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18 results for “organelle genome”
Organelle Genome Utilities benchmark data
<p>test_Lamiaceae.zip: Benchmark result of Lamiaceae plastid data. Includes original sequences and analyze result from OGU.<br>test_1M_out.zip: Benchmark result of 1 million random GenBank records. Includes original sequences and analyze result from OGU.<br>test_308_angiosperm.zip: Benchmark result of 308 angiosperm family's plastid genomes. Includes original sequences and analyze result from OGU.<br>test_rodents.zip: Benchmark result of 307 mitochondria genomes from rodents. Includes original sequences and analyze result from OGU.<br>CDS and spacer tree of angiosperm plastid data.zip: Sequences and maximum likelihood trees of angiosperm plastid CDS and spacers. Built with IQTREE2.</p> <p>OGU-source code.zip: three versions of source code of OGU. </p>
Dataset for "Whole-genome de novo assemblies reveal structural variations and organelle-to-nucleus DNA transfers in Asian and African rice""
<p>DXCWR_O.rufipogon_scaffolded_anchored.fa.gz</p> <p>--Scaffolded and anchored genome assembly for <em>O. rufipogon</em> DXCWR.</p> <p>DXCWR_O.rufipogon_scaffolded_anchored.gff.gz</p> <p>--Gene annotation for the genome assembly DXCWR_O.rufipogon_scaffolded_anchored.fa.</p> <p>DXCWR_O.rufipogon_scaffolded_anchored_repeatmasker.gff.gz</p> <p>--Repeat annotation for the genome assembly DXCWR_O.rufipogon_scaffolded_anchored.fa.</p> <p>IRGC104165_O.glaberrima_scaffolded_anchored.fa.gz</p> <p>--Scaffolded and anchored genome assembly for <em>O. glaberrima</em> IRGC104165.</p> <p>IRGC104165_O.glaberrima_scaffolded_anchored.gff.gz</p> <p>--Gene annotation for the genome assembly IRGC104165_O.glaberrima_scaffolded_anchored.fa.</p> <p>IRGC104165_O.glaberrima_scaffolded_anchored_repeatmasker.gff.gz</p> <p>--Repeat annotation for the genome assembly IRGC104165_O.glaberrima_scaffolded_anchored.fa.</p> <p>W1411_O.barthii_scaffolded_anchored.fa.gz</p> <p>--Scaffolded and anchored genome assembly for <em>O. barthii</em> W1411.</p> <p>W1411_O.barthii_scaffolded_anchored.gff.gz</p> <p>--Gene annotation for the genome assembly W1411_O.barthii_scaffolded_anchored.fa.</p> <p>W1411_O.barthii_scaffolded_anchored_repeatmasker.gff.gz</p> <p>--Repeat annotation for the genome assembly W1411_O.barthii_scaffolded_anchored.fa.</p> <p>W2014_O.nivara_scaffolded_anchored.fa.gz</p> <p>--Scaffolded and anchored genome assembly for <em>O. nivara</em> W2014.</p> <p>W2014_O.nivara_scaffolded_anchored.gff.gz</p> <p>--Gene annotation for the genome assembly W2014_O.nivara_scaffolded_anchored.fa.</p> <p>W2014_O.nivara_scaffolded_anchored_repeatmasker.gff.gz</p> <p>--Repeat annotation for the genome assembly W2014_O.nivara_scaffolded_anchored.fa.</p>
Phylogenomics and biogeography of Torreya (Taxaceae) – Integrating data from three organelle genomes, morphology, and fossils and a practical method for reducing missing data from RAD-seq
<p><span>Restriction site-associated DNA sequencing (RAD-seq) enables obtaining thousands of genetic markers for phylogenomic studies. However, RAD-seq data are subject to allele dropout (ADO) due to polymorphisms at enzyme cutting sites. We developed a new pipeline, RADADOR, to mitigate the ADO in outgroups by recovering missing loci from previously published transcriptomes in our study of a gymnosperm genus </span><em>Torreya</em><span>. Using the supplemented RAD-seq data in combination with plastome and mitochondrial gene sequences, morphology, and fossil records, we reconstructed the phylogenetic and biogeographic histories of the genus and test hypotheses on diversity anomaly in eastern Asian-North American floristic disjunction. Our results showed that our pipeline recovered many loci missing from the outgroup, and the improved data yielded a more robust phylogeny for </span><em>Torreya</em><span>. Using the fossilized-birth-death model and divergence-extinction-cladogenesis method we resolved detailed biogeographic history of </span><em>Torreya</em><span> that suggested a Jurassic origin in the Laurasia and differential speciation and extinction among continents accounting for the modern diversity anomaly biased toward Eastern Asia (EA). The history also supported a vicariance origin of the modern </span><em>Torreya</em><span> from a widespread ancestor in EA and NA in the mid-Eocene, cross-Beringia exchange in the early Paleogene before the vicariant isolation, in contrast to the "Out of NA" pattern common to gymnosperms and in contrast to the "Out of EA" hypothesis previously proposed for the genus. Furthermore, we observed phylogenetic discordance between the nuclear and plastid phylogenies on </span><em>T. jackii</em><span>, suggesting differential lineage sorting of plastid genomes among </span><em>Torreya</em><span> species or plastid genome capture in </span><em>T. jackii</em><span>.</span></p>
Phylogenomics and biogeography of Torreya (Taxaceae) – Integrating data from three organelle genomes, morphology, and fossils and a practical method for reducing missing data from RAD-seq
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Data From: Oatk - a de novo assembly tool for complex plant organelle genomes
<p>This reposity hosts the data for 195 plant organelle genome assemblies generated in the manuscript "Oatk: a de novo assembly tool for complex plant organelle genomes". The sequence data were produced by the Tree of Life programme at the Sanger Institute, mostly from the Darwin Tree of Life (DToL) project, including 24 monocots, 154 eudicots, 16 mosses and one liverwort. See SAMPLE_LIST file for descriptions of these species.</p> <p>In each species subfolder, below files are included.</p> <ol> <li><code>PLTD.fasta</code> Plastome assembly file in FASTA format</li> <li><code>PLTD.annot.bed</code> Plastome assembly annotation file in BED format</li> <li><code>MITO.fasta</code> Mitogenome assembly file in FASTA format</li> <li><code>MITO.annot.bed</code> Mitogenome assembly annotation file in BED format</li> <li><code>MBG.gfa</code> Genome assembly file in GFA format generated with MBG</li> <li><code>PMAT.gfa</code> Genome assembly file in GFA format generated with OATK</li> <li><code>OATK.gfa</code> Genome assembly file in GFA format generated with PMAT (may not exist)</li> </ol> <p> </p> <p>Updates in the New Version:</p> <p>In the previous version, our raw PacBio HiFi read pre-processing pipeline had screened out some reads that it erroneously thought contained HiFi adapter sequence, which led to the gaps in the Hibiscus plastomes. We now fixed this and have rerun all the assemblies that led to any linear organelle components (37 species). All plastomes remain unchanged except for the three Hibiscuses, which are now also circular. Thirteen mitogenomes changed, with six of them now becoming circular.</p>
Genotype data of 1970 Pedunculate oak trees (Quercus robur L.) in 13 European countries at 381 gene loci covering the nuclear and organelle genome
<p>The data set is the result of genetic inventory on 1970 Pedunculate oak trees from 197 locations in Europe. The samples are from the countries: Belarus, Bosnia, Bulgaria, Croatia, Finland, France, Germany, Hungary, Italy, Latvia, Poland, Russia and Ukraine. At each location ten individual trees were collected. The data set includes the location ID and geographic coordinates of each sampled tree (longitude and latitude in decimal degrees) and the genotype data. All samples were screened with a targeted sequencing approach on a set of 381 polymorphic loci (356 nuclear SNPs, 3 nuclear InDels, 17 chloroplast SNPs and five mitochondrial SNPs).</p> <p>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.</p>
Genotype data of 970 Pedunculate oak trees (Quercus robur L.) in Russia and neighbouring countries at 385 gene loci covering the nuclear and organelle genome
<p>The data set is the result of genetic inventory on 970 Pedunculate oak trees from 97 locations in Russia, Belarus, Ukraine and Latvia representing the eastern part of the natural species range. The data set includes the sample IDs, geographic coordinates of each sampled tree (longitude and latitude in decimal degrees) and the genotype data. All samples were screened with a set of 385 gene markers covering the nuclear (n=364) and the organelle genomes (chloroplast: n=14, mitochondria: n=7) by use of a genotyping by sequencing approach. With exception of three INDELs (Insert and Deletion mutations) all gene markers are SNPs (Single nucleotide Polymorphism).</p>
Genotype data of 970 Pedunculate oak trees (Quercus robur L.) in Russia and neighbouring countries at 385 gene loci covering the nuclear and organelle genome
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Data from: Connections across open water: A bi-organelle, genomics-scale assessment of Atlantic-wide population dynamics in a pelagic, endangered apex predator shark (Isurus oxyrinchus)
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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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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>
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>
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>
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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Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species
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Supplementary files for manuscript: Acacia organelle genome assembly
<p>Supplementary files to accompany manuscript regarding genome assembly of organelles from <em>Acacia pycnantha. </em></p> <p>This manuscript assembles a mitochondrial genome (the mitome) and a chloroplast genome (the plastome). Results are referred to in the manuscript, and included here. </p> <p>For each organelle genome, there are 14 assemblies in fasta format, and associated GFA format file if available (not all stages produce this file), as well as the Spades GFA from Unicycler. For each Unicycler assembly there is a set of annotation files that include GenBank and GFF3 formats, and outputs from HMMER, ARAGORN, and tRNAscan-SE. There is also a bam file of reads mapped to alternate assembly paths for the mitome to explore the 90 Kbp contig of interest. A copy of the assembly script (assembler.sh) is included and is also available at this repository - https://github.com/AnnaSyme/organelle-assembly - with instructions on how to run the script and the required inputs and tools.</p> <p>(This Zenodo version is an update, with some duplicated files removed from the annotation folders, and information about the files now included.) </p>
Genome-wide rearrangement of protein translation levels for cell and organelle proliferation in a simple unicellular alga
GEO Series GSE273424. Cyanidioschyzon merolae. 4 samples. Type: Other.
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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)
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DANDI Archive for NWB datasets
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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.