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1,715 results for “Arabidopsis thaliana; Arabidopsis”
Data for: Weaker selection on genes with treatment-specific expression consistent with a limit on plasticity evolution in Arabidopsis thaliana
<p>Differential gene expression between environments often underlies phenotypic plasticity. However, environment-specific expression patterns are hypothesized to relax selection on genes, and thus limit plasticity evolution. We collated over 27 terabases of RNA-sequencing data on <em>Arabidopsis thaliana</em> from over 300 peer-reviewed studies and 200 treatment conditions to investigate this hypothesis. Consistent with relaxed selection, genes with more treatment-specific expression have higher levels of nucleotide diversity and divergence at nonsynonymous sites but lack stronger signals of positive selection. This result persisted even after controlling for expression level, gene length, GC content, the tissue specificity of expression, and technical variation between studies. Overall, our investigation supports the existence of a hypothesized trade-off between the environment specificity of a gene's expression and the strength of selection on said gene in <em>A. thaliana</em>. Future studies should leverage multiple genome-scale datasets to tease apart the contributions of many variables in limiting plasticity evolution.</p>
Revealing the lipidome and proteome of Arabidopsis thaliana plasma membrane
<p>This table contains peaks aera values from GC-MS, TLC-GC-MS and LC-MS for characterization of Arabidopsis thaliana plasma membrane. These data were used for Fig. 6, 7, 8, 9 and S1, S2, S3 and S4 of Bahammou et al. 2023: Revealing the lipidome and proteome of Arabidopsis thaliana plasma membrane</p>
Genome-wide association study of aphid abundance highlights a locus affecting plant growth and flowering in Arabidopsis thaliana
<div> <div>Plant life-history traits, such as size and flowering, contribute to shaping variation in herbivore abundance. Although plant genes involved in physical and chemical traits have been well studied, less is known about the loci linking plant life-history traits and herbivore abundance. Here, we conducted a genome-wide association study (GWAS) of aphid abundance in a field population of <em>Arabidopsis thaliana</em>. This GWAS of aphid abundance detected a relatively rare but significant variant on the third chromosome of <em>A. thaliana</em>, which was also suggestively but non-significantly associated with the presence or absence of inflorescence. Out of candidate genes near this significant variant, a mutant of a ribosomal gene (AT3G13882) exhibited slower growth and later flowering than a wild type under laboratory conditions. A no-choice assay with the turnip aphid, <em>Lipaphis erysimi</em>, found that aphids were unable to successfully establish on the mutant. Our genome-wide association study of aphid abundance unexpectedly found a locus affecting plant growth and flowering.</div> </div>
Stiffness transitions in new walls post-cell division differ between Marchantia polymorpha gemmae and Arabidopsis thaliana leaves
<p>Plant morphogenesis is governed by the mechanics of the cell wall–a stiff and thin polymeric box that encloses the cells. The cell wall is a highly dynamic composite material. New cell walls are added during cell division. As the cells continue to grow, the properties of cell walls are modulated to undergo significant changes in shape and size without breakage. Spatial and temporal variations in cell wall mechanical properties have been observed. However, how they<br> relate to cell division remains an outstanding question. Here we combine time-lapse imaging with local mechanical measurements via atomic force microscopy to systematically map the cell wall’s age and growth, with their stiffness. We make use of two systems, <em>M. polymorpha</em> gemmae, and <em>A. thaliana</em> leaves. We first characterise the growth and cell division of <em>M. polymorpha</em> gemmae. We then demonstrate that cell division in <em>M. polymorpha</em> gemmae results in<br> the generation of a temporary stiffer and slower growing new wall. In contrast, this transient phenomenon is absent in <em>A. thaliana</em> leaves. We provide evidence that this different temporal behaviour has a direct impact on the local cell geometry via changes in the junction angle. These results are expected to pave the way for developing more realistic plant morphogenetic models and to advance the study into the impact of cell division on tissue growth.</p>
Data from: Genome-wide association mapping within a local Arabidopsis thaliana population more fully reveals the genetic architecture for defensive metabolite diversity
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Plastid and peroxisome movement tracks in the root cells of Arabidopsis thaliana
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Genome-wide association study of aphid abundance highlights a locus affecting plant growth and flowering in Arabidopsis thaliana
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Data from: Predicting fitness in future climate: Insights from temporally replicated field experiments in Arabidopsis thaliana
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Data for: Weaker selection on genes with treatment-specific expression consistent with a limit on plasticity evolution in Arabidopsis thaliana
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Tandem Tag Assay Optimized for Semi-automated in vivo Autophagic Activity Measurement in Arabidopsis thaliana roots
<p>This is demo data set for AuTToFlux, the semi-automated assay for <em>in vivo</em> autophagic activity measurement in <em>Arabidopsis thaliana</em> roots.</p> <p>The protocol and software required for the assay are available here: <a href="https://github.com/jonasoh/AuTToFlux">https://github.com/jonasoh/AuTToFlux</a></p>
GWAS output for early salt stress responses in Arabidopsis thaliana accessions
<p>The output of the Genome Wide Association Study for early responses to salt stress in Arabidopsis accessions. The "_gwas2029.rda" files contain associations found for each trait using single models, where the first part of file name describes the phenotype (e.g. ROUNDNESS), the first number describes the day after stress application, the subsequent C/S indicated whether the association was performed with the trait scored at Control / Salt Stress conditions respectively. The "mtmm_final.rda" files contain the associations found between two traits, indicated as above in the first part of the file name. </p>
Data from: Genetic basis of photosynthetic responses to cold in two locally adapted populations of Arabidopsis thaliana
Local adaptation is common, but the traits and genes involved are often unknown. Physiological responses to cold probably contribute to local adaptation in wide-ranging species, but the genetic basis underlying natural variation in these traits has rarely been studied. Using a recombinant inbred (495 lines) mapping population from locally adapted populations of Arabidopsis thaliana from Sweden and Italy, we grew plants at low temperature and mapped quantitative trait loci (QTLs) for traits related to photosynthesis: maximal quantum efficiency (Fv/Fm), rapidly reversible photoprotection (NPQfast), and photoinhibition of PSII (NPQslow) using high-throughput, whole-plant measures of chlorophyll fluorescence. In response to cold, the Swedish line had greater values for all traits, and for every trait, large effect QTLs contributed to parental differences. We found one major QTL affecting all traits, as well as unique major QTLs for each trait. Six trait QTLs overlapped with previously published locally adaptive QTLs based on fitness measured in the native environments over 3 years. Our results demonstrate that photosynthetic responses to cold can vary dramatically within a species, and may predominantly be caused by a few QTLs of large effect. Some photosynthesis traits and QTLs probably contribute to local adaptation in this system.
Climate biogeography of Arabidopsis thaliana: Linking distribution models and individual variation
<p>Patterns of individual variation are key to testing hypotheses about the mechanisms underlying biogeographic patterns. If species distributions are determined by environmental constraints, then populations near range margins may have reduced performance and be adapted to harsher environments. Model organisms are potentially important systems for biogeographical studies, given the available range‐wide natural history collections, and the importance of providing biogeographical context to their genetic and phenotypic diversity. We fit occurrence records to climate data and then projected the distribution of <em>Arabidopsis</em> under the last glacial maximum, current, and future climates. We confronted model predictions with individual performance measured on 2194 herbarium specimens, and we asked whether predicted suitability was associated with life history and genomic variation measured on ~900 natural accessions. The most important climate variables constraining the <em>Arabidopsis</em> distribution were winter cold in northern and high-elevation regions and summer heat in southern regions. Herbarium specimens from regions with lower habitat suitability in both northern and southern regions were smaller, supporting the hypothesis that the distribution of <em>Arabidopsis</em> is constrained by climate‐associated factors. Climate anomalies partly explained interannual variation in herbarium specimen size, but these did not closely correspond to local limiting factors identified in the distribution model. Late‐flowering genotypes were absent from the lowest suitability regions, suggesting slower life histories are only viable closer to the centre of the realized niche. We identified glacial refugia farther north than previously recognized, as well as refugia concordant with previous population genetic findings. Lower latitude populations, known to be genetically distinct, are most threatened by future climate change. The recently colonized range of Arabidopsis was well‐predicted by our native‐range model applied to certain regions but not others, suggesting it has colonized novel climates. Integration of distribution models with performance data from vast natural history collections is a route forward for testing biogeographical hypotheses about species distributions and their relationship with evolutionary fitness across large scales.</p>
Data set - Photosynthetic light harvesting and thylakoid organization in a CRISPR/Cas9 Arabidopsis thaliana LHCB1 knockout mutant.
<p>This data set was produced at the University of Neuchâtel, it cointains the raw data relative to the manuscript entitled "Photosynthetic light harvesting and thylakoid organization in a CRISPR/Cas9 Arabidopsis thaliana LHCB1 knockout mutant."</p> <p>The report presents the difference in terms of protein accumulation, light harvesting, electron transport and thylakoid structure between the WT line (Col0) of <em>Arabidopsis thaliana </em>and a newly generated line that contains multiple mutations in all the genes coding for the light harvesting protein LHCB1, named L1ko.</p> <p>Paper_raw_data.xlsx contains the data utilised to produce the figures presented in the paper.</p> <p>Fluorescence_data.xlsx contains the raw fluorescence traces in excel format for three experiments. The data of the measurments performed with the multispeq are also available here: https://photosynq.org/projects/etr_in_lab_test_protocols</p> <p>Chloroplasts_TEM_WT_L1KO.zip contains all the electron microscopy pictures, at full resolution analysed for the report.</p> <p> </p> <p> </p>
Proteolytic cleavage of Arabidopsis thaliana phosphoenolpyruvate carboxykinase-1 modifies its allosteric regulation
<p>Phospho<i>enol</i>pyruvate carboxykinase (PEPCK) plays a crucial role in gluconeogenesis. In this work, we analyze the proteolysis of <i>Arabidopsis thaliana</i> PEPCK1 (<i>Ath</i>PEPCK1) in germinating seedlings. We found that the amount of <i>Ath</i>PEPCK1 protein peaks at 24-48 hours post-imbibition. Concomitantly, we observed shorter versions of <i>Ath</i>PEPCK1, putatively generated by metacaspase-9 (<i>Ath</i>MC9). To study the impact of <i>Ath</i>MC9 cleavage on the kinetic and regulatory properties of <i>Ath</i>PEPCK1, we produced truncated mutants based on the reported <i>Ath</i>MC9 cleavage sites. The Δ19 and Δ101 truncated mutants of <i>Ath</i>PEPCK1 showed similar kinetic parameters and the same quaternary structure than the WT. However, activation by malate and inhibition by glucose 6-phosphate were abolished in the Δ101 mutant. We propose that proteolysis of <i>Ath</i>PEPCK1 in germinating seedlings operates as a mechanism to adapt the sensitivity to allosteric regulation during the sink-to-source transition.</p>
Arabidopsis thaliana Col-CEN complete Chromosome 2 numt sequences and alignments
<p>Data associated with the assembly of complete chromosome 2 nuclear insertion of mitochondrial DNA (numt) from the <em>Arabidopsis thaliana</em> accession Columbia (Col-CEN). A full report of this project can be obtained in a manuscript titled "<strong>Complete sequence of a 641-kb insertion of mitochondrial DNA in the <em>Arabidopsis thaliana </em>nuclear genome</strong>".</p>
Historical Arabidopsis thaliana genomes from across its native range.
<p>We report short-read Illumina sequencing of 131 <em>Arabidopsis thaliana </em>herbarium specimens across its native range collected from 1820 to 2010. Sequencing depth averaged ~6X across these genomes. Sequences from the herbarium samples showed the expected degradation patterns typical of ancient DNA with endogenous DNA content between 18.01-88.26% (mean 56%; median 74%) and enrichment of cytosine to thymine substitutions at fragment ends. We provide access to the sequences upon request.</p>
Variation and plasticity in life-history traits and fitness of wild Arabidopsis thaliana populations are not related to their genotypic and ecological diversity
<p>Despite its implications for population dynamics and evolution, the relationship between genetic and phenotypic variation in wild populations remains unclear. Here, we estimated variation and plasticity in life-history traits and fitness of the annual plant <em>Arabidopsis thaliana</em> in two common garden experiments that differed in environmental conditions. We used up to 306 maternal inbred lines from six Iberian populations characterized by low and high genotypic (based on whole-genome sequences) and ecological (vegetation type) diversity. Low and high genotypic and ecological diversity was found in edge and core Iberian environments, respectively. Given that selection is expected to be stronger in edge environments and that ecological diversity may enhance both phenotypic variation and plasticity, we expected genotypic diversity to be positively associated with phenotypic variation and plasticity. However, maternal lines, irrespective of the genotypic and ecological diversity of their population of origin, exhibited a substantial amount of phenotypic variation and plasticity for all traits. Furthermore, all populations harbored maternal lines with canalization (robustness) or sensitivity in response to harsher environmental conditions in one of the two experiments. Overall, we conclude that the environmental attributes of each population probably determine their genotypic diversity, but all populations maintain substantial phenotypic variation and plasticity for all traits, which represents an asset to endure in changing environments.</p>
Gene Enrichment Map Data from gProfiler Analysis - Selected MPK Interactions of Arabidopsis thaliana
<p>Gene enrichment analysis results for the selected predicted MPK interactions are included in the supplementary materials.</p>
Continental-scale associations of Arabidopsis thaliana phyllosphere members with host genotype and drought
<p><strong><span>Plants are colonized by distinct pathogenic and commensal microbiomes across different regions of the globe, but the factors driving their geographic variation are largely unknown. Using 16S rDNA and shotgun sequencing, we characterized the associations of the <em>Arabidopsis thaliana</em> leaf microbiome with host genetics and climate variables from 267 populations in the species’ native range across Europe. Comparing the distribution of the 575 major bacterial amplicon variants (phylotypes), we discovered that microbiome composition in <em>A. thaliana</em> segregates along a latitudinal gradient. The latitudinal clines in microbiome composition are predicted by metrics of drought, but also by the spatial genetics of the host. To validate the relative effects of drought and host genotype we conducted a common garden field study, finding 10% of the core bacteria to be affected directly by drought, and 20% to be affected by host genetic associations with drought. These data provide a valuable resource for the plant microbiome field, with the identified associations suggesting that drought can directly and indirectly shape genetic variation in A. thaliana via the leaf microbiome.</span></strong></p>
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International Brain Laboratory public data
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OpenNeuro
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