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1,715 results for “Arabidopsis thaliana; Arabidopsis”
Supplementary File to "Both binding strength and evolutionary accessibility affect the population frequency of transcription factor binding sequences in Arabidopsis thaliana" (Genome Biology and Evolution)
<p>This data is supplementary file 1 of the following publication:</p> <p>Schweizer G, Wagner A. "Both binding strength and evolutionary accessibility affect the population frequency of transcription factor binding sequences in Arabidopsis thaliana" (Genome Biology and Evolution)</p>
Spatio-temporal dynamics of genetic variation at the quantitative and molecular levels within a natural Arabidopsis thaliana population
<p><span>Evolutionary change begins at the population scale. Therefore, understanding adaptive variation requires the identification of the factors maintaining and shaping standing genetic variation at the within-population level. Spatial and temporal environmental heterogeneity represent ecological drivers of within-population genetic variation, determining the evolutionary trajectory of populations along with random processes. Here, we focused on the effects of </span><span>spatio-temporal heterogeneity on quantitative and molecular variation in a natural population of the annual plant <em>Arabidopsis thaliana</em>.</span></p> <p><span>We sampled 1,093 individuals from a Spanish <em>A. thaliana </em>population across an area of 7.4 ha for 10 years (2012-2021). Based on a sample of 279 maternal lines, we estimated spatio-temporal variation in life-history traits and fitness from a common garden experiment. We genotyped 884 individuals with nuclear microsatellites to estimate spatio-temporal variation in genetic diversity. We assessed spatial patterns by estimating spatial autocorrelation of traits and fine-scale genetic structure. We analyzed the relationships between phenotypic variation, geographic location and genetic relatedness, as well as the effects of environmental suitability and genetic rarity on phenotypic variation. </span></p> <p><span>The common garden experiment indicated that there was more temporal than spatial variation in life-history traits and fitness. Despite the differences among years, genetic distance in ecologically relevant traits (e.g. flowering time) tended to be positively correlated to genetic distance among maternal lines, whilst isolation by distance was less important. Genetic diversity exhibited significant spatial structure at short distances, which were consistent among years. Finally, genetic rarity, and not environmental suitability, accounted for genetic variation in life-history traits.</span></p> <p><span>Synthesis. Our study highlighted the importance of repeated sampling to detect the large amount of genetic diversity at the quantitative and molecular levels that a single <em>A. thaliana</em> population can harbor. Overall, population genetic attributes estimated from our long-term monitoring scheme (genetic relatedness and genetic rarity), rather than biological (dispersal) or ecological (vegetation types and environmental suitability) factors, emerged as the most important drivers of within-population structure of phenotypic variation in <em>A. thaliana.</em></span></p>
Draft genome sequences of Arabidopsis thaliana-associated micro-organisms from Reijerscamp soil, the Netherlands
<p><strong>Methodological summary and relevant references</strong></p> <p>Compressed tar archive containing 447 draft bacterial genomes and their annotations used in several studies including Fourie <em>et al</em>. (2024; in review) and Selten et al. (2024; in prep). Genome sequences are obtained by Illumina-only sequencing of microbial cultures. Illumina reads were demultiplexed and cleaned with cutadapt (version 2.8) (Martin, 2011) and assembled into genomes using A5 (A5-miseq version 20160825) (Coil et al., 2014). Genome contamination and heterogeneity was checked with CheckM (version 1.1.3) (Parks et al., 2015) and any genomes with multiple single copy gene occurrences were subjected to MaxBin (version 2.2.7) (Wu et al., 2014) to separate the genomes from contaminated bacterial cultures. Any non-bacterial contigs in the genome assemblies were removed using MMSeqs2 (version 13.45111) (Steineigger & Schöding, 2017). Open reading frames were found and annotated by PROKKA (version 1.14.6) (Seemann, 2014) and EggNOG (version 2.1.4-2) (Cantalapiedra et al., 2021) respectively. Microbial cultures were derived from <em>Arabidopsis thaliana</em> roots grown in Reijerscamp soil, described in Stringlis <em>et al</em>., 2018 https://doi.org/10.1073/pnas.1722335115.</p> <p><strong>The uploaded files are</strong></p> <ol> <li>Genome assemblies</li> <li>Prokka gene predictions in GFF3 format</li> <li>Predicted transcripts from genes in (2)</li> <li>Predicted proteins from genes in (2), and</li> <li>EggNOG annotations for the proteins in (4)</li> </ol> <p><strong>Genomes and annotations pending upload om NCBI GenBank (April 2024)</strong></p>
Potential Interactions of the 20 Arabidopsis thaliana Mitogen-Activated Protein Kinases (MPKs)
<p>A comprehensive dataset detailing potential interactions of the 20 <em>Arabidopsis thaliana</em> MPKs.</p>
Supplementary tables for manuscript Dynamics of alternative polyadenylation in single root cells of Arabidopsis thaliana
<p>Supplementary tables for manuscript Dynamics of alternative polyadenylation in single root cells of Arabidopsis thaliana</p>
Relate-inferred genealogies for 66 longread Arabidopsis thaliana genomes
<p>Relate-inferred genealogies for 66 longread Arabidopsis thaliana genomes.</p> <p>The genomes are the samples used in Wlodzimierz et al. 2023 (https://doi.org/10.1038/s41586-023-06062-z). </p> <p>longread-trees.tar.gz contains the output of Relate's estimate population size command (<a href="https://myersgroup.github.io/relate/modules.html#CoalescenceRate">https://myersgroup.github.io/relate/</a>modules.html#CoalescenceRate), including an anc/mut/dist/coal file for every chromosome. It also constains a tskit tree sequence (https://tskit.dev/) for each chromosome, converted from anc/mut.</p> <p>Thal_ref_Boec_Lyra_Malc_outgroups_nodupes_orthoonly.maf is the multi-species alignment (kindly provided by Tyler Kent, Adrian Platts, and the Brassicales Map Alignment Project (DOE-JGI, http://bmap.jgi.doe.gov/)) that we used to polarize the alleles.</p> <p>Snakefile is the code we used to generate the genealogies.</p>
Crystal structure of the LRR ectodomain from the plant immune receptor kinase SOBIR1 from Arabidopsis thaliana - native dataset
<p>This dataset includes the raw X-ray diffraction images collected on 02.02.2018 at beam line PXIII of the Swiss Light Source (SLS) Villigen, Switzerland. The dataset includes a .bz2 archive of the XDS processing, the resulting XDS_ASCII.HKL contains the integrated intensities. The corresponding coordinates and crystallographic structure factors have been deposited with the Protein Data Bank (http://rcsb.org) with ID 6R1H.</p>
Crystal structure of the LRR ectodomain from the plant immune receptor kinase SOBIR1 from Arabidopsis thaliana - sulphur SAD datasets
<p>This dataset includes the raw X-ray diffraction images collected on 06.11.2017 at beam line PXIII of the Swiss Light Source (SLS) Villigen, Switzerland. The archive native_images.tar contains a native dataset to 1.75 Å resolution (λ=1.033201 Å, 1 360° wedge at 0.1° oscillation). The archive ssad_images.tar contains redundant sulphur single-wavelength anomalous dispersion (SAD) data (λ= 2.078524 Å, 3 360° wedges at 0.1° oscillation) to 3.12 Å resolution. The xds_nat_ssad.tar.bz2 includes a .bz2 archive of the XDS processing for native and sulphur SAD data. Data were scaled together in xscale, the resulting xscale.hkl and nat1.hkl contain the integrated intensities and crystallographic structure factors. The corresponding coordinates have been deposited with the Protein Data Bank (http://rcsb.org) with ID 6R1H.</p>
The development of Arabidopsis thaliana under phosphate limiting conditions: The role of Strigolactones
<p>Phosphate (P) is one of the most limiting nutrients for plant development and is involved in photosynthesis, energy transmission and cell division amongst others. P occurs in organic and inorganic form but plants are only able to take up inorganic phosphate. Plants have evolved various mechanisms to deal with nutrient deficiencies. Recently research has been done on Strigolactones (SLs), carotenoid derived plant hormones. SL biosynthesis is upregulated under P deficiency and regulates branching, stem thickness, root architecture and leaf senescence. In this study, we looked at the role of SLs on development of <em>Arabidopsis thaliana </em>under P deprivation. A SL biosynthesis mutant (P450) and two SL perception mutants (D14, U-box) were examined when treated with and without phosphate. The effects of P deprivation on bolting time, biomass and photosynthetic capacity were examined. Photosynthetic capacity was measured by Pulse Amplitude Modulation (PAM). Significant differences between the treatment groups and genotypes were found in dry weight and Quantum Yield of Photosystem II (Y(II)), but no conclusion could be drawn from the overall results.</p>
Relate-inferred genealogies for 1552 Arabidopsis thaliana samples
<p>Relate-inferred genealogies for 1552 Arabidopsis thaliana samples.</p> <p>The genealogies for each of the 5 autosomes are given as .anc.gz and .mut.gz files.</p> <p>Each chromosome also has a .dist and .coal file, giving the space between mutations (accounting for genomic mask) and the inferred coalescence rates (inferred from trees on that chromosome only for the sake of computation time).</p> <p>keep.poplabels gives the IDs of the samples, in the order given to Relate. Since we filter out heterozygous sites, there is only one sample for each diploid individual.</p> <p>Pipeline given in Snakefile with Python environment given in requirements.txt.</p> <p>Genetic data from Durvasula et al 2017 (https://www.pnas.org/doi/abs/10.1073/pnas.1616736114), https://www.ebi.ac.uk/ena/browser/view/PRJEB44201?show=analyses.</p> <p>The .maf file is the multi-species alignment (kindly provided by Tyler Kent, Adrian Platts, and the Brassicales Map Alignment Project (DOE-JGI, http://bmap.jgi.doe.gov/)) that we used to polarize the alleles.</p> <p>Please don't hesitate to get in touch with questions.</p> <p>Matt</p>
Data from: Independent FLC mutations as causes of flowering time variation in Arabidopsis thaliana and Capsella rubella
Capsella rubella is an inbreeding annual forb closely related to Arabidopsis thaliana, a model species widely used for studying natural variation in adaptive traits such as flowering time. Although mutations in dozens of genes can affect flowering of A. thaliana in the laboratory, only a handful of such genes vary in natural populations. Chief among these are FRIGIDA (FRI) and FLOWERING LOCUS C (FLC). Common and rare FRI mutations along with rare FLC mutations explain a large fraction of flowering-time variation in A. thaliana. Here we document flowering time under different conditions in 20 C. rubella accessions from across the species' range. Similar to A. thaliana, vernalization, long photoperiods and elevated ambient temperature generally promote flowering. In this collection of C. rubella accessions, we did not find any obvious loss-of-function FRI alleles. Using mapping-by-sequencing with two strains that have contrasting flowering behaviors, we identified a splice-site mutation in FLC as the likely cause of early flowering in accession 1408. However, other similarly early C. rubella accessions did not share this mutation. We conclude that the genetic basis of flowering-time variation in C. rubella is complex, despite this very young species having undergone an extreme genetic bottleneck when it split from C. grandiflora a few tens of thousands of years ago.
Data from: Temporal variation in genetic diversity and effective population size of Mediterranean and subalpine Arabidopsis thaliana populations
Currently there exists a limited knowledge on the extent of temporal variation in population genetic parameters of natural populations. Here we study the extent of temporal variation in population genetics by genotyping 151 genome-wide SNP markers polymorphic in 466 individuals collected from nine populations of the annual plant Arabidopsis thaliana during four years. Populations are located along an altitudinal climatic gradient from Mediterranean to subalpine environments in NE Spain, which has been shown to influence key demographic attributes and life-cycle adaptations. Genetically, A. thaliana populations were more variable across space than over time. Common multilocus genotypes were detected several years in the same population, whereas low-frequency multilocus genotypes appeared only one year. High-elevation populations were genetically poorer and more variable over time than low-elevation populations, which might be caused by a higher overall demographic instability at higher altitudes. Estimated effective population sizes were very low but also showed a significant decreasing trend with increasing altitude, suggesting a deeper impact of genetic drift at high-elevation populations. In comparison with single-year samplings, repeated genotyping over time captured substantially higher amount of genetic variation contained in A. thaliana populations. Furthermore, repeated genotyping of populations provided novel information on the genetic properties of A. thaliana populations and allowed hypothesizing on their underlying mechanisms. Therefore, including temporal genotyping programs into traditional population genetic studies can significantly increase our understanding of the dynamics of natural populations.
Supporting Data for "Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes"
<p>This dataset contains supporting files referenced by the following publication:</p> <p>• Rabanal FA, Gräff M, Lanz C, Fritschi K, Llaca V, Lang M, Carbonell-Bejerano P, Henderson I, Weigel D. <strong>Pushing the limits of HiFi assemblies reveals centromere diversity between two <em>Arabidopsis thaliana</em> genomes</strong>. <em>Nucleic Acids Research</em>. doi: 10.1093/nar/gkac1115</p> <p> </p> <p>Directory structure:</p> <ul> <li><strong>Bionano_optical_maps_based_assemblies</strong>: this directory contains results from the Bionano optical map based scaffolding for the main long-read assemblers analysed in the study for <em>Arabidopsis thaliana</em> accession Ey15-2 (9994): <ul> <li><strong>9994.CLR_Canu</strong></li> <li><strong>9994.HiFi_FALCON</strong></li> <li><strong>9994.HiFi_HiCanu</strong></li> <li><strong>9994.HiFi_Hifiasm</strong></li> <li><strong>9994.HiFi_IPA</strong></li> <li><strong>9994.HiFi_Peregrine</strong></li> </ul> </li> </ul> <p> </p> <ul> <li><strong>Col-0_HiFi-Hifiasm_assembly</strong>: this directory contains the Pacbio HiFi based chromosome level assembly (fasta file) and repeat annotation (gff file) of <em>Arabidopsis thaliana</em> accession Col-0 (6909). </li> </ul> <p> </p> <ul> <li><strong>Ey15-2_HiFi-Hifiasm_plus_CLR-Canu_assembly</strong>: this directory contains the Pacbio HiFi+CLR based chromosome level assembly (fasta file) and repeat annotation (gff file) of <em>Arabidopsis thaliana</em> accession Ey15-2 (9994). </li> </ul> <p> </p> <ul> <li><strong>Naish2021_Wang2021_repeat_annotation</strong>: this directory contains the repeat annotation (gff files) for the <em>Arabidopsis thaliana</em> Col-0 (6909) assemblies performed by Naish <em>et al.</em> (doi: 10.1126/science.abi7489) and Wang <em>et al.</em> (doi: 10.1016/j.gpb.2021.08.003). </li> </ul> <p> </p> <ul> <li><strong>TAIR10_masked</strong>: this directory contains the repeat-hard-masked version of the TAIR10 <em>Arabidopsis thaliana</em> Col-0 (6909) reference genome that was used for in silico scaffolding of contigs with RagTag (<a href="http://github.com/malonge/RagTag">https://github.com/malonge/RagTag</a>).</li> </ul> <p> </p>
Seed dormancy varies widely among Arabidopsis thaliana populations both between and within Fennoscandia and Italy
<p>The timing of germination is a key life-history trait in plants, which is strongly affected by the strength of seed dormancy. Continental-wide genetic variation in seed dormancy has been related to differences in climate and the timing of conditions suitable for seedling establishment. However, for predictions of adaptive potential and consequences of climatic change, information is needed regarding the extent to which seed dormancy varies within climatic regions and the factors driving such variation. We quantified dormancy of seeds produced by 17 Italian and 28 Fennoscandian populations of <em>Arabidopsis thaliana</em> when grown in the greenhouse and at two field sites in Italy and Sweden. To identify possible drivers of among-population variation in seed dormancy, we examined the relationship between seed dormancy and climate at the site of population origin, and between seed dormancy and flowering time. Seed dormancy was on average stronger in the Italian compared to the Fennoscandian populations, but also varied widely within both regions. Estimates of seed dormancy in the three maternal environments were positively correlated. Among Fennoscandian populations, seed dormancy tended to increase with increasing summer temperature and decreasing precipitation at the site of population origin. In the smaller sample of Italian populations, no significant association was detected between mean seed dormancy and climate at the site of origin. The correlation between population mean seed dormancy and flowering time was weak and not statistically significant within regions. The correlation between seed dormancy and climatic factors in Fennoscandia suggests that at least some of the among-population variation is adaptive and that climate change will affect selection on this trait. The weak correlation between population mean seed dormancy and flowering time indicates that the two traits can evolve independently.</p>
Images of colony growth for 224 Arabidopsis thaliana bacterial strains on 46 carbon sources
<p>This repository contains all data necessary to score colony growth on agar plates using the software tool 'platescan' (github.com/MicrobiologyETHZ/platescan) for the strains presented in Schäfer, Pacheco, et al.</p> <p>The growth of the 224 strains was split into 3 screens. Rounds 1, 2, and half of 3 comprised the core of the screen for all strains, and the second half of 3 comprised the validation set for computing the false discovery rate. The directories containing the images, as well as their corresponding metadata files, are named accordingly:</p> <p> pictures_7dps_screen_*: folders contain pictures of screening plates to assess growth on tested garbon sources. Pictures were taken 7 days after spotting strains on the plates.</p> <p> *_d7_filenames.txt: files link the picture filename to the carbon source that was tested. In addition the screening round and the plate number within the screening round is indicated.</p> <p> strain_metadata_screen*.txt: files indicate the position of the strains on the test plates [row (alphabetical), row (numbered), column (numbered)] and additional comments relevant for analysis (swarmer). Screen_nr and plate_number allow to link data to the corresponding pictures.</p> <p>This repository additionally includes a script to perform downstream processing of the platescan software output,</p> <p> plate_scan_analysis.R.</p> <p>and a file reporting the latescan output values that were manually overwritten due to contamination or poor image quality</p> <p> manual_correction.txt.</p>
Genome-Wide Association Studies meta-analysis uncovers NOJO and SGS3 novel genes involved in Arabidopsis thaliana primary root development and plasticity
<p>Postembryonic primary root growth relies on meristems that harbour multipotent stem cells that produce new cells that will duplicate and provide all the different root cell types. <em>Arabidopsis thaliana</em> primary root growth has become a model for evo-devo studies due to its simplicity and facility to record cell proliferation and differentiation. To identify new genetic components relevant to primary root growth, we used a Genome-Wide Association Studies (GWAS) meta-analysis approach using data published in the last decade. In this work, we performed intra and inter-studies analyses to discover new genetic components that could participate in primary root growth. We used 639 accessions from nine different studies and performed different GWAS tests ranging from single studies and pairwise analysis with high correlation associations, analyzing the same number of accessions in different studies to using the daily data of the root growth kinetic of the same research. We found that primary root growth changes were associated with 41 genomic loci, of which six (14.6%) have been previously described as inhibitors or promoters of primary root growth. The knockdown of genes associated with two of these loci: a gene that participates in Trans-acting siRNAs (tasiRNAs) processing <em>Suppressor of Gene Silencing</em> (<em>SGS3</em>) and a gene with a Sterile Alpha Motif (SAM) confirmed their participation as repressors of primary root growth. As none has been shown to participate in this developmental process before, our GWAS analysis identified new genes that participate in primary root growth. Overall, our findings provide novel insights into the genomic basis of root development and further demonstrate the usefulness of GWAS meta-analyses in non-human species.</p>
Fig. 5 in Labdane diterpenoids from the heartwood of Leucosceptrum canum that impact on root growth and seed germination of Arabidopsis thaliana
Fig. 5. Biological function of leucolactones A-K (1–11) on the growth and development of Arabidopsis thaliana. (A) Seed germination rate of A. thaliana on MS-agar plates in the presence of 10, 20, 30, 40 μM compound 8. Different letters represent significant differences (one-way ANOVA followed by Tukey's test, P <0.05). (B–D) A. thaliana seedlings after 5 days on MS-agar plates containing 0.1% ethanol (B), 10 μM compound 8 (C), 20 μM compound 8 (D); (E–F) Effect of compound 8 on auxin reporter of A. thaliana DR5::GUS after 24 h incubation in solution with 0.1% ethanol (E) or 20 μM compound 8 (F). The images were representatives of at least three independent experiments with>25 seedlings examined for each experiment.
Fig. 8 in Rosmarinic acid and hesperidin regulate gas exchange, chlorophyll fluorescence, antioxidant system and the fatty acid biosynthesis-related gene expression in Arabidopsis thaliana under heat stress
Fig. 8. The changes of the relative expression of WRI1 (A), BCCP2 (B), FAD2 (C), FAD3 (D) genes encoding after rosmarinic acid (RA, 100 μM) and/or hesperidin (HP, 100 μM) with/without heat stress (38 ◦C) in A. thaliana leaves. Multivariate data analyses of gene expression analysis under investigation.
Fig. 5 in Rosmarinic acid and hesperidin regulate gas exchange, chlorophyll fluorescence, antioxidant system and the fatty acid biosynthesis-related gene expression in Arabidopsis thaliana under heat stress
Fig. 5. The changes of the relative band intensity of different types of glutathione S-transferase activity isoenzymes (GST, A) and GST activity (B), and glutathione peroxidase activity (GPX, C) after rosmarinic acid (RA, 100 μM) and/or hesperidin (HP, 100 μM) with/without heat stress (38 ◦C) in A. thaliana leaves.
Fig. 1 in Rosmarinic acid and hesperidin regulate gas exchange, chlorophyll fluorescence, antioxidant system and the fatty acid biosynthesis-related gene expression in Arabidopsis thaliana under heat stress
Fig. 1. The average absorption per active reaction center (ABS/RC), the electron transport flux per active reaction center (ETo/RC), the flux of trapped exciton per active reaction center (TRo/RC), and the energy flow on the acceptor side of PSI ((Ro), The number of QA-reducing reaction centers per PSII antenna chlorophyll ((ΦPo/(1-ΦPo)), the efficiency with which a trapped exciton transfers an electron to the photosynthetic electron transfer chain ((ΨEo/(1-ΨEo)), the number of QA- reducing reaction centers per PSII antenna chlorophyll (γRC/(1-γRC)), the ratio of total dissipation to the number of active reaction centers (DIo/RC). The relative variable fluorescence intensity at J (VJ) and I step (VI), the performance index based on light absorption (PIABS), and the performance index (potential) for energy conservation from exciton to PSI and acceptor reduction (PItotal) were determined in A. thaliana leaves following treatment with rosmarinic acid (RA, 100 μM) and/or hesperidin (HP, 100 μM) with/without heat stress (38 ◦ C).
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