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373 results for “Chloroplast”
Dataset for "Antisense transcription from neighboring genes interferes with the expression of mNeonGreen as a functional in vivo fluorescent reporter in the chloroplast of Chlamydomonas reinhardtii."
<p>Plasmid sequences for "Antisense transcription from neighboring genes interferes with the expression of mNeonGreen as a functional in vivo fluorescent reporter in the chloroplast of Chlamydomonas reinhardtii."</p>
Genotypes and geographic positions of 5797 European white oaks from 636 locations genotyped at 355 nuclear SNPs and 28 maternally inherited SNPs of the chloroplast and mitochondria
<p class="MsoNormal"><span>The data set is the result of genetic inventory on 5797 white oaks collected at 636 locations all over Europe. The oaks trees were assigned in forest inventories as <em>Quercus robur</em> </span><em>L.</em> <span>(3342), <em>Quercus petraea </em></span><em>Matt</em>. <span>(2090), <em>Quercus pubescens </em></span><em>Willd</em>. <span>(170) or as unspecified <em>Quercus</em>. spp. (195). The sampling had a focus on central and east Europe as well as the Black Sea and Caucasus region. All individuals were genotyped at 355 nuclear SNPs and 28 maternally inherited SNPs of the chloroplast and mitochondria. The combination of the maternally inherited SNPs resulted in 26 different haplotypes. </span></p> <p class="MsoNormal"><span>The genotype of each individual is one row in the csv-file "genotypes". The genotypes at the nuclear markers are diploid and represented by two columns per gene marker. The genetic information at the organelle genome is haploid. For each of these gene markers one column is used. Genotypes are coded by Arabic numbers. The meaning of the numbers is explained in the table "coding genotypes" in a second csv-file. Each Individual has a unique "Genotype_ID" and a "Thuenen_Sample_ID". The "Thuenen_Sample_ID" is a unique ID that serves to identify the sample in our depository at the Thuenen Institute of Forest Genetics. Each individual has data on the geographic origin given as "Longitude" and "Latitude" in decimal degrees. For each individual the putative oak species ("Putative species") as it has been assigned in the forest inventories is given. The numbers of the "Haplotype" represent the multilocus combination of the mitochondrial and chloroplast SNPs of that individual.</span></p>
The alignments of chloroplast genome sequences and nuclear ribosomal DNA fragments of six oak species sampled in the hot-dry valley of the Jinsha River, southwestern China
<p>Both chloroplast (cp) genome sequences and nuclear ribosomal (nr) DNA were assembled using GetOrganelle v.1.7.6.1 for 18 oak trees sampled in the Panzhihua Cycad National Nature Reserve, Sichuan Province, China. These trees belong to six oak species, including Quercus cocciferoides, Q. dolicholepis, Q. franchetii, Q. griffithii, Q. longispica, and Q. variabilis. We used PhyloSuite v.1.1.152 to extract coding sequences (CDSs), tRNA genes, rRNA genes, introns, and intergenic spacers (IGSs) of the 18 oak cp genomes. These sequences were aligned separately using MAFFT v.7.3.13 and manually adjusted with BioEdit v.7.2.5. Length variations in mononucleotide repeats were excluded and inversions were replaced with their reverse complements because of their tendency for homoplasy. Other indels were coded as binary characters according to the simple gap coding method using GapCoder. Separate assignments were concatenated according to their respective positions in the cp genome to obtain the alignments of LSC, SSC, IRb, and the whole cp genome.</p>
Membrane mesh and tomogram of the Chlamydomonas chloroplast
<p>Membrane mesh and tomogram of the Chlamydomonas chloroplast. These data were originally published in <a href="https://doi.org/10.7554/eLife.53740">Wietrzynski and Schaffer et al., eLife, 2020</a>. The tomograms were accessed from <a href="https://www.ebi.ac.uk/emdb/EMD-10780">EMD-10780</a>.</p>
The complete chloroplast genome of Mimusops elengi (Sapotaceae)
<p><span>The first complete chloroplast genome sequences of <i><span>Mimusops elengi</span></i> (Sapotaceae) were reported in this study. The cpDNA of <i><span>M</span></i><i><span>.</span></i><i><span> elengi</span></i> is 159,719 bp in length, contains a large single-copy region (LSC) of 88,935 bp and a small single-copy region (SSC) of 18,606 bp, which were separated by a pair of inverted repeat (IR) regions of 26,089 bp. The genome contains 132 genes, including 87 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the whole genome is 36.8%. Phylogenetic analysis of 12 chloroplast genomes within the family Sapotaceae suggests that the sister relationship of <i><span>Autranella</span></i> and <i><span>Tieghemella</span></i><span> is strongly supported. </span><i><span>Minusops</span></i> genus is close to <i><span>Autranella</span></i> and <i><span>Tieghemella</span></i>, although the support value is still low.</span></p>
Supplementary Materials from the article Characterization and molecular evolution analysis of Periploca forrestii inferred from its complete chloroplast genome sequence
<p>Table S1. Base composition of chloroplast genome in <em>P. forrestii</em>, Table S2. The lengths of introns and exons for the splitting genes, Table S3. The GC content of the codons from <em>P. forrestii </em>chloroplast genome, Table S4. Preferred codons in chloroplast genome of <em>P. forrestii</em>, Table S5. Long repeat sequences in the <em>P. forrestii </em>chloroplast genome, Figure S1. Codon bias analysis of P. forrestii chloroplast genome. (A) Neutrality plot analysis; (B) Analysis of PR2 bias plot; (C) Analysis on ENC and GC3 relationship.</p>
Comparative analysis of chloroplast genomes of Sanguisorba species and insights into phylogenetic implications and molecular dating
<pre class="js_message_plain ng-binding"><em>Sanguisorba</em> is a small genus, which consists of about 15 species widely distributed in North America and Eurasia. Previous studies on <em>Sanguisorba</em> are useful for understanding of phylogeny and chloroplast (cp) genome evolution of <em>Sanguisorba</em>. However, the cp genome resources of <em>Sanguisorba</em> are still limited, and the phylogeny and molecular dating for <em>Sanguisorba</em> and its relatives still need further explored. Here, we reported four cp genomes of <em>Sanguisorba</em> and conducted comparative analysis of the four <em>Sanguisorba</em> cp genomes plus five previously published ones. The nine cp genomes of <em>Sanguisorba</em> have typical tetrad quadripartite structure, with a total length of 154 282 to 155 730 bp, and their gene content, gene structure, and gene order are relatively conservative. The analysis of single copy (SC)/inverted repeat (IR) boundaries shows very slight boundary differences in <em>Sanguisorba</em> cp genomes. Eight variation hotspots were screened as excellent candidate markers of <em>Sanguisorba</em>. Phylogenetic analysis indicated <em>Sanguisorba</em> was monophyletic and was a member of tribe Agrimonieae subtribe Sanguisorbinae. Within <em>Sanguisorba</em>, <em>S. filiformis</em> is a sister group of six other taxa in the present sampling. Estimation of the divergence times indicated that subtribes Agrimoniinae and Sanguisorbinae diverged at the transition between the Oligocene and the Miocene, and divergent times of Agrimonieae genera ranged from the late Miocene to the Middle Pleistocene. This study enriches the available cp genome resources of <em>Sanguisorba</em>, and it is of great significance to further study the phylogeny and evolution of <em>Sanguisorba</em> and its relatives.</pre>
The dataset of five chloroplast regions used in: A contribution to Gymnosphaera (Cyatheaceae) in mainland Asia: Two new species, reinstatement of Cyathea bonii, and their phylogenetic positions
<p><em>Gymnosphaera</em> represents a minor lineage within the scaly tree-fern family Cyatheaceae. Tropical and subtropical mainland Asia is a main distribution area of <em>Gymnosphaera</em>. However, the species diversity of <em>Gymnosphaera</em> is currently incompletely known in mainland Asia due to lacking critical revision. Here we present new findings of species diversity and their relationships with mainland Asian <em>Gymnosphaera</em> based on field surveys, the examination of herbarium collections, and phylogenetic analyses of sequences of multiple chloroplast and nuclear regions. Two new species, <em>G. saxicola</em> from southwestern Yunnan and <em>G. bachmaensis</em> from central Vietnam are established. Traditionally recognized <em>G. podophylla </em>is revealed to be a complex, from which <em>G. bonii</em> is reinstated as a distinct species. Our phylogenetic analyses identified four clades within <em>Gymnosphaera</em> in mainland Asia: <em>G. denticulata</em> clade, <em>G. gigantea</em> clade, <em>G. podophylla </em>clade, and <em>G. salletii </em>clade. The new species <em>G. saxicola,</em> which is special for its saxicolous habitat, was resolved as a sister to <em>G. austroyunnanensis</em> in the <em>G. salletii</em> clade. The newly discovered <em>G. bachmaensis</em>, which is characterized especially by the spathulate frond, was positioned in the <em>G. podophylla</em> clade, being sister to <em>G. bonii</em>. The mountainous region from south-central Vietnam northwards to western Yunnan is a diverse center of <em>Gymnosphaera</em> and more species of this group are probably to be discovered there.</p>
Baraminology of Cucurbitaceae based on chloroplast genome analysis
<p>The gourd family (Cucurbitaceae) is an economically important and diverse group of plants, with approximately 1000 species. Previous analysis of hybridization data and nuclear ITS regions in 70 species of 14 genera of the family Cucurbitaceae identified seven putative holobaramins.</p><p>The present study expands upon this previous analysis by analyzing the sequence similarity of the chloroplast genome between 30 species from Cucurbitaceae. The clustering analysis showed six putative holobaramins: <i>Gynostemma</i>, <i>Gomphogyne</i>+<i>Hemsleya</i>,<i> Cucurbita</i>, <i>Cucumis</i>, <i>Citrullus</i>, <i>Coccinia grandis</i>+<i>Hodgsonia macrocarpa</i>+<i>Lagenaria siceraria</i>+<i>Momordica charantia</i>+<i>Siraitia grosvernorii</i>+<i>Trichosanthes kirilowii</i>. All six groups had a significant p-value except <i>Gomphogyne</i>+<i>Hemsleya</i>. Of these, Gynostemma and <i>Gomphogyne</i>+<i>Hemsleya</i> are two new putative holobaramins. </p><p>The present study is the second of its kind, after an analysis of chloroplast genomes in Liliales. This study used both hybridization data and chloroplast genome sequences that supported each other's results. Future chloroplast genome studies could be performed on plant groups that have enough species with mitochondrial genomes.</p>
Figure 2 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 2. Maximum Likelyhood tree showing the phylogenetic relationship between individuals.
Fig. 1 in Chloroplast genome of the conserved Aster altaicus var. uchiyamae B2015-0044 as genetic barcode
Fig. 1. Plastid genomic map of Aster altaicus var. uchiyamae.
Fig. 1 in Chloroplast genome of white wild chrysanthemum, Dendranthema sp. K247003, as genetic barcode
Fig. 1. Plastid genomic map of Dendranthema sp. K247003.
Structural Basis for Redox Regulation of Cytoplasmic and Chloroplastic Triosephosphate Isomerases from Arabidopsis thaliana
<p>Mass spectrometry raw data files for the determination of the molecular weight of the intact proteins.</p> <p>López-Castillo LM, Jiménez-Sandoval P, Baruch-Torres N, Trasviña-Arenas CH, Díaz-Quezada C, Lara-González S, Winkler R and Brieba LG (2016) Structural Basis for Redox Regulation of Cytoplasmic and Chloroplastic Triosephosphate Isomerases from <em>Arabidopsis thaliana</em>. <em>Front. Plant Sci</em>. 7:1817. doi: 10.3389/fpls.2016.01817</p>
Results for chloroplast assembler benchmarking
<p>Output fasta files produced by the different tools for real data (retry is a subset of real to test for consistency) and simulated data.</p>
Dataset: Light-regulated chloroplast morphodynamics in a single-celled dinoflagellate
<p>This repository contains the files for Figures 1-4 of the manuscript and SI figures 2-4. Every folder contains a readme file with further description. Folders contain analyzed and raw microscopy data. </p>
Photosynthesis from stolen chloroplasts can support sea slug reproductive fitness
<p>Some sea slugs are able to steal functional chloroplasts (kleptoplasts) from their algal food sources, but the role and relevance of photosynthesis to the animal host remain controversial. While some researchers claim that kleptoplasts are slowly digestible 'snacks', others advocate that they enhance the overall fitness of sea slugs much more profoundly. Our analysis show light-dependent incorporation of <sup>13</sup>C and <sup>15</sup>N in the albumen gland and gonadal follicles of the sea slug <i>Elysia timida</i>, representing translocation of photosynthates to kleptoplast-free reproductive organs. Long-chain polyunsaturated fatty acids with reported roles in reproduction were produced in the sea slug cells using labelled precursors translocated from the kleptoplasts. Finally, we report reduced fecundity of <i>E. timida</i> by limiting kleptoplast photosynthesis. The present study indicates that photosynthesis enhances the reproductive fitness of kleptoplast-bearing sea slugs, confirming the biological relevance of this remarkable association between a metazoan and an algal-derived organelle.</p>
Data for: Alignments of chloroplast DNA and ITS of tribe Adonideae
<p><span>The Euro-Siberian steppe flora consists of warm- and cold-adapted species, which may have responded differently to Pleistocene glacials and interglacials. Genotyping-by-sequencing individuals from across the distribution range of the pheasant's eye (<em>Adonis vernalis</em>), we aimed to gain insight into steppe florogenesis based on the species' evolutionary history. Although the primary area of origin of the species group comprising <em>A. vernalis</em>, <em>A. villosa</em> and <em>A. volgensis</em> is in Asia, our results indicate that <em>A. vernalis</em> itself is not of Asian origin but evolved in southern (incl. Southeastern) Europe during the Pleistocene, with Spanish populations being clearly genetically distinct<a> </a></span><span>from the Southeastern European populations. We inferred<a> </a></span><span>that <em>A. vernalis</em> migrated eastwards from the sub-Mediterranean forest-steppes of Southeastern Europe into the continental forest-steppe zone. Eastern European populations</span><span> had the highest private allelic richness, indicating long-term large population sizes in this region. As a thermophilic species, <em>A. vernalis</em> seems unlikely to have survived in the cold deserts of the Last Glacial Maximum in Western Siberia, so this region was likely</span><span> (re)colonized postglacially. Overall, our results reinforce the importance of identifying the area of origin and the corresponding ecological requirements of steppe plants in order to understand the composition of today's steppe flora.</span></p>
Chloroplast genome assemblies and comparative analyses of commercially important Vaccinium berry crops
<p><em>Vaccinium</em> is a large genus of shrubs that includes a handful of economically important berry crops. Given the numerous hybridizations and polyploidization events, the taxonomy of this genus has remained the subject of long debate. In addition, berries and berry-based products are liable to adulteration, either fraudulent or unintentional due to misidentification of species. The availability of more genomic information could help achieve higher phylogenetic resolution for the genus, provide molecular markers for berry crop identification, and a framework for efficient genetic engineering of chloroplasts. Therefore, in this study, we assembled five <em>Vaccinium</em> chloroplast sequences representing the economically relevant berry types: northern highbush blueberry (<em>V. corymbosum</em>), southern highbush blueberry (<em>V. corymbosum</em> hybrids), rabbiteye blueberry (<em>V. virgatum</em>), lowbush blueberry (<em>V. angustifolium</em>), and bilberry (<em>V. myrtillus</em>). Comparative analyses showed that the <em>Vaccinium</em> chloroplast genomes exhibited an overall highly conserved synteny and sequence identity among them. Polymorphic regions included the expansion/contraction of inverted repeats, gene copy number variation, simple sequence repeats, indels, and single nucleotide polymorphisms. Based on their in silico discrimination power, we suggested variants that could be developed into molecular markers for berry crop identification. Phylogenetic analysis revealed multiple origins of highbush blueberry plastomes, likely due to the hybridization events that occurred during northern and southern highbush blueberry domestication.</p>
The role of chloroplast movement in C4 photosynthesis: A theoretical analysis using a 3-D reaction-diffusion model for maize
<p>Chloroplast movement within mesophyll (M) cells in C<sub>4</sub> plants is hypothesized to enhance the CO<sub>2</sub> concentrating mechanism (CCM), but this is difficult to verify experimentally. A three-dimensional (3-D) leaf model can help analyze how chloroplast movement influences the operation of CCM. The first volumetric reaction-diffusion model of C<sub>4</sub> photosynthesis that incorporates: detailed 3-D leaf anatomy, light propagation, ATP and NADPH production and CO<sub>2</sub>, O<sub>2</sub> and bicarbonate concentration driven by diffusional and assimilation/emission processes, was developed and implemented for maize leaves to simulate various chloroplast movement scenarios within M cells: the movement of all M chloroplasts towards bundle-sheath (BS) cells (aggregative movement) and movement of only those of interveinal M cells towards BS cells (avoidance movement). Light absorbed by bundle-sheath (BS) chloroplasts relative to M chloroplasts increased in both cases. Avoidance movement decreased light absorption by M chloroplasts considerably. Consequently, total ATP and NADPH production and net photosynthesis rate increased for aggregative movement and decreased for avoidance movement case compared to the default case of no chloroplast movement at high light intensities. Leakiness increased in both chloroplast movement scenarios due to the imbalance in energy production and demand in M and BS cells. These results suggest the need to design strategies for coordinated increases in electron transport and Rubisco activities for an efficient CCM at very high light intensities.</p>
Multiple paternally inherited chloroplast capture events associated with Taxus speciation in the Hengduan Mountains
<p><strong>Template files and estimation files in Fastsimcoal2 for 16 models. Each model corresponded with the same name in Fig S2 and Fig S3. And SNP file, plastome matrix and transcriptome matrixes</strong></p>
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