (R_rate_max_perN, mg d<sup>-1</sup> mg<sup>-1</sup>) were estimated together with the flowering time (FT, days after germination) and specific leaf area (SLA, m<sup>2</sup> kg<sup>-1</sup>) in 137 Arabidopsis thaliana accessions selected from the 1001 genomes project accession list. The dataset contains genotype means for every measured accession.</p>
Sphingolipids are involved in Pieris brassicae egg-induced cell death in Arabidopsis thaliana
<p>This table contains mean + SEM values of sphingolipid levels by LC-MS analysis in Arabidopsis thaliana (wild-type and mutant lines) and Brassica nigra (wild-type) in response to egg extract of Pieris brassicae, as well as P-values for selected comparisons by Welsch t-test. These data were used for Fig. 7 and Fig. 8 of Groux et al. 2022</p> <p> </p> <p> </p> <p> </p>
Phenotypic plasticity and genetic diversity in a polyploid Arabidopsis complex
<p class="MsoNormal"><span>Polyploid species possess more than two sets of chromosomes and may show high gene redundancy, hybrid vigor and masking of deleterious alleles compared to their parent species. Following this, it is hypothesized that this makes them better at adapting to novel environments than their parent species, possibly due to phenotypic plasticity. The allopolyploid <em>Arabidopsis suecica </em>and its parent species <em>A. arenosa</em> and <em>A. thaliana</em> were chosen as a model system to investigate relationships between phenotypic plasticity, fitness and genetic variation. Particularly, we test if <em>A. suecica</em> is more plastic, show higher genetic diversity and/or have higher fitness than its parent species. Wild Norwegian populations of each species were analyzed for phenotypic responses to differences in availability of nutrient, water and light, while genetic diversity was assessed through analysis of AFLP markers. <em>Arabidopsis arenosa</em> showed a higher level of phenotypic plasticity and higher levels of genetic diversity than the two other species, probably related to its outbreeding reproduction strategy. Furthermore, a general positive relationship between genetic diversity and phenotypic plasticity was found. Low genetic diversity were found in the inbreeding <em>A. thaliana</em>. Geographic spacing of populations might explain the clear genetic structure in <em>A. arenosa</em>, while the lack of structure in <em>A. suecica </em>could be due to coherent populations. Fitness measured as allocation of resources to reproduction, pointed towards <em>A. arenosa</em> having lower fitness under poor environmental conditions. <em>Arabidopsis </em><em>suecica</em>, on the other hand, showed tendencies towards keeping up fitness under different environmental conditions. </span></p>
Effects of sub-lethal single, simultaneous, and sequential abiotic stresses on phenotypic traits of Arabidopsis thaliana
<p>Data and code from: "Effects of sub-lethal single, simultaneous, and sequential abiotic stresses on phenotypic traits of Arabidopsis thaliana" published at Annals of Botany PLANTS. This is a dataset on phenotypic traits of Arabidopsis in response to different abiotic stresses and a reproducible R script to generate all figures and tables in the publication.</p>
Volumetric imaging of Arabidopsis thaliana root cells
<p><em>Arabidopsis thaliana</em> seeds were surface sterilized, germinated and grown in Murashigue and Skoog medium at pH 5.7 and supplemented with vitamins (0.1 mg l-1 pyridoxine, 0.1 mg l-1 nicotinic acid), 0.8% agar, and 1% sucrose. Plants were grown at 21°C, 16/8-hour light/dark periods at 105 µmol/m<sup>2</sup>s<sup>2</sup> light intensity.</p> <p>Using a Zeiss Axiovert 200M microscope and a C-APO 63X, 1.2NA objective (Oberkochen, Germany), confocal volumetric imaging of the plant material was performed, with a pixel size of 404 nm and Z step size of 500 nm. Excitation of the sample was provided by a 488 nm laser, and a filter cube with 525/45 nm and 630/92 nm bandpass filters was used for yellow and red emission light collection, respectively.</p> <p>An inverted Olympus FV1000-IX81 confocal microscope equipped with a LUMFLN×60, 1.3NA S objective was used for root cell nuclear imaging. Sample excitation was achieved with a 543 nm laser and a BA560-660 filter was used for emission light collection. Pixel size was 41 nm, with a Z step size of 100 nm.</p> <p>A custom-built selective plane illumination microscopy (SPIM) system was used for imaging of primary root cells expressing p35s:H2B-R-RF. Sample excitation was achieved with a 561 nm laser using stroboscopic illumination. Emission was filtered via a multi-bandpass emission filter (Semrock, FF01-446/523/600/677-25 BrightLine). Volumetric imaging was done by mounting the sample on a four dimensional (XYZ, and Y rotation) motorized stage (Picard Industries). A sCMOS sensor (Hamamatsu, ORCA-Flash4.0 V2) was used for signal recording. The OpenSPIM plugin of µmanager (v.1.4 for windows) was used for control of acquisition parameters, sample translation and stroboscopic illumination. Collected images had a pixel size of 0.325µm, Z step size of 100 nm and a Y rotation step of 1.8°.</p> <p>Experimental procedures were approved by the Bioethics Committee of the Biotechnology Institute of the National Autonomous University of Mexico.</p>
Historical Arabidopsis thaliana genomes from Germany
<p>We report short-read Illumina sequencing of 35 <em>Arabidopsis thaliana</em> herbarium specimens collected in Southern Germany from 1817 to 1957. The historical genomes were sequenced to an average depth of ~7X. The herbarium-derived sequences showed patterns of degradation typical of ancient DNA with average read lengths of 78 bp, endogenous DNA content between 26%-93% (mean 72%; median 74%) and enrichment of cytosine to thymine substitutions at the read’s termini. We provide the sequences to the public with open access.</p>
Evolutionary potential under heat and drought stress at the southern range edge of North American Arabidopsis lyrata
<p>The warm edges of species' distributions are vulnerable to global warming. Evidence is the recent range retraction from there found in many species. It is unclear why populations cannot easily adapt to warmer, drier, or combined hot and dry conditions and locally persist. Here, we assessed the ability to adapt to these stressors in the temperate species <em>Arabidopsis lyrata</em>. We grew plants from replicate seed families of a central population with high genetic diversity under a temperature and precipitation regime typical of the low-latitude margin or under hotter and/or drier conditions within naturally occurring amplitudes. We then calculated genetic variance-covariance (G-) matrices of traits depicting growth and allocation as well as selection vectors to compare the predicted adaptation potential under the different climate-stress regimes. We found that the sum of genetic variances and genetic correlations were not significantly different under stress as compared to benign conditions. However, under drought and heat drought, the predicted ability to adapt was severely constrained due to strong selection and selection pointing in a direction with less multivariate genetic variation. The much-reduced ability to adapt to dry and hot-dry conditions is likely to reduce the persistence of populations at the low-latitude margin of the species' distribution and contribute to the local extinction of the species under further warming.</p>
Raster Image Correlation Spectroscopy and Brightness Measurements of AtLEA proteins from Arabidopsis thaliana
<p>Temporal sequences of various fluorescent leaves were captured using a confocal scanning microscope (Olympus FV1000 inverted microscope), equipped with a 1.3 NA oil immersion 60X objective and the photon counting detection mode. Utilizing a 488 nm laser at 0.1% power and GFP filters/cubes, each temporal sequence involved the acquisition of 100 frames of 64x64 pixels, with a dwell time of 10 μs (1.76 ms per line, 130.24 ms per frame) and a pixel size of 66 nm (50X digital zoom). The interval between frames was set at 131.6 ms.</p> <p>Five plants were analyzed, each expressing one of four distinct genetic constructs fused to complementary fragments of Yellow Fluorescent Protein: pYFN-4-/5pYFC-4-5 (representing the complete AtLEA4-5 protein), pYFN-4-51-77/pYFC-4-51-77 (associated with the N-terminal region of AtLEA4-5), pYFN-4-578-158/pYFC-4-578-158 (relating to the C-terminal region of AtLEA4-5), and pYFN-pYFC (serving as the control). The raw data (*.oib files) were collected during three imaging sessions within a one-week period:</p> <p>- 220618 raw oib dataset.zip</p> <p>- 220622 raw oib dataset.zip</p> <p>- 220623 raw oib dataset.zip</p> <p>Images were converted to *.tif format using FIJI/ImageJ for further analysis and were archived in "tif dataset RICS NB LEAs.zip," excluding files with excessive movement of biological specimens. These images were then subjected to "Raster Image Correlation Spectroscopy" and "Number and Brightness" techniques for analysis.</p> <p>Notation:</p> <p>- h1, h2, h3, h4, h5: Replicates (plants) expressing one of four specific genetic constructs fused to complementary fragments of Yellow Fluorescent Protein.</p> <p>- 45: Fused to the full-length AtLEA4-5 protein (pYFN-4-/5pYFC-4-5).</p> <p>- 4h: Fused to the N-terminal region of AtLEA4-5 (pYFN-4-51-77/pYFC-4-51-77).</p> <p>- rc: Fused to the C-terminal region of AtLEA4-5 (pYFN-4-578-158/pYFC-4-578-158).</p> <p>- ct: The control condition (pYFN-pYFC).</p>
Indirect genetic effects are shaped by demographic history and ecology in Arabidopsis thaliana
<p><em>This folder contains data & code used for the study "Indirect genetic effects are shaped by demographic history and ecology in Arabidopsis thaliana"</em></p> <p>All data analyzed in the study are stored in the folder "data":</p> <ul> <li>"pheno_file.csv": the main phenotypic file corresponding to the experiment with paired plants used to estimate Indirect Genetic Effects.</li> <li>"pheno_file_single_plants.csv": phenotypic file with measurements of plant biomasses in the absence of competition (single plants)</li> <li>"call_method_75_TAIR9.csv": genomic data (SNPs) for each accession from the RegMap panel (ref [1])</li> <li>"Data_geo_RegMap_accessions.csv": geographic localization of each accession from the RegMap panel (ref [2])</li> <li>"igeGWAS_scores.csv": Genome-Wide Association Study (GWAS) results reporting for each SNP from the RegMap panel the p-value and estimated effect sizes of their direct and indirect genetic effects</li> <li>"1001_accessions_info.csv": geographic localization and admixture group for each accession from the 1001 genomes project (ref [3])</li> <li>"snp_data_all_samples.txt": allelic value of each accession from the 1001 genomes project at the eleven top SNPs associated with IGE</li> <li>"sample_names.txt": names of accessions listed in the file "snp_data_all_samples.txt"</li> <li>"climatic_data.csv": climatic data for each accessions from the 1001 genomes project (ref [4])</li> <li>"candidate_genes_all.csv": list of all genes (and associated GO terms) with a non-synonymous, nonsense, or frameshift mutation in close proximity (distance < half LD decay distance) and high linkage (r2>0.5) with a SNP significantly associated with IGE</li> <li>"genes.coord.bed": list of all genes in a +- 500 kb around top IGE SNPs and their coordinates</li> <li>"AllGenes_fst.GeneID.txt": pairwise Fst computed between each pair of admixture groups, for all genes annotated in the genome of A. thaliana</li> </ul> <p>"ABBA_BABA" subfolder contains ABBA_BABA statistics computed for each individual chromosome (Chr1-Chr5) using genomic windows of 20 kb with at least 250 SNPs per windows. ABBA-BABA statistics were computed using custom python scripts from https://github.com/simonhmartin/genomics_general</p> <p><br> "GEA" subfolder contains Genome-Environment Association results, with one file per chromosome x climatic variable. Climatique variable are indexed, following the order listed in the file "Climatic_variables.txt" within the subfolder "GEA". GEA analysis were run with the gemma program: https://github.com/genetics-statistics/GEMMA.</p> <p><br> "LD_IGE_SNPs" subfolders contains the list of SNPs located at +- 2Mb of a significant IGE SNP (one file per IGE SNP, named "SNPalias_LDSimplified.csv") and their linkage (r2) with the IGE SNP. It also contains the file "LD_windows_sizes.csv" with the half LD decay distances for all significant IGE SNP.</p> <p>All analysis performed to produce the tables and figures presented in the study (main manuscript & supplementary information) were done with the R script "Arabidopsis_IGE_analysis.R", which uses "manhattan_custom.R" as a source function to produce custom manhattan plots.</p> <p> </p> <p><strong>REFERENCES:</strong></p> <p>[1] Horton MW, Hancock AM, Huang YS, Toomajian C, Atwell S, Auton A, Muliyati NW, Platt A, Sperone FG, Vilhjálmsson BJ, et al. 2012. Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel. Nature Genetics 44: 212–216.</p> <p>[2] Anastasio AE, Platt A, Horton M, Grotewold E, Scholl R, Borevitz JO, Nordborg M, Bergelson J. 2011. Source verification of mis-identified Arabidopsis thaliana accessions. The Plant Journal 67: 554–566.</p> <p>[3] 1001 Genomes Consortium. 2016. 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell 166: 481–491.</p> <p>[4] Ferrero-Serrano Á, Assmann SM. 2019. Phenotypic and genome-wide association with the local environment of Arabidopsis. Nature Ecology & Evolution 3: 274–285.</p>
Data from: Genome-wide association mapping within a local Arabidopsis thaliana population more fully reveals the genetic architecture for defensive metabolite diversity
<p>A paradoxical finding from genome-wide association studies (GWAS) in plants is that variation in metabolite profiles typically maps to a small number of loci, despite the complexity of underlying biosynthetic pathways. This discrepancy may partially arise from limitations presented by geographically diverse mapping panels. Properties of metabolic pathways that impede GWAS by diluting the additive effect of a causal variant, such as allelic and genic heterogeneity and epistasis, would be expected to increase in severity with the geographic range of the mapping panel. We hypothesized that a population from a single locality would reveal an expanded set of associated loci. We tested this in a French <em>Arabidopsis thaliana</em> population (< 1 km transect) by profiling and conducting GWAS for glucosinolates, a suite of defensive metabolites that have been studied in depth through functional and genetic mapping approaches. For two distinct classes of glucosinolates, we discovered more associations at biosynthetic loci than previous GWAS with continental-scale mapping panels. Candidate genes underlying novel associations were supported by concordance between their observed effects in the TOU-A population and previous functional genetic and biochemical characterization. Local populations complement geographically diverse mapping panels to reveal a more complete genetic architecture for metabolic traits.</p>
Arabidopsis RNA-seq seedling small training set (chr1 100k)
<p>Arabidopsis seedling small training set for RNA-seq. FastQ files for reads mapping to the first 100k of the first chromosome of Arabidopsis are included. The sequencing was done using Illumina, 100 paired-end mode. </p>
Salt stress responses in 9 Arabidopsis accessions
<p>The dataset is used as an example dataset for the MVApp, previously published the results in Awlia et al., 2016 Frontiers in Plant Science.</p>
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