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307 results for “Nuclear DNA”
Multiplexed DNA-FISH imaging dataset, drosophila embryos, nuclear cycles 11-14
<p>Multiplexed DNA-FISH imaging dataset from Drosophila embryos at nuclear cycles 11-14.</p> <p>Examples on how to load and use this dataset can be found at this <a href="https://github.com/NollmannLab/Goetz_etal">GitHub repository</a>.</p> <p><strong>Data processing details</strong></p> <p>Barcodes were segmented using a neural network (<a href="https://github.com/stardist/stardist"><em>stardist</em></a>) specifically trained for the detection of 3D diffraction limited spots produced by our microscope. To extract the position of the barcode with sub-pixel accuracy, a subsequent 3D Gaussian fit of the regions segmented by <em>stardist</em> was performed with Big-FISH (<a href="https://github.com/fish-quant/big-fish">https://github.com/fish-quant/big-fish</a>). Barcode localizations with intensities lower than 1.5 times that of the background were filtered out.</p> <p>Nuclei were segmented from projected DAPI images using <em><a href="https://github.com/stardist/stardist">stardist</a> </em>with a neural network trained for detection of nuclei from <em>Drosophila</em> embryos under our imaging conditions. Barcodes were then attributed to single nuclei by using the XY coordinates of the barcodes and the DAPI masks of the nuclei. Finally, pairwise distance matrices were calculated for each single nucleus.</p> <p><strong>Processed data in Figures</strong></p> <p>This new version of the dataset contains the raw data for each of the figures in the manuscript:</p> <p><strong>Associated publication</strong></p> <p><strong>Multiple parameters shape the 3D chromatin structure of single nuclei at the doc locus in </strong><em>Drosophila</em>.</p> <p>Markus Götz, Olivier Messina, Sergio Espinola, Jean-Bernard Fiche, Marcelo Nollmann</p> <p>Nature Communications (2022).</p>
Begomovirus DNA-B Movement Protein and Nuclear Shuttle Protein Ref-Seq Datasets
<p>Multiple Sequence Alignment of proteins encoded on begomovirus DNA-B (movement protein and nuclear shuttle protein; n=131). One isolate per species based on ICTV reference list.</p> <p> </p>
FIG. 3 in Intraindividual variation in nuclear DNA content in Durvillaea antarctica (Chamisso) Hariot, Macrocystis pyrifera (Linnaeus) C. Agardh and Lessonia spicata (Suhr) Santelices (Phaeophyceae)
FIG. 3. — Developmental stages of sporangia in Macrocystis pyrifera (Linnaeus) C. Agardh stained with DAPI: A-C, four-nucleate sporangium (4-ns) and sporangial mother cells (smc); D, mature sporangia. Scale bars: A-D, 5 μm.
FIG. 1 in Intraindividual variation in nuclear DNA content in Durvillaea antarctica (Chamisso) Hariot, Macrocystis pyrifera (Linnaeus) C. Agardh and Lessonia spicata (Suhr) Santelices (Phaeophyceae)
FIG. 1. — Cells of Durvillaea antarctica (Chamisso) Hariot stained with DAPI: A, mitotic figure (mf) of dividing cortical cells (cc); B, uninucleate cortical cells; C, D, mature antheridia (ma), antheridia germinative cells (agc), antheridium (a) and four-nucleate antheridium (4-na); E, five-nucleate antheridium (5-na); F, antheridia germinative cells. Scale bars: A-D, 5 μm.
Fig. 3. Maximum likelihood tree constructed from 38 nuclear rDNA ITS1 and ITS2 sequences from Apiaceae genus Daucus and relatives using a in Molecular phylogeny of Daucus (Apiaceae): Evidence from nuclear ribosomal DNA ITS sequences
Fig. 3. Maximum likelihood tree constructed from 38 nuclear rDNA ITS1 and ITS2 sequences from Apiaceae genus Daucus and relatives using a transition/transversion rate ratio of 1.6. Branch lengths are proportional to the number of expected nucleotide substitutions per site.
Fig. 2 in Molecular phylogeny of Daucus (Apiaceae): Evidence from nuclear ribosomal DNA ITS sequences
Fig. 2. Neighbor-joining tree inferred form the analysis of 39 nuclear rDNA ITS1 and ITS2 sequences from Apiaceae genus Daucus and its relatives using a transition/transversion rate ratio of 1.6. Branch lengths are proportional to distance estimated from the two parameter method of Kimura. Numbers at nodes indicate bootstrap values for 100 replicate analyses. On this tree, bootstrap values <20% are not indicated.
Fig. 1 in Molecular phylogeny of Daucus (Apiaceae): Evidence from nuclear ribosomal DNA ITS sequences
Fig. 1. Strict consensus of 11 parsimony trees derived from equally-weighted parsimony analysis of combined nuclear DNA ITS1 and ITS2 sequences from Daucus and its relatives using all unambiguously-aligned positions (CIs with and without uninformative characters= 0.6613 and 0.5817; RI=0.8387). From the left to the right, names of taxa, sections, and clades are given. Numbers above the nodes indicate the number of times a monophyletic group occurred in 100 bootstrap replicates; AutoDecay values are given below.
FIGURE 5 in A subspecies of marbled newt (Triturus marmoratus) in the Iberian Peninsula newly resolved from congruent nuclear and mitochondrial DNA data
FIGURE 5 The Iberian Peninsula with the ranges of Triturus pygmaeus in light red and T. rudolfi in brown (Arntzen, 2023, 2024). Populations of the counterpart species T. marmoratus are coloured according to the dominant mitochondrial haplogroups with colours as in the legend and fig. 4. The solid or interrupted black line shows the northern range of T. m. harmannis ssp. nov., as determined by the green, yellow and blue sections in fig. 1. Note that haplogroups 1 and 2 are associated with T. m. marmoratus and that haplogroups 3, 4 and 5 are associated with T. m. harmannis ssp. nov. Haplogroup 6 is associated with T. pygmaeus and T. rudolfi (for details see table 2). Areas shown in white fall outside the documented range of the T. marmoratus species group and areas shown in grey are distant from a sampled locality.
FIGURE A1 in A subspecies of marbled newt (Triturus marmoratus) in the Iberian Peninsula newly resolved from congruent nuclear and mitochondrial DNA data
FIGURE A1 Holotype of Triturus marmoratus harmannis ssp. nov. at right and ventral view. Size bar is 1 cm. Stored at the Museo Nacional de Ciencias Naturales, Madrid, Spain under catalogue number 51792.
FIGURE 3 in A subspecies of marbled newt (Triturus marmoratus) in the Iberian Peninsula newly resolved from congruent nuclear and mitochondrial DNA data
FIGURE 3 Histogram of scores along the first axis for the discriminant analysis of size corrected morphometric data for Triturus marmoratus marmoratus (shaded bars) and T. m. harmannis ssp. nov. (open bars). This first discriminant axis is most strongly correlated with extremity lengths and not the other characters. Highest loadings on the second axis are for head length and head width (results not shown).
FIGURE 1 in A subspecies of marbled newt (Triturus marmoratus) in the Iberian Peninsula newly resolved from congruent nuclear and mitochondrial DNA data
FIGURE 1 Classification and geographical distribution of European marbled and pygmy newts from a panel of 32–33 nuclear genetic markers (data from Kazilas et al., 2024). (A) HIests plot with ancestry and heterozygosity for within marbled newts (top panel, with Triturus m. marmoratus left and T. m. harmannis ssp. nov. to the right) and for pygmy newts (bottom panel, with T. rudolfi to the left and T. pygmaeus to the right). (B) Investigated Iberian populations shown by black dots with surrounding areas coloured as in A. Areas shown in white fall outside the documented range of the T. marmoratus species group and areas in shown grey are distant from a sampled locality. The open square symbol in the Lisbon Peninsula corresponds to the open round symbol in A.
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.
Genome-scale target capture of mitochondrial and nuclear environmental DNA from water samples
<p>Environmental DNA (eDNA) provides a promising supplement to traditional sampling methods for population genetic inferences, but current studies have almost entirely focused on short mitochondrial markers. Here, we develop one mitochondrial and one nuclear set of target capture probes for the whale shark (<i>Rhincodon typus</i>) and test them on seawater samples collected in Qatar to investigate the potential of target capture for eDNA-based population studies. The mitochondrial target capture successfully retrieved ~235x (90x-352x per base position) coverage of the whale shark mitogenome. Using a minor allele frequency of 5%, we find 29 variable sites throughout the mitogenome, indicative of at least five contributing individuals. We also retrieved numerous mitochondrial reads from an abundant non-target species mackerel tuna<i> </i>(<i>Euthynnus affinis</i>), showing a clear relation between sequence similarity to the capture probes and the number of captured reads. The nuclear target capture probes retrieved only few reads and polymorphic variants from the whale shark, but we successfully obtained millions of reads and thousands of polymorphic variants with different allele frequencies from <i>E</i>. <i>affinis</i>. We demonstrate that target capture of complete mitochondrial genomes and thousands of nuclear loci is possible from aquatic eDNA samples. Our results highlight that careful probe design, taking into account the range of divergence between target and non-target sequences as well as presence of non-target species at the sampling site, is crucial to consider. Environmental DNA sampling coupled with target capture approaches provide an efficient means with which to retrieve population genomic data from aggregating and spawning aquatic species.</p>
Data from: Strong selective effects of mitochondrial DNA on the nuclear genome
<p>Oxidative phosphorylation, the primary source of cellular energy in eukaryotes, requires gene products encoded in both the nuclear and mitochondrial genomes. As a result, functional integration between the genomes is essential for efficient adenosine triphosphate (ATP) generation. Although within populations this integration is presumably maintained by coevolution, the importance of mitonuclear coevolution in key biological processes such as speciation and mitochondrial disease has been questioned. In this study, we crossed populations of the intertidal copepod <i>Tigriopus californicus</i> to disrupt putatively coevolved mitonuclear genotypes in reciprocal F<sub>2</sub> hybrids. We utilized inter-individual variation in developmental rate among these hybrids as a proxy for fitness to assess the strength of selection imposed on the nuclear genome by alternate mitochondrial genotypes. Developmental rate varied among hybrid individuals, and <i>in vitro </i>ATP synthesis rates of mitochondria isolated from high fitness hybrids were approximately two-fold greater than those of mitochondria isolated from low fitness individuals. We then used Pool-seq to compare nuclear allele frequencies for high or low fitness hybrids. Significant biases for maternal alleles were detected on five (of 12) chromosomes in high fitness individuals of both reciprocal crosses, whereas maternal biases were largely absent in low fitness individuals. Therefore, the most fit hybrids were those with nuclear alleles that matched their mitochondrial genotype on these chromosomes, suggesting that mitonuclear effects underlie individual-level variation in developmental rate and that inter-genomic compatibility is critical for high fitness. We conclude that mitonuclear interactions can have profound impacts on both physiological performance and the evolutionary trajectory of the nuclear genome.</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>
MALDI-TOF MS data: Species delimitation of Hexacorallia and Octocorallia around Iceland using nuclear and mitochondrial DNA and proteome fingerprinting
<p>Cold-water corals build up reef structures or coral gardens and play an important role for many organisms in the deep sea. Climate change, deep-sea mining, and bottom trawling are severely compromising these ecosystems, making it all the more important to document the diversity, distribution, and impacts on corals. This goes hand in hand with species identification, which is morphologically and genetically challenging for Hexa- and Octocorallia. Morphological variation and slowly evolving molecular markers both contribute to the difficulty of species identification. In this study, a fast and cheap species delimitation tool for Octocorallia and Scleractinia of the Northeast Atlantic was tested based on 49 specimens. Two nuclear markers (ITS2 and 28S rDNA) and two mitochondrial markers (COI and mtMutS) were sequenced. The sequences formed the basis of a reference library for comparison to the results of species delimitation based on proteomic analysis using the MALDI-TOF MS method. The genetic methods were able to distinguish 17 of 18 presumed species. The MALDI-TOF MS method was able to distinguish 7 species. Species that could not be distinguished from one another still achieved good signals but were not represented by enough specimens for comparison. Therefore, it is predicted that with an extensive reference library of proteome spectra for Scleractinia and Octocorallia, MALDI-TOF MS may provide a rapid and cost-effective alternative for species discrimination in corals.</p>
Data and scripts for the manuscript of svaRetro and svaNUMT: modular packages for annotating retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data
<p>This upload include data and scripts supporting the results described in the manuscript of <em>svaRetro and svaNUMT: modular packages for annotating retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data</em><em>. </em>Detailed description of the contents can be found in README.txt.</p>
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