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81 results for “Organelle”
Data from: Nitrogen fixing organelle in a marine alga
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Genotype data of 1970 Pedunculate oak trees (Quercus robur L.) in 13 European countries at 381 gene loci covering the nuclear and organelle genome
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Supplementary data for: Encyclopaedia of family A DNA polymerases localized in organelles: Evolutionary contribution of bacteria including the proto-mitochondrion
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In vivo timelapse imaging and analysis of Golgi satellite organelle distribution and movement in the neural progenitor cells of the brain
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Data for: Photosystems in the eye-like organelles of heterotrophic warnowiid dinoflagellates
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Sex‐dimorphic effects of biogenesis of lysosome‐related organelles complex‐1 deficiency on mouse perinatal brain development
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Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species
C4 photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photosynthetic diversification are blurred. The grass Alloteropsis semialata is an exception, as this species encompasses C4 and non-C4 populations. Using phylogenomics and population genomics, we infer the history of dispersal and secondary gene flow before, during, and after photosynthetic divergence in A. semialata. We further analyse the genome composition of individuals with varied ploidy levels to establish the origins of polyploids in this species. Detailed organelle phylogenies indicate limited seed dispersal within the mountainous region of origin and the emergence of a C4 lineage after dispersal to warmer areas of lower elevation. Patterns of differentiation across nuclear genomes highlight repeated secondary gene flow. In particular, the nuclear genome associated with the C4 phenotype was swept into a distantly related maternal lineage probably via unidirectional pollen flow. Multiple segmental allopolyploidy events mediated additional secondary genetic exchanges between photosynthetic types. Overall, our results show that limited dispersal and isolation allowed lineage divergence, with photosynthetic innovation happening after migration to new environments, and pollen-mediated gene flow led to the rapid spread of the derived C4 physiology away from its region of origin.
Test datasets for organelle genome assembly
<p>This is the PacBio HiFi data for the Arabidopsis thaliana organelle genomes extracted from the Darwin Tree of Life (<a href="https://www.darwintreeoflife.org">DToL, https://www.darwintreeoflife.org</a>) project sample ddAraThal4 (<a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJEB51511">https://www.ncbi.nlm.nih.gov/bioproject/PRJEB51511</a>). The data was downsampled to a coverage of ~800x for the chloroplast and ~100x for the mitochondrion.</p>
Molecular dynamics trajectories related to manuscript: SARS-CoV-2 nsp3 and nsp4 are minimal constituents of a pore spanning replication organelle
<p>This dataset contains two folders, each with sequentially numbers coordinates files for all-atom molecular dynamics trajectories related to the manuscript "SARS-CoV-2 nsp3 and nsp4 are minimal constituents of a pore spanning replication organelle" by Zimmermann et al. Each folder contains PDB and PSF files specifying the components of each system depicted in Fig. S10 of that manuscript as well as 200 sequentially named DCD files, each containing 5 nanoseconds of a 1 microsecond trajectory.</p>
Dasyclonium species delimitation with organelle genomes
<p>Datasets for our paper on scaling up species delimitation from single genes to whole organelle genomes, using the red alga Dasyclonium as a case study. The dataset includes assembled contigs for each specimen and alignments for named chloroplast-encoded genes.</p>
Organelle calcium-derived voltage oscillations in pacemaker neurons drive the motor program for food-seeking behavior in Aplysia
<p><span>An atypical neuronal pacemaker mechanism, based on rhythmic intracellular calcium store release in an identified pair of interneurons (B63) and resulting oscillation of the neurons' membrane potential, acts as an autonomous releaser for the irregular occurrences of the <span>motor program for food-seeking behavior</span> in Aplysia. The rhythmic variations of the membrane potential in B63 neurons were analyzed by Fast Fourier Transform (FFT) analysis in a cycle period bandwidth of 512 s to 8 s. The resulting power spectral density periodograms were used to identify oscillation periods of peak magnitude. The periodograms were computed from the FFT frequency spectrograms by converting the frequency band (in Hz) to its reciprocal, period (in secs). These analysis were performed in isolated buccal ganglia preparations bathed in artifical sea water (ASW), in 'Low Ca+Co' saline to block chemical synapses, or in 'Low Ca+Co' saline and after an intracellular injection of organelle membrane calcium channel blocker heparin into either the bilateral B63 or B31 neurons. The oscillations of B63 membrane potential that were recorded in ASW persisted in 'Low Ca+Co', but were suppressed after heparin injection specifically into B63.</span></p>
Figure 2 in Apocrine secretion of the egg hull in oogenesis and exclusion of sperm organelles at fertilization make reproduction in Chitonida (Mollusca) unique
Figure 2. (A) Portion of Figure 1C enlarged to show a region (boxed area) of apical bleb formation and aposome release from oocyte (O) into the forming hull (H). Scale bar = 2 µm. Inset: centriole (C) with rootlets in cytoplasm of late oocyte. Scale bar = 0.3 µm. (B) 3D image of microapocrine secretion from the oocyte (O) to the forming hull (H) created from an area similar to that in box in (A). Image was formed from 12 digitized serial sections entered into 'Reconstruct'. (C) TEM of Littorina sitkana bursa copulatrix, showing macroapocrine secretions (MS) being released from the cell surface (CS) to the lumen. Scale bar = 10 μm.
Figure 1 in Apocrine secretion of the egg hull in oogenesis and exclusion of sperm organelles at fertilization make reproduction in Chitonida (Mollusca) unique
Figure 1. (A) Scanning electron micrograph (SEM) of oocyte type with closed hull cupules (C) found in some species of Acanthochitona and Cyanoplax. The example is Cyanoplax dentiens. Scale bar = 40 µm. (B) Transmission electron micrograph (TEM) of section of later stage oocyte (O) of A. garnoti showing characteristic form of closed cupules (C). FC, follicle cell. Scale bar = 10 µm. (C) TEM of forming hull cupule (H) of A. garnoti showing three areas of microapocrine secretion (arrows) from surface of oocyte (O). FN, follicle cell nucleus. Scale bar = 5 µm. (D) TEM of one region of microapocrine secretion release below the forming hull (H). Note elongate apical blebs (AB), like microvilli, extending from cell membrane of oocyte (O). Micro-aposomes are pinched off and released into the intercellular space, where the hull is forming. Note also: rare Golgi vesicle exocytosis (arrow). Scale bar = 1 µm. (E) TEM detail of
Figure 3 in Apocrine secretion of the egg hull in oogenesis and exclusion of sperm organelles at fertilization make reproduction in Chitonida (Mollusca) unique
Figure 3. (A) SEM of egg of Stenosemus albus exhibiting the spinous hull typical of Chitonina. Scale bar = 50 µm. (B) SEM of portion of egg of S. albus showing sperm (arrow) penetrating one of a series of pores in the hull (P) located at the bases of spines. Scale bar = 5 μm. (C) Tip of needle-like extension of sperm of S. albus, showing acrosomal vesicle (AV) and tip of nuclear filament (N). Scale bar = 0.1 µm. (D) Light micrograph (LM) taken with Nomarski optics of
Organelle reads from Acacia pycnantha
<p>Organelle reads from <em>Acacia pycnantha</em>, to accompany a manuscript. This manuscript assembles a mitochondrial genome (the mitome) and a chloroplast genome (the plastome). </p> <p>In this repository, there are six files of sequencing reads. These were extracted from the full <em>Acacia pycnantha</em> data set, in NCBI under BioProject PRJNA752212.</p> <p><strong>How were these reads extracted? </strong></p> <p>For full detail, see manuscript sections: Extraction and assembly of organelle-only Nanopore reads, round 1 and round 2, and Extraction of organelle-only Illumina reads, in https://www.biorxiv.org/content/10.1101/2020.12.22.423164v1</p> <p><strong> Summary:</strong></p> <p>Extraction and assembly of organelle-only Nanopore reads, round 1</p> <p>To extract the organelle-only reads from the full read sets, we used a set of known sequences from related taxa as “baits”. For the plastome, we used three coding sequences from Acacia ligulata (NC_026134.2) in FASTA nucleotide format. We chose the genes rbcL, matK and ndhF as these are all likely to be plastid-only genes and are also well conserved. The rbcL and matK genes are usually located at either end of the LSC region, and ndhF is usually in the SSC region; these are well spaced around the plastid so that long reads should be extracted with roughly even coverage. As the mitome is much larger than the plastome, we used all 38 of the coding sequences from the mitome Acacia ligulata (NC_040998.1). </p> <p>We mapped the raw Nanopore reads (~5.5 million) to the baits with minimap2 and used samtools to extract mapped reads. We then used Filtlong to keep only the longest of the extracted reads up to a coverage of X250, because assembly becomes more fragmented or not possible when coverage is too high (and preliminary tests confirmed this with our data). For the plastome, we extracted ~28,000 reads, downsampled to 901 reads, longest ~121 Kbp; for the mitome, we extracted ~14,000 reads, no downsampling as coverage did not meet cutoff (X250), longest ~105 Kbp. Extracted Nanopore reads were assembled with Flye and the assembly was polished with two rounds of Racon.</p> <p>Extraction and assembly of organelle-only Nanopore reads, round 2</p> <p>We used this first assembly as the baits file for the next round of extracting organelle reads from the original full read set. In Minimap2, we set a minimum match value to 5000, as preliminary tests showed that more leniency here resulted in too many reads extracted to assemble properly. Again we kept only the longest reads to a target coverage of X250. From the ~5.5 million raw reads, for the plastome, we extracted ~70,000 reads (approx twice as many as in round 1), downsampled to 864 reads, longest ~121,000 bp (same as round 1); for the mitome, we extracted ~14,000 reads (similar to round 1), downsampled slightly to ~12,000 reads, longest ~105 Kbp (same as round 1). As in the first round, these reads were then assembled with Flye and polished with two rounds of Racon. In testing, further rounds of Racon polishing made little difference.</p> <p><strong>These are read sets:</strong></p> <ul> <li> <p><strong>mitome_nano_extracted_long2.fq.gz</strong></p> </li> <li> <p><strong>plastome_nano_extracted_long2.fq.gz</strong></p> </li> </ul> <p> </p> <p>Extraction of organelle-only Illumina reads</p> <p>Using the Round 2 assembly as baits, we then extracted organelle-only reads from the filtered and trimmed Illumina reads (~410 million read pairs). The extracted read sets were then randomly downsampled to a coverage of X250 using Rasusa. For the plastome, this resulted in ~26 million read pairs, downsampled to ~130,000 read pairs; for the mitome, this resulted in ~23 million read pairs, downsampled to ~670,000 read pairs. </p> <p><strong>These are read sets:</strong></p> <ul> <li> <p><strong>mitome_R1_extracted_subset.fq.gz</strong></p> </li> <li> <p><strong>mitome_R2_extracted_subset.fq.gz</strong></p> </li> <li> <p><strong>plastome_R1_extracted_subset.fq.gz</strong></p> </li> <li> <p><strong>plastome_R2_extracted_subset.fq.gz</strong></p> </li> </ul> <p> </p>
Complete organelle genomes of Korean fir, Abies koreana and phylogenomics of the gymnosperm genus Abies using nuclear and cytoplasmic DNA sequence data
<span>Background</span> <p><em><span>Abies koreana</span></em><span> E. H. Wilson is an endangered evergreen coniferous tree that is native to high altitudes in South Korea and susceptible to the effects of climate change. Hybridization and reticulate evolution have been reported in the genus; therefore, multigene datasets from nuclear and cytoplasmic genomes are needed to better understand its evolutionary history.</span></p> <span>Results</span> <p><span>Using Illumina NovaSeq6000 and Oxford Nanopore Technologies (ONT) PromethION platforms, we generated complete mitochondrial (1,174,803 bp) and plastid (121,341 bp) genomes from <em>A. koreana</em>. The mitochondrial genome is highly dynamic, transitioning from cis- to trans-splicing and breaking the conserved gene clusters. In the case of the plastome, the ONT reads revealed two structural conformations of <em>A. koreana</em>. The short inverted repeats (1,186 bp) of the <em>A. koreana</em> plastome are associated with the different structural types. Transcriptomic sequencing revealed 1,356 sites of C-to-U RNA editing in the 41 mitochondrial genes. Using <em>A. koreana</em> as a reference, we additionally produced nuclear ribosomal DNA and organelle genomic sequences from eight Abies species and generated multiple datasets for maximum likelihood and network analyses. Three sections (<em>Balsamea</em>, <em>Momi</em>, and <em>Pseudopicea</em>) were well grouped in the nuclear phylogeny, but the phylogenomic relationships showed conflicting signals in the mitochondrial and plastid genomes, indicating a complicated evolutionary history that may have included introgressive hybridization.</span></p> <span>Conclusions</span> <p><span>These results illustrate that phylogenomic analyses based on the sequences from differently inherited organelle genomes resulted in conflicting trees. Organellar capture, organellar genome recombination, and incomplete lineage sorting in an ancestral heteroplasmic individual can contribute to phylogenomic discordance. We provide strong support for the relationships within <em>Abies</em> and new insights into the phylogenomic complexity of this genus.</span></p>
Data associated with the publication "Assembling membraneless organelles from de novo designed proteins"
<p>Raw data used in the manuscript "Assembling membraneless organelles from de novo designed proteins"</p>
Complete organelle genomes of Korean fir, Abies koreana and phylogenomics of the gymnosperm genus Abies using nuclear and cytoplasmic DNA sequence data
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Organelle calcium-derived voltage oscillations in pacemaker neurons drive the motor program for food-seeking behavior in Aplysia
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Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.