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13 results for “Spirodela polyrhiza”
Data from: Latitudinal variation in norms of reaction of phenology in the greater duckweed Spirodela polyrhiza
<p>Variable environments may result in the evolution of adaptive phenotypic plasticity when cues reliably indicate an appropriate phenotype-environment match. Although adaptive plasticity is well established for phenological traits expressed across environments, local differentiation in norms of reaction is less well studied. The switch from the production of regular fronds to overwintering "turions" in the greater duckweed <i>Spirodela polyrhiza</i> is vital to fitness and is expressed as a norm of reaction induced by falling temperatures associated with the onset of winter. However, the optimal norm of reaction to temperature is expected to differ across latitudes. Here, we test the hypothesis that a gradient in the length and predictability of growing seasons across latitudes results in the evolution of reaction norms characterized by earlier turion production at higher latitudes. We test this by collecting <i>S. polyrhiza</i> from replicate populations across seven latitudes from Ontario to Florida, and then assessing differentiation in thermal reaction norms of turion production along a common temperature gradient. As predicted, northern populations produce turions at lower birth order and earlier; a significant latitude-by-temperature interaction suggests that reaction norm differentiation has occurred. Our results provide evidence of differentiation in reaction norms across latitudes in a phenological trait, and we discuss how the adaptive significance of this plasticity might be further tested.</p>
Data from: Genetic mechanism of non-targeted-site resistance to diquat in Spirodela polyrhiza
<p>Understanding non-target-site resistance (NTSR) to herbicides represents a pressing challenge as NTSR is widespread in many weeds. Using the giant duckweed (<em>Spirodela polyrhiza</em>) as a model, we systematically investigated genetic and molecular mechanisms of diquat resistance, which can only be achieved via NTSR. Screening the diquat resistance among 138 genotypes suggested more than 8.5-fold resistance differences. Further experiments suggested that diquat uptake and antioxidant-related processes jointly contributed to diquat resistance in <em>S. polyrhiza</em>. Using a genome-wide association approach, we identified candidate genes that are associated with diquat resistance in <em>S. polyrhiza</em>, which includes a homolog of dienelactone hydrolase.</p>
Data from: Genetic mechanism of non-targeted-site resistance to diquat in Spirodela polyrhiza
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Data from: Latitudinal variation in norms of reaction of phenology in the greater duckweed Spirodela polyrhiza
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Data for: Birth order as a source of within-genotype diversification in the clonal duckweed, Spirodela polyrhiza (Araceae: Lemnoideae)
<p>Organismal persistence attests to adaptive response to environmental variation. Diversification bet hedging, in which risk is reduced at the cost of expected fitness, is increasingly recognized as an adaptive response, yet mechanisms by which a single genotype generates diversification remain obscure. The clonal greater duckweed, <i>Spirodela polyrhiza </i>(L.), facultatively expresses a seed-like but vegetative form, the "turion", that allows survival through otherwise lethal conditions. Turion reactivation phenology is a key fitness component, yet little is known about turion reactivation phenology in the field, or sources of variation. Here, using floating traps deployed in the field, we find a remarkable extent of variation in natural reactivation phenology that cannot be explained solely by spring cues, occurring over a period of at least 200 days. Under controlled laboratory conditions, we find support for the hypothesis that turion phenology is influenced jointly by phenotypic plasticity to temperature and diversification within clones. Turion "birth order" consistently accounted for a difference in reactivation time of 46 days at temperatures between 10° and 18°C, with early birth-order turions reactivating more rapidly than late birth-order turions. These results should motivate future work to formally evaluate turion phenology variance as a bet-hedging trait.</p>
Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza.
<p><span>The dataset contains all the original raw files for images, including protein and RNA blots, DNA and protein sequences used for phylogenetic trees, do plots…, and any other type of source data, sorted by figure and figure panel. Plasmids generated for this study have been deposited in Addgene. They are listed below together with previously existing plasmids obtained from Addgene and used in this study. NGS data has been deposited on NCBI SRA, accession numbers of datasets used in each figure are listed accordingly in this document. Ready-to-visualize using IGV software files of all NGS datasets together with the S. polyrhiza 9509 gene and TE annotations are also provided. The content of each file is:</span></p> <p><span> </span></p> <p><strong><span>FIGURE 3:</span></strong></p> <p><span>- </span><strong><span>3A</span></strong><span>: Picture of Spirodela polyrhiza (used as well in S19A, S26B, D).</span></p> <p><span> </span></p> <p><strong><span>FIGURE 5:</span></strong></p> <p><span>- </span><strong><span>5A:</span></strong><span> Western blot raw TIFF image files for the detection of H3K9me1, H3K9me2 and H3 in Arabidopsis and Spirodela.</span></p> <p><span> </span></p> <p><strong><span>FIGURE 7:</span></strong></p> <p><span>- </span><strong><span>7A:</span></strong><span> Western blot and Coomassie raw TIFF image files for the detection of FHA-AtAGO4_gDNA and FHA-SpAGO4a_cDNA in input and IP fractions from transient expression in <em>N. benthamiana</em>.</span></p> <p><span>- </span><strong><span>7D:</span></strong><span> Raw scan image files of <em>N. benthamiana</em> leaves infiltrated with RUBY or Scarlet hairpin (hpScarlet) and Northern blots raw TIFF image files for the detection of siRNAs produced by RUBY and hpScarlet transiently expressed in <em>N. benthamiana</em>.</span></p> <p><span>- </span><strong><span>7E:</span></strong><span> Raw scan image files of Spirodela cultures in dishes infiltrated with RUBY or Scarlet hairpin (hpScarlet) and Northern blots raw TIFF image files for the detection of siRNAs produced by RUBY and hpScarlet transiently expressed in Spirodela.</span></p> <p><strong><span> </span></strong></p> <p><strong><span>SUPPLEMENTAL FIGURE S6:</span></strong></p> <p><span>- </span><span>Protein sequences, and their alignment, of several angiosperm DRB proteins, including those identified in the <em>S. polyrhiza</em>9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).</span></p> <p><strong><span> </span></strong></p> <p><strong><span>SUPPLEMENTAL FIGURE S7:</span></strong></p> <p><span>- </span><span>Protein sequences, and their alignment, of several angiosperm RDR proteins, including those identified in the <em>S. polyrhiza</em>9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).</span></p> <p><strong><span> </span></strong></p> <p><strong><span>SUPPLEMENTAL FIGURE S8:</span></strong></p> <p><span>- </span><span>Protein sequences, and their alignment, of several angiosperm DCL proteins, including those identified in the <em>S. polyrhiza</em>9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).</span></p> <p><strong><span> </span></strong></p> <p><strong><span>SUPPLEMENTAL FIGURE S9:</span></strong></p> <p><span>- </span><span>Protein sequences, and their alignment, of several angiosperm AGO proteins, including those identified in the <em>S. polyrhiza</em>9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).</span></p> <p><strong><span> </span></strong></p> <p><strong><span>SUPPLEMENTAL FIGURE S10:</span></strong></p> <p><span>- </span><span>DNA sequence of the Spirodela (Sp9509) Chromosome 7 fragment containing the AGO5 cluster.</span></p> <p><strong><span> </span></strong></p> <p><strong><span>SUPPLEMENTAL FIGURE S11:</span></strong></p> <p><span>- </span><span>Protein sequences, and their alignment, of several angiosperm SHH proteins, including those identified in the <em>S. polyrhiza</em>9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).</span></p> <p><strong><span> </span></strong></p> <p><strong><span>SUPPLEMENTAL FIGURE S12:</span></strong></p> <p><span>- </span><span>Protein sequences, and their alignment, of several angiosperm Snf2 remodelers proteins, including those identified in the <em>S. polyrhiza</em> 9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).</span></p> <p><strong><span> </span></strong></p> <p><strong><span>SUPPLEMENTAL FIGURE S13:</span></strong></p> <p><span>- </span><span>Protein sequences, and their alignment, of several angiosperm Class V SET-domain containing proteins, including those identified in the <em>S. polyrhiza</em> 9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).</span></p> <p><strong><span> </span></strong></p> <p><strong><span>SUPPLEMENTAL FIGURE S14:</span></strong></p> <p><span>- </span><span>Protein sequences, and their alignment, of several angiosperm DNA methyltransferase proteins, including those identified in the <em>S. polyrhiza</em> 9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).</span></p> <p><strong><span> </span></strong></p> <p><strong><span>SUPPLEMENTAL FIGURE S15:</span></strong></p> <p><span>- </span><span>Protein sequences, and their alignment, of several angiosperm RNA pol large subunit proteins, including those identified in the <em>S. polyrhiza</em> 9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).</span></p> <p><strong><span> </span></strong></p> <p><strong><span>SUPPLEMENTAL FIGURE S16:</span></strong></p> <p><span>- </span><span>Protein sequences, and their alignment, of several angiosperm SPT5 and SPT5L proteins, including those identified in the <em>S. polyrhiza</em> 9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).</span></p> <p><strong><span> </span></strong></p> <p><strong><span>SUPPLEMENTAL FIGURE S17:</span></strong></p> <p><span>- </span><span>Protein sequences, and their alignment, of several animal and plant Uhrf/VIM proteins, including those identified in the <em>S. polyrhiza</em> 9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).</span></p> <p><strong><span> </span></strong></p> <p><strong><span>SUPPLEMENTAL FIGURE S18:</span></strong></p> <p><span>- </span><strong><span>S18A_B:</span></strong><span> Protein sequences, and their alignment, of several angiosperm SUVH4 and SUVH5/6 proteins, including those identified in the <em>S. polyrhiza</em> 9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).</span></p> <p><span>- </span><strong><span>S18C_D:</span></strong><span> Protein sequences, and their alignment, of several angiosperm ASI1 proteins, including those identified in the <em>S. polyrhiza</em> 9509 genome, used to build phylogenetic tree in fasta (.fa) format. Machine readable tree file is also provided in Nexus format (.nxs).</span></p> <p><strong><span> </span></strong></p> <p><strong><span>SUPPLEMENTAL FIGURE S19:</span></strong></p> <p><span>- </span><span>Picture of Arabidopsis (used as well in S26 A,C).</span></p> <p><strong><span> </span></strong></p> <p><strong><span>SUPPLEMENTAL FIGURE S24:</span></strong></p> <p><span>- </span><strong><span>S24C:</span></strong> <span>Raw TIFF image files of the coomassie staining of histone acid-extraction protein samples run on SDS-PAGE gel.</span></p> <p><span>- </span><strong><span>S24D:</span></strong><span> Excel files with mass-spectrometry data used for quantification of histone modifications in Arabidopsis and Spirodela.</span></p> <p><span> </span></p> <p><strong><span>SUPPLEMENTAL FIGURE S27:</span></strong></p> <p><span>- </span><strong><span>S27A:</span></strong> <span>Raw czi and TIFF image files of Arabidopsis interphase nuclei stained with DAPI.</span></p> <p><span>- </span><strong><span>S27B:</span></strong> <span>Raw czi and TIFF image files of Spirodela interphase nuclei stained with DAPI.</span></p> <p><span> </span></p> <p><strong><span>SUPPLEMENTAL FIGURE S34:</span></strong></p> <p><span>- </span><span>DNA sequence files (fasta) of TEs used to generate dot plots</span><span>.</span></p> <p><span> </span></p> <p><strong><span>SUPPLEMENTAL FIGURE S35:</span></strong></p> <p><span>- </span><strong><span>S35A:</span></strong> <span>Western blot and Coomassie raw TIFF image files for the detection of FHA-AtAGO4_gDNA and FHA-SpAGO4a_gDNA in input and IP fractions from transient expression in <em>N. benthamiana</em>.</span></p> <p><span>- </span><strong><span>S35B:</span></strong> <span>Intron-annotated genomic DNA sequences of At<em>AGO4 </em>and Sp<em>AGO4a</em> in GenBank (.gbk) format.</span></p> <p><span>- </span><strong><span>S35C:</span></strong><span> Raw image file of EtBr staining of agarose gel electrophoresis of 5’OH-RACE prior to gel excision and cloning.</span></p> <p><span>- </span><strong><span>S35D:</span></strong> <span>Western blot and Coomassie raw TIFF image files for the detection of FHA-AtAGO4_gDNA and FHA-SpAGO4a_cDNA in input and IP fractions from transient expression in <em>N. benthamiana</em>.</span></p> <p><span> </span></p> <p><strong><span>SUPPLEMENTAL FIGURE S36:</span></strong></p> <p><span>- </span><span>DNA sequence files (fasta) of TEs used to generate dot plots</span><span>.</span></p> <p><span> </span></p> <p><strong><span>SUPPLEMENTAL FIGURE S38:</span></strong></p> <p><span>- </span><span>Pictures of Spirodela during pretreatment, manual and vacuum agroinfiltration and RUBY transient expression</span><span>.</span></p> <p><span> </span></p> <p><strong><span>GENOME BROWSER TRACKS:</span></strong></p> <p><span>- </span><span>The following Integrative Genomics Viewer browser (</span><a href="https://igv.org/"><span>https://igv.org</span></a><span>) tracks are provided:</span></p> <p><span>SPIRODELA</span></p> <p><span>· </span><span>Spirodela 9509 genome (this study)</span></p> <p><span>· </span><span>Spirodela gene annotations (V3.0)</span></p> <p><span>· </span><span>Spirodela TE annotations (this study)</span></p> <p><span>· </span><span>Spirodela H3K9me1 as log2[H3K9me1/H3] (this study)</span></p> <p><span>· </span><span>Spirodela H3K9me2 as log2[H3K9me2/H3] (this study)</span></p> <p><span>· </span><span>Spirodela H3K27me3 as log2[H3K27me3/H3] (this study)</span></p> <p><span>· </span><span>Spirodela H3K4me3 as log2[H3K4me3/H3] (this study)</span></p> <p><span>· </span><span>Spirodela H3K9me1 as log2[H3K9me1/H3] for H3K27me1 (this study)</span></p> <p><span>· </span><span>Spirodela H3K9me2 as log2[H3K9me2/H3] ] for H3K27me1 (this study)</span></p> <p><span>· </span><span>Spirodela H3K27me3 as log2[H3K27me3/H3] ] for H3K27me1 (this study)</span></p> <p><span>· </span><span>Spirodela TraPR purified 21-nt small RNAs (+ strand) (this study)</span></p> <p><span>· </span><span>Spirodela TraPR purified 21-nt small RNAs (- strand) (this study)</span></p> <p><span>· </span><span>Spirodela TraPR purified 22-nt small RNAs (+ strand) (this study)</span></p> <p><span>· </span><span>Spirodela TraPR purified 22-nt small RNAs (- strand) (this study)</span></p> <p><span>· </span><span>Spirodela TraPR purified 24-nt small RNAs (+ strand) (this study)</span></p> <p><span>· </span><span>Spirodela TraPR purified 24-nt small RNAs (- strand) (this study)</span></p> <p><span>· </span><span>Spirodela Illumina RNA seq coverage (this study)</span></p> <p><span>· </span><span>Spirodela Illumina RNA seq reads (this study)</span></p> <p><span>· </span><span>Spirodela PacBio Iso-seq coverage (this study)</span></p> <p><span>· </span><span>Spirodela PacBio Iso-seq reads (this study)</span></p> <p><span> </span></p> <p><span>ARABIDOPSIS</span></p> <p><span>· </span><span>Arabidopsis Col-0 genome (TAIR10)</span></p> <p><span>· </span><span>Arabidopsis gene annotations (TAIR10)</span></p> <p><span>· </span><span>Arabidopsis TE annotations (TAIR10)</span></p> <p><span>· </span><span>Arabidopsis seedlings H3K9me1 as log2[H3K9me1/H3] (this study)</span></p> <p><span>· </span><span>Arabidopsis seedlings H3K9me2 as log2[H3K9me2/H3] (this study)</span></p> <p><span>· </span><span>Arabidopsis seedlings H3K27me3 as log2[H3K27me3/H3] (this study)</span></p> <p><span>· </span><span>Arabidopsis seedlings H3K4me3 as log2[H3K4me3/H3] (this study)</span></p> <p><span>· </span><span>Arabidopsis seedlings TraPR purified 21-nt small RNAs (+ strand) (this study)</span></p> <p><span>· </span><span>Arabidopsis seedlings TraPR purified 21-nt small RNAs (- strand) (this study)</span></p> <p><span>· </span><span>Arabidopsis seedlings TraPR purified 22-nt small RNAs (+ strand) (this study)</span></p> <p><span>· </span><span>Arabidopsis seedlings TraPR purified 22-nt small RNAs (- strand) (this study)</span></p> <p><span>· </span><span>Arabidopsis seedlings TraPR purified 24-nt small RNAs (+ strand) (this study)</span></p> <p><span>· </span><span>Arabidopsis seedlings TraPR purified 24-nt small RNAs (- strand) (this study)</span></p> <p><span> </span></p> <p><strong><span>NGS DATASETS:</span></strong></p> <p><span> </span></p> <p><span>All the NGS data generated for this study can be found under the SRA BioProject ID PRJNA1164696. The data was used to generate the following figure panels:</span></p> <p><span>- </span><span>Figures: 1A-H, 2A-F, 3A-E, 4A-H, 5D-J, 6A-G, 7B, 7F-H</span></p> <p><span>- </span><span>Supplemental Figures: S1, S3, S4, S19, S20, S22, S23, S26, S28, S29, S30, S31, S32, S33, S35, S36, S37, S38.</span></p> <p><span> </span></p> <p><span>Publicly available sequencing data (from indicated datasets) was used to generate the following figures:</span></p> <p><span>- </span><span>Figure 2A-F (Arabidopsis gene expression): GSM6892968</span></p> <p><span> </span></p> <p><strong><span>MASS SPECTROMETRY DATA:</span></strong></p> <p><span> </span></p> <p><span>The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD050443. Data was used to generate:</span></p> <p><span>- </span><span>Supplemental Figure 24D</span></p> <p><span> </span></p> <p><strong><span>PLASMIDS:</span></strong></p> <p><span> </span></p> <p><span>The following plasmids generated in this study can be retrieved from Addgene under the following ID#:</span></p> <p><span>- </span><span>p35S:FHA-AtAGO4_gDNA: #216838</span></p> <p><span>- </span><span>p35S:FHA-SpAGO4a_gDNA: #216841</span></p> <p><span>- </span><span>p35S::FHA-SpAGO4a_cDNA: #216842</span></p> <p><span> </span></p> <p><span>The following plasmids used in this study were retrieved from Addgene under the following ID#:</span></p> <p><span>- </span><span>p35S:RUBY: #160908</span></p> <p><span>- </span><span>pZmUbq:RUBY: #160909</span></p> <p><span>- </span><span>p35S:GFP-GUS: #167122</span></p> <p><span> </span></p> <p><span>The following plasmids were a gift from Dr. Marco Incarbone (Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, Potsdam 14476, Germany).</span></p> <p><span>- </span><span>pAtUBQ:hpScarlet</span></p>
Data for: Birth order as a source of within-genotype diversification in the clonal duckweed, Spirodela polyrhiza (Araceae: Lemnoideae)
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Data from: Plastic particles adsorb to the roots of freshwater vascular plant Spirodela polyrhiza but do not impair growth
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Data from: Hiding in plain sight: Koshicola spirodelophila gen. et sp. nov. (Chaetopeltidales, Chlorophyceae), a novel green alga associated with the aquatic angiosperm Spirodela polyrhiza
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Unusual predominance of maintenance DNA methylation in Spirodela polyrhiza
GEO Series GSE161234. Spirodela polyrhiza. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing.
Genome-wide characterization of aquaporins in Spirodela polyrhiza and expression of aquaporin gene family under high temperature stress
GEO Series GSE206791. Spirodela polyrhiza. 12 samples. Type: Expression profiling by high throughput sequencing.
Discovery of novel and conserved microRNAs in Spirodela polyrhiza by deep sequencing
GEO Series GSE55208. Spirodela polyrhiza. 1 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Spirodela polyrhiza root and frond phosphate starvation RNA-Seq
GEO Series GSE226143. Spirodela polyrhiza. 16 samples. Type: Expression profiling by high throughput sequencing.
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