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373 results for “Chloroplast”
Simulated Arabidopsis thaliana sequencing datasets for chloroplast assembler benchmarking
<p><strong>Changes</strong></p> <ul> <li>Fixed non-circular sampling from chloroplast and mitochondrion in version 1.1.0</li> <li>Fixed off-by-one error in reverse read in version 1.0.0</li> </ul> <p><strong>Purpose and Documentation</strong></p> <p>See: <a href="https://github.com/chloroExtractorTeam/benchmark">github.com/chloroExtractorTeam/benchmark</a></p> <p><strong>Original data</strong><br> The original <em>Arabidopsis thaliana </em>sequences were downloaded from TAIR: </p> <p>The Arabidopsis Information Resource (<a>TAIR</a>) on www.arabidopsis.org, Mar 22, 2019 available under the <a href="http://www.arabidopsis.org/doc/about/tair_terms_of_use/417">TAIR Terms of Use</a> </p> <p><em>Tanya Z. Berardini, Leonore Reiser, Donghui Li, Yarik Mezheritsky, Robert Muller, Emily Strait and Eva Huala. "The Arabidopsis Information Resource: Making and mining the "gold standard" annotated reference plant genome." genesis 2015 <a href="https://doi.org/10.1002/dvg.22877">doi:10.1002/dvg.22877</a></em></p> <p><strong>Programs used to generate this data</strong><br> - <a href="https://github.com/shenwei356/seqkit">seqkit</a> (v0.10.1): Shen W, Le S, Li Y, Hu F (2016) "SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation." PLOS ONE 11(10): e0163962. <a href="https://doi.org/10.1371/journal.pone.0163962">doi:10.1371/journal.pone.0163962</a></p> <p> </p>
Chloroplast redox state changes indicate cell-to-cell signalling during the hypersensitive response
<p>We performed detailed spatiotemporal analysis of chloroplast redox response to potato virus Y (PVY) infection in resistant <em>Ny</em><em>‐</em><em>1</em>-gene-bearing potato and its transgenic counterpart with impaired SA accumulation and compromised resistance. We found that the chloroplasts are highly oxidized in the cells adjacent to the cell death zone at different stages after virus inoculation in both genotypes. This hypothesis is further supported by highly induced formation of stroma filled tubules that extend from chloroplasts (stromules) in the cells adjacent to signalling cells. This dataset s a deposit of all the raw microscopy images of the study, plus the relevant metadata in ISA-tab compliant folder structure. </p> <p>After receiving reviews, we have made an additional experiment using a ROS inhibitor. The raw and processed data for this is in a separate file: _S_chlROS_inhibitor.zip</p> <p><br> <br> </p> <p><strong>Additional information about the microscopy images in this data deposit </strong></p> <ol> <li>Images of which name ends with <strong>ch00/ch01/ch02</strong> are maximum projections from Z-stacks for each ROI for each of three channels: chlorophyll fluorescence (ch00), GFP fluorescence after excitation with 405 nm laser line (ch01) and GFP fluorescence after excitation with 488 laser line (ch02), exported from Leica LAS X software.</li> <li>Only mesophyll cells are included in z-stack, except for the experiments with GFP-tagged PVY where additional z-stacks including both mesophyll and epidermal cells were produced ( »_2« added in the image name, see images with the comment »epidermal cells included in z-stack« in S_PhenodataRedox).</li> <li>Images of which name ends with <strong>ch00.tif</strong> and <strong>ch00.tif_ratio</strong> are analysed images, obtained using in-house Matlab script. These images were obtained by the analysis of ch00/ch01/ch02 images with the following steps: conversion to grayscale, filtering out pixels of low intensity, conversion to binary format using spatial adaptive thresholding, a round or erosion and dilation to remove single pixel noise around the chloroplasts, followed by size-based segmentation of individual chloroplasts. The ratios of fluorescence intensities 405/488 were then calculated for each pixel belonging to the chloroplast masks obtained in the previous step. Results were calculated per image (normalized to the fraction of pixels belonging to chloroplasts) and per individual chloroplast in each image.</li> <li>In the experiments with GFP-tagged PVY, due to high background signal in the cell death zone as a result of virus derived GFP fluorescence, signal in the 488 channel and 405/488 ratio (images named »scaled 488« and »405/488 in chloroplasts« in ch00.tif_ratio) in the cell death zone are not accurate.</li> <li>Figures of which name ends with <strong>ch00.tif_spatial_ROI1/ROI2</strong> show the 405/488 ratios in ROI1 or ROI2, determined for each pixel inside chloroplast masks for each Bin. See Image analysis in Methods for details.</li> <li>Experiment names and image names correspond to the names in S_PhenodataRedox. Details regarding experimental set-up and transgenic lines used are specified in S_PhenodataRedox.</li> </ol> <p>The Zenodo_reanalysis.zip file contains processed microscopic images in a new red/blue colormap. </p>
Chloroplast motion under dim light conditions
<p><em>Elodea densa </em>was kept in an aquatic culture. Ambient light conditions were applied 1h before image acquisition. <br> Imaging preparation: a low-light adapted leaf was detached and placed between two glass slides.<br> Lower cell layer is displayed. <br> Microscopy: Bright field microscopy was performed with a Nikon TI2 microscope using a halogen light source and a red-light 620nm cut-on wavelength filter at low light intensities of 7.2 W/cm^2 in combination with a Photometrics BSI Express sCMOS camera with high quantum yield to enable imaging every 1s with a $63\times$ water-immersion objective (NA=1.2) and pixel resolution of 0.1µm/px. <br> <br> Description:<br> Chloroplast.zip:<br> Contains ome.tiff files for 3600 frames of chloroplast motion (total duration 1h)<br> The dense chloroplasts (dark circular objects) inside the plant cells move by actin-mediated propulsion mechanism. <br> <br> 211013_CP_rawLabelMeasures.csv:<br> Analysis of segmented data (3600 frames) <br> <br> 211013_CP_tracks_vel.csv:<br> Trajectories (with velocities) constructed by trackpy from center-of-mass positions of the 211013_CP_rawLabelMeasures.csv. <br> Velocities where calculated using the first derivative of 3rd order Savitzky-Golay filtered data (Kernel width 11s). </p> <p><br> <br> </p>
The chloroplast genomes of Sanicula (Apiaceae): plastome structure, comparative analyses, and phylogenetic relationships
<p><em>Sanicula</em> (Apiaceae subfamily Saniculoideae) is a taxonomically difficult genus of medicinal value. Its distribution center is in China, where there are 18 species (11 of which are endemic). To provide plastid genome resources, whole chloroplast genomes of five <em>Sanicula</em> species (<em>S. flavovirens</em>, <em>S. giraldii</em>, <em>S. lamelligera</em>, <em>S. odorata</em>, and <em>S. rubriflora</em>) were sequenced and compared to the previously published <em>S. orthacantha</em> plastome. These genomes exhibit a typical quadripartite structure. All contain 129 different genes, including 84 protein-coding, 37 tRNA, and 8 rRNA genes. Loci <em>rpl2</em>, <em>matK</em>, <em>psbA</em>, and <em>ycf1</em> are the most variable. Results of maximum likelihood analysis of 90 whole plastome sequences from Apioideae and Saniculoideae and the outgroup <em>Hydrocotyle</em> (Araliaceae) reveal sectional relationships in <em>Sanicula</em> different from the traditional classification system, support the monophyly of Apioideae and its sister group relationship to Saniculoideae, and show concordant topologies to nrDNA ITS and other plastome-based phylogenies. <em>Sanicula orthacantha</em> and <em>S. chinensis</em> form a clade sister group to <em>S. lamelligera</em> and <em>S. odorata</em>, consecutively. These four species comprise a clade sister group to the clade of <em>S. rubriflora</em> and <em>S. flavovirens</em>, with this entire group sister to <em>S. giraldii</em>. The plastid genome resources provided herein will be important for future systematic, evolutionary, phylogenomic, and population-level studies of <em>Sanicula</em>.</p>
Figure 1 in An investigation on the chloroplast and nuclear genomes of taxa belong to the subgenus Dracunculus (Bess.) Rydb. of Artemisia L. (Asteraceae) in Turkey
Figure 1. Geographic distribution of four species of the subgenus Dracunculus in Turkey (A. campestris (), A. marschalliana (), A. araratica () and A. scoparia () (Civelek et al., 2010, Kursat 2010).
Fig. 3 in Chloroplast genome of the conserved Aster altaicus var. uchiyamae B2015-0044 as genetic barcode
Fig. 3. The variable sites in the chloroplast genomes of Aster altaicus var. uchiyamae. Variable sequences are marked in red. GG: Yeoju, Gyeonggi Province, CB: Cheongju, Chungcheongbuk Province.
Fig. 2 in Chloroplast genome of the conserved Aster altaicus var. uchiyamae B2015-0044 as genetic barcode
Fig. 2. The sequence alignment of variable sites in the chloroplast genomes of Aster altaicus var. uchiyamae. Variable sequences are marked in red. GG: Yeoju, Gyeonggi Province, CB: Cheongju, Chungcheongbuk Province.
Fig. 2 in Chloroplast genome of white wild chrysanthemum, Dendranthema sp. K247003, as genetic barcode
Fig. 2. Comparison of chloroplast genomes of Dendranthema sp. K247003 and D. boreale IT121002 using mVISTA program. Grey arrows and thick black lines above the alignment indicate genes with their orientation and the position of the IRs, respectively. The Yscale represents the percent identity between 50-100%. Genome regions are color-coded: Coding regions in blue; noncoding sequences (CNS) in red.
FIG. 3. — Bayesian consensus tree inferred from concatenated chloroplast rps4 in Pterygoneurum sampaianum (Guim.) Guim.: range extension to Africa, first mentions in France, confirmation of specific status and improved morphological circumscription
FIG. 3. — Bayesian consensus tree inferred from concatenated chloroplast rps4-trnS and trnM-trnV sequence data of the analysed dataset of Pottiaceae subfam. Pottioideae, partitioned between DNA sequence and indel data. Posterior probability from BI is displayed above the branches; bootstrap support (656 replications) from ML analysis is displayed below the branches.
Fig. 3 in Evolution of Polyscias sect. Tieghemopanax (Araliaceae) based on nuclear and chloroplast DNA sequence data
Fig. 3. — Strict consensus of 10,000 most parsimonious trees resulting from the analysis of 58 ITS sequences; tree length = 725 steps; consistency index = 0.518; retention index = 0.734. Clades denoted by brackets are those referred to in text. Values along branches are bootstrap percentages. Placement of Polyscias elegans (discussed in text) is denoted by an asterisk. Labels for the Tieghemopanax group and other clades in "Polyscias sensu lato" follow PLUNKETT et al. (2001).
Fig. 2 in Evolution of Polyscias sect. Tieghemopanax (Araliaceae) based on nuclear and chloroplast DNA sequence data
Fig. 2. — The single most parsimonious tree resulting from the combined analysis of ITS + trnL-trnF + 5S spacer sequences, based on the identical 24-taxon sampling as used in Fig. 1; tree length = 349 steps; consistency index = 0.663; retention index = 0.770. Values along nodes are bootstrap percentages; nodes with dashed branches have bootstraps below 70%. Identical or near identical clades (labeled A-E) from Fig. 1 are also labeled, as is the placement of Polyscias sambucifolia and P. microbotrys (asterisks), as discussed in text. Outgroups indicated by "OG."
Fig. 4 in Evolution of Polyscias sect. Tieghemopanax (Araliaceae) based on nuclear and chloroplast DNA sequence data
Fig. 4. — Strict consensus of 156 most parsimonious trees resulting from the analysis of 40 trnL-trnF sequences; tree length = 122 steps; consistency index = 0.938; retention index = 0.972. Values along branches are bootstrap percentages. Placement of Polyscias elegans (discussed in text) is denoted by an asterisk. Labels for the Tieghemopanax group and other clades in "Polyscias sensu lato" follow PLUNKETT et al. (2001).
Fig. 5 in Evolution of Polyscias sect. Tieghemopanax (Araliaceae) based on nuclear and chloroplast DNA sequence data
Fig. 5. — Strict consensus of 156 most parsimonious trees resulting from the analysis of 26 5S spacer sequences; tree length = 147 steps; consistency index = 0.744; retention index = 0.849. Values along branches are bootstrap percentages.
Data from: Chloroplast genomes of six Colocasia species (Araceae) including taro
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The chloroplast genomes of Sanicula (Apiaceae): plastome structure, comparative analyses, and phylogenetic relationships
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Chloroplast genome sequencing reads from snow gum
<p>Tutorial data for chloroplast genome assembly: fastq reads from illumina and nanopore sequencing for the snow gum, <em>Eucalyptus pauciflora</em>.</p> <p>Data from: Wang, W., Schalamun, M., Morales-Suarez, A. et al. Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case. BMC Genomics 19, 977 (2018) doi:10.1186/s12864-018-5348-8</p> <p>Data hosted at NCBI under accession numbers: illumina (SRR7153063) and nanopore (SRR7153095). Additional illumina file SRR7153071 not used here. </p> <p>This is how the files have been changed from the original datasets: </p> <p>Using the Galaxy platform (usegalaxy.org): </p> <ul> <li> <p>Each dataset was separately mapped to the NCBI Reference Sequence for <em>Eucalyptus pauciflora </em>chloroplast NC_039597.1, using BWA-MEM. </p> </li> <li> <p>Unmapped reads were filtered out using a SAMtools flag. </p> </li> <li> <p>Bam files were converted to fastq files.</p> </li> <li> <p>Each fastq file was then reduced in size:</p> </li> <li> <p>snow-gum-illumina-cp-reduced: has the first 62,500 reads only. Note that original pairing of reads has not been preserved so consider these to be unpaired reads for this tutorial.</p> </li> <li> <p>snow-gum-nanopore-cp-reduced: has only reads that are longer than 90,000 bp.</p> </li> </ul>
Data from: Multi-scale spatial genetic structure within and between populations of wild cherry trees in nuclear genotypes and chloroplast haplotypes
Spatial genetic structure (SGS) of plants mainly depends on the effective population size and gene dispersal. Maternally inherited loci are expected to have higher genetic differentiation between populations and more intensive SGS within populations than biparentally inherited loci because of smaller effective population sizes and fewer opportunities of gene dispersal in the maternally inherited loci. We investigated biparentally inherited nuclear genotypes and maternally inherited chloroplast haplotypes of microsatellites in 17 tree populations of three wild cherry species under different conditions of tree distribution and seed dispersal. As expected, inter-population genetic differentiation was 6–9 times higher in chloroplast haplotypes than in nuclear genotypes. This difference indicated that pollen flow 4–7 times exceeded seed flow between populations. However, no difference between nuclear and chloroplast loci was detected in within-population SGS intensity due to their substantial variation among the populations. The SGS intensity tended to increase as trees became more aggregated, suggesting that tree aggregation biased pollen and seed dispersal distances toward shorter. The loss of effective seed dispersers, Asian black bears, did not affect the SGS intensity probably because of mitigation of the bear loss by other vertebrate dispersers and too few tree generations after the bear loss to alter SGS. The findings suggest that SGS is more variable in smaller spatial scales due to various ecological factors in local populations.
Data from: Chloroplast Primers for Clade-Wide Phylogenetic Studies of Thalictrum (Ranunculaceae)
• Premise of the study: Chloroplast primers were developed for phylogenetic and comparative studies in Thalictrum (Ranunculaceae). • Methods and Results: We assembled and annotated the complete plastome sequence of Thalictrum thalictroides by combining multiple whole genome sequencing libraries. Using transcriptome-sequencing libraries, we also assembled a partial plastome of the related species T. hernandezii. From the newly assembled plastomes and one previously sequenced plastome, we designed and validated 28 primer pairs to target variable portions of the chloroplast genome in Thalictrum. Furthermore, we tested the validated primers in 62 species of Thalictrum and three species of closely related genera. The total alignment length of the 28 regions was 15,268 bp with 2,443 variable sites and 92% character occupancy. • Conclusions: The newly developed chloroplast primers pairs showed to improve the phylogenetic resolution (bootstrap support and tree certainty) in Thalictum and are a great resource for future phylogenetic and evolutionary studies in group and its close relatives in Thalictroideae.
Data from: Relationships in the Lupinus albifrons species complex (Fabaceae) based on two highly variable chloroplast regions
The perennial lupines of western North America, previously suggested to be monophyletic, comprise an apparently rapid and recent species radiation concentrated in the California Floristic Province. The Lupinus albifrons species complex consists of a number of closely related yet morphologically variable taxa within the larger group of perennial lupines. We used sequence data from two rapidly evolving noncoding chloroplast regions to analyze relationships in the perennial lupines, with special emphasis on the Lupinus albifrons species complex. Sampling from throughout the ranges of species thought to be closely related to Lupinus albifrons, we found that this group is characterized by high genetic diversity not only between species, but also within species and even within populations. The results of this study call into question the monophyly of the western North American perennials. Only two taxa clearly emerge as deserving recognition at the species or subspecies level based on the molecular data: Lupinus paynei from Simi Valley, California, and Lupinus excubitus from eastern California and the San Gabriel Mountains. Although some taxonomic conclusions can be extrapolated from this study, overall, these results warn against undersampling in phylogenetic studies of recently evolved groups.
1,825 Oryza chloroplast genomes
<p>1,825 complete or near-complete chloroplast genomes of Oryza species.</p> <p>Reconstruction based on previously published data (PRJEB2829; PRJEB2578; PRJEB2052; PRJEB6180).</p> <p>Includes O. rufipogon, O. sativa (temperate japonica, tropical japonica, indica, aus, aromatic).</p> <p>Reference: Civan P, Brown T. Genetic origins of cultivated rice (<em>Oryza sativa</em> L.) and the role of gene flow during its domestication. <em>In preparation.</em></p>
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