Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
35
datasets available to search
ShareScore release 0.9.0
Dataset results
35 results for “repetitive DNA”
Data from: Repetitive DNA profiles reveal evidence of rapid genome evolution and reflect species boundaries in ground beetles
Genome architecture is a complex, multidimensional property of an organism defined by the content and spatial organization of the genome's component parts. Comparative study of entire genome architecture in model organisms is shedding light on mechanisms underlying genome regulation, evolution, and diversification; but such studies require costly analytical approaches which make extensive comparative study impractical for most groups. However, lower-cost methods that measure a single architectural component (e.g., distribution of one class of repeats) have potential as a new data source for evolutionary studies insofar as that measure correlates with more complex biological phenomena, and for which it could serve as part of an explanatory framework. We investigated copy number variation (CNV) profiles in ribosomal DNA (rDNA) as a simple measure reflecting the distribution of rDNA subcomponents across the genome. We find that signatures present in rDNA CNV profiles strongly correlate with species boundaries in the <i>breve</i> species group of <i>Bembidion</i>, and vary across broader taxonomic sampling in <i>Bembidion</i> subgenus <i>Plataphus</i>. Profiles of several species show evidence of re-patterning of rDNA-like sequences throughout the genome, revealing evidence of rapid genome evolution (including among sister pairs) not evident from analysis of traditional data sources such as multi-gene data sets. Major re-patterning of rDNA-like sequences has occurred frequently within the evolutionary history of <i>Plataphus</i>. We confirm that CNV profiles represent an aspect of genomic architecture (i.e., the linear distribution of rDNA components across the genome) via fluorescence in-situ hybridization. In at least one species, novel rDNA-like elements are spread throughout all chromosomes. We discuss the potential of copy number profiles of rDNA, or other repeats, as a low-cost tool for incorporating signal of genomic architecture variation in studies of species delimitation and genome evolution.
FIGURE 1 in Cytomolecular investigations using repetitive DNA probes contribute to the identification and characterization of Characidium sp. aff. C. vidali (Teleostei: Characiformes)
FIGURE 1 | Characidium sp. aff. C. vidali karyotypes arranged from mitotic metaphases after to conventional Giemsa staining and C-banding. A. and C. male karyotypes. B. and D. female karyotypes. B chromosomes are in the boxes. In evidence a preserved specimen under study. Photo of Characidium sp. aff. C. vidali by Bruno F. Melo.
FIGURE 3 in Cytomolecular investigations using repetitive DNA probes contribute to the identification and characterization of Characidium sp. aff. C. vidali (Teleostei: Characiformes)
FIGURE 3 | Metaphase plates of Characidium sp. aff. C. vidali after fluorescent in situ hybridization (FISH) with four microsatellite motifs. B chromosomes present in the species are indicated. Scale bar = 10 µm.
FIGURE 2 in Cytomolecular investigations using repetitive DNA probes contribute to the identification and characterization of Characidium sp. aff. C. vidali (Teleostei: Characiformes)
FIGURE 2 | Metaphase of Characidium sp. aff. C. vidali after FISH with histone H3 (green) and H4 (red) probe. Synteny marked in par 10. Scale bar = 10 µm.
FIGURE 4 in Cytomolecular investigations using repetitive DNA probes contribute to the identification and characterization of Characidium sp. aff. C. vidali (Teleostei: Characiformes)
FIGURE 4 | Metaphase of Characidium sp. aff. C. vidali after fluorescent in situ hybridization (FISH); A. With a telomeric probe (TTAGGG) n. B. After sequential C-banding. The arrows indicate Interstitial Telomeric Sites (ITS), and asterisks highlight double-ITS marks; B = B-chromosomes; Z, W = sex chromosomes. Scale bars = 10 µm.
Data from: Repetitive DNA profiles reveal evidence of rapid genome evolution and reflect species boundaries in ground beetles
Open the record for dataset details and reuse information.
Data from: Optimizing exome captures in species with large genomes using species-specific repetitive DNA blocker
Open the record for dataset details and reuse information.
Repetitive DNA annotation of Cladosporium fulvum Race 5
<p>This dataset consists of repetitive DNA annotation of the genome of <em>Cladosporium fulvum i</em>solate Race 5 (GenBank GCA_020509005.2). Repeats were identified with two versions of RepeatModeler v1.0.11 and v2.0.2. The repeat libraries obtained by both versions are in distinct files: RM1_lib.fasta and RM2_lib.fasta for versions 1 and 2 of RepeatModeler, respectively. The repeat libraries were used to mask the genome of <em>C. fulvum</em> Race 5 using RepeatMasker v4.1.2-p1. The obtained locations of repeats are shown in the GFF files.</p> <p>This dataset is associated with the following publication: A chromosome-scale genome assembly of the tomato pathogen <em>Cladosporium fulvum</em> reveals a compartmentalized genome architecture and the presence of a dispensable chromosome. <em>Microbial Genomics</em>, 2022.</p>
Figure 5 in Karyotype stasis but species-specific repetitive DNA patterns in Anguis lizards (Squamata: Anguidae), in the evolutionary framework of Anguiformes
Figure 5. Evolutionary trends and patterns of repeat distribution in the karyotype of Anguis and Pseudopus. The summary presents: the distribution pattern of interstitial telomeric repeats (ITRs) in macrochromosomes (red arrowheads), the presence of constitutive heterochromatin in the centromeric region of chromosome No. 2 (black arrowheads), and the number and topology of 18S rDNA sites (green signals). Phylogenetic relationships follow Gvoždík et al. (2023). Although all six species share 2n = 44 and macrochromosome morphology differs only subtly, several species-specific repeat accumulation patterns have been observed. A, The common ancestor of Anguis and Pseudopus had 10 macro- and 12 microchromosome pairs, and its metacentric chromosome No. 1 likely possessed ITRs in the centromeric region. B, Accumulation of ITRs on chromosomes Nos 2, 4, and 7, and heterochromatin on chromosome No. 2; translocation and accumulation of rDNA sites on microchromosomes in the Anguis ancestor. C, Accumulation (in A. cephallonica) or elimination (in the A. fragilis species complex ancestor) of ITRs on pair Nos 5 and 9 and of rDNA sites on one of the microchromosome pairs. An asterisk indicates two possible directions of chromosomal changes. D, Elimination of ITRs on pair No. 1 in the A. fragilis species complex ancestor. E, Elimination of ITRs on chromosomes Nos 2 and 7; elimination of heterochromatin on chromosome No. 2 in the common ancestor of A. colchica and A. graeca. F, Accumulation of ITRs on chromosome No. 3 in the ancestor of A. fragilis and A. veronensis. Anguis veronensis represents a composite ITR pattern of A. cephallonica and A. fragilis, providing support for the hypothesis of past contact between Italian and Peloponnese slow worms (Gvoždík et al. 2023), with remnants of these interactions likely persisting. An alternative hypothesis proposes a shared repeat pattern among all Anguis species, wherein the detection of ITRs depends on the repeat abundance and reveals accumulations only above the detection limit.
Figure 2 in Karyotype stasis but species-specific repetitive DNA patterns in Anguis lizards (Squamata: Anguidae), in the evolutionary framework of Anguiformes
Figure 2. Distribution of constitutive heterochromatin (first column from the less side), GC/AT-positive regions (second column), telomeres and ITRs (third column), and 18S rDNA gene clusters (fourth column) in Anguis and Pseudopus (males, UN for unknown sex). First column (A, E, I, M, Q, U): presence (full arrowhead) and absence (empty arrowhead) of centromeric heterochromatin in chromosome pair No. 2. Second column (B, F, J, N, R, V): diffused GC+ pattern in distal part of pair No. 2 (empty arrowhead) or strong signal (full arrowhead) in the telomeric region of pair No. 1. Third column (C, G, K, O, S, W): ITRs (full arrowhead). Fourth column (D, H, L, P, T, X): hybridization of 18S rDNA on three pairs of microchromosomes (full arrowheads) and additional weak signal on another microchromosome pair (empty arrowheads). Where available, females do not differ from males and are shown in Supporting Information (Fig. S3).
Figure 4 in Karyotype stasis but species-specific repetitive DNA patterns in Anguis lizards (Squamata: Anguidae), in the evolutionary framework of Anguiformes
Figure 4. Chromosome painting with Varanus komodoensis (VKO) macrochromosome probes on Anguis fragilis (AFR) and Pseudopus apodus (PAP) chromosomes. The probe identity is indicated (number and letter correspond to VKO chromosome and flow-sorted peak, respectively). Arrowheads mark the hybridization signal on the AFR (A–E) and PAP (F) homeologous chromosomes. Note that each of the probes VKO 1, 2, and 3 marks two different pairs of chromosomes, whereas the probes VKO 6 + 7 and 8 + 7 mark different arms of the same chromosome pair. The hybridization signal of the probes VKO 6 + 7 and 8 + 7 does not clearly overlap in Anguis, but it marks chromosome pair No. 7 in Pseudopus.
Figure 3 in Karyotype stasis but species-specific repetitive DNA patterns in Anguis lizards (Squamata: Anguidae), in the evolutionary framework of Anguiformes
Figure 3. Male (A, C, E, G) and female (B, D, F, H) comparative genomic hybridization in four Anguis species. Male-specific DNA is labelled with fluorescein d-UTP (green), and female-specific DNA with Cy3 d-UTP (red). The yellow regions reflect regions of accumulated repetitive elements existing in equilibrium in the male and female genomes. Slightly reddish (E, F) or greenish (G, H) regions indicate certain enrichment of the repetitive fraction in the genome of one of the individuals.
Figure 1 in Karyotype stasis but species-specific repetitive DNA patterns in Anguis lizards (Squamata: Anguidae), in the evolutionary framework of Anguiformes
Figure 1. Karyograms of Anguis and Pseudopus. Male karyograms are shown, the karyograms of A. veronensis and P. apodus are from a juvenile of unknown sex. All tested individuals including females share the karyotype of 2n = 44 consisting of 20 macrochromosomes and 24 microchromosomes. Where available, karyograms of both sexes are shown in Supporting Information Figure S1. Scale bar = 10 µm. Photos on the right, not to scale.
Figure 6 in Karyotype stasis but species-specific repetitive DNA patterns in Anguis lizards (Squamata: Anguidae), in the evolutionary framework of Anguiformes
Figure 6. Schematic illustration of the homeology of the Varanus and Anguis + Pseudopus macrochromosomes with respect to the putative toxicoferan ancestor. The simplified arrangement of the macrochromosomes of the toxicoferan ancestor follows the hypothesis of Deakin and Ezaz (2019). Based on the fission(s) leading to Varanus and Anguis, we can assume that both lizards exhibit a derived stage of macrochromosome organization rather than variants of the putative ancestral arrangement of their common anguiform ancestor. The homeology of VKO 5 and AFR 6 (red and white hatched) is tentative and requires further evidence. The colour code depicts the chromosome homeology.
Data for: The role of repetitive DNA in re-patterning of major rDNA clusters in Lepidoptera
<p><span>Genes for major ribosomal RNAs (rDNA) are present in multiple copies organized in tandem arrays. Number and position of rDNA loci can change dynamically and their re-patterning is presumably driven by repetitive sequences. We explored a peculiar rDNA organization in several representatives of Lepidoptera with either extremely large or numerous rDNA clusters. We combined molecular cytogenetics with analyses of second and third generation sequencing data to show that rDNA spreads as a transcription unit and reveal association between rDNA and various repeats. Furthermore, we performed comparative long read analyses between the species with derived rDNA distribution and moths with a single rDNA locus, which is considered ancestral. Our results suggest that satellite arrays, rather than mobile elements, facilitate homology-mediated spread of rDNA via either integration of extrachromosomal rDNA circles or ectopic recombination. The latter arguably better explains preferential spread of rDNA into terminal regions of lepidopteran chromosomes as efficiency of ectopic recombination depends on proximity of homologous sequences to telomeres.</span></p>
Repeatome turnover meets stable chromosomes: repetitive DNA sequences mark speciation and gene pool boundaries in sugar beet and wild beets
<p>The present repository provides zipped archives containing the results of the RepeatExplorer2 runs of individual as well as comparative repeat analyses in beet genomes.</p> <p> </p> <p>Sugar beet (<em>Beta vulgaris</em> subsp. <em>vulgaris</em>) and its crop wild relatives share a base chromosome number of nine and similar chromosome morphologies. Yet, interspecific breeding is impeded by chromosome and sequence divergence that is still not fully understood. Since repetitive DNA sequences represent the fastest evolving parts of the genome, they likely impact genomic variability and contribute to the separation of beet gene pools. Hence, we investigated if innovations and losses in the repeatome can be linked to chromosomal differentiation and speciation.</p> <p>We traced genome- and chromosome-wide evolution across sugar beet and twelve wild beets comprising all sections of the beet genera <em>Beta </em>and <em>Patellifolia</em>. For this, we combined data from short and long read sequencing, flow cytometry, and cytogenetics to build a comprehensive data framework for our beet panel that spans the complete scale from DNA sequence to chromosome up to the genome. Genome sizes and repeat profiles reflect the separation of the beet species into three gene pools. These gene pools harbor repeats with contrasting evolutionary patterns: We identified section- and species-specific repeat emergences and losses, e.g. of the retrotransposons causal for genome expansions in the section <em>Corollinae</em>/<em>Nanae</em>. Since most genomic variability was found in the satellite DNAs, we focused on tracing the 19 beetSat families across the three beet sections/genera. These taxa harbor evidence for contrasting strategies in repeat evolution, leading to contrasting satellite DNA profiles and fundamentally different centromere architectures, ranging from chromosomal uniformity in <em>Beta</em> and <em>Patellifolia</em> species to the formation of patchwork chromosomes in <em>Corollinae/Nanae</em> species. </p> <p>We show that repetitive DNA sequences are causal for genome size expansion and contraction across the beet genera, providing insights into the genomic underpinnings of beet speciation. Satellite DNAs in particular vary considerably among beet taxa, leading to the evolution of distinct chromosomal setups. These differences likely contribute to the barriers in beet breeding between the three gene pools. Thus, with their isokaryotypic chromosome sets, beet genomes present an ideal system for studying the link between repeats, genome variability, and chromosomal differentiation/evolution and provide a theoretical basis for understanding barriers in crop breeding.</p>
Data for: The role of repetitive DNA in re-patterning of major rDNA clusters in Lepidoptera
Open the record for dataset details and reuse information.
Data from: Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements
Cytosine DNA methylation (mC) is a genome modification that can regulate the expression of coding and non-coding genetic elements. However, little is known about the involvement of mC in response to environmental cues. Using whole genome bisulfite sequencing to assess the spatio-temporal dynamics of mC in rice grown under phosphate starvation and recovery conditions, we identified widespread phosphate starvation-induced changes in mC, preferentially localized in transposable elements (TEs) close to highly induced genes. These changes in mC occurred after changes in nearby gene transcription, were mostly DCL3a-independent, could partially be propagated through mitosis, however no evidence of meiotic transmission was observed. Similar analyses performed in Arabidopsis revealed a very limited effect of phosphate starvation on mC, suggesting a species-specific mechanism. Overall, this suggests that TEs in proximity to environmentally induced genes are silenced via hypermethylation, and establishes the temporal hierarchy of transcriptional and epigenomic changes in response to stress.
Data from: Survey sequencing reveals elevated DNA transposon activity, novel elements, and variation in repetitive landscapes among vesper bats
The repetitive landscapes of mammalian genomes typically display high Class I (retrotransposon) transposable element (TE) content, usually around half of the genome. In contrast, the Class II (DNA transposon) contribution is typically small (<3% in model mammals). Most mammalian genomes also exhibit a precipitous decline in Class II activity beginning roughly 40 million years ago (Ma). The first signs of more recently active mammalian Class II TEs were obtained from the little brown bat, Myotis lucifugus and are reflected by higher genome content (~5%). To aid in determining taxonomic limits and potential impacts of this elevated Class II activity, we performed 454 survey sequencing of a second Myotis species as well as four additional taxa within the family Vespertilionidae and an outgroup species from Phyllostomidae. Graph-based clustering methods were used to reconstruct the major repeat families present in each species and novel elements were identified in several taxa. Retrotransposons remained the dominant group with regard to overall genome mass. Elevated Class II TE composition (3-4%) was observed in all five vesper bats while less than 0.5% of the phyllostomid reads were identified as Class II derived. Differences in satellite DNA and Class I TE content are also described among vespertilionid taxa. These analyses present the first cohesive description of TE evolution across closely related mammals, revealing genome-scale differences in TE content within a single family.
Data from: Super-resolution imaging of a 2.5 kb non-repetitive DNA in situ in the nuclear genome using molecular beacon probes
High-resolution visualization of short non-repetitive DNA in situ in the nuclear genome is essential for studying looping interactions and chromatin organization in single cells. Recent advances in fluorescence in situ hybridization (FISH) using Oligopaints probes enabled super-resolution imaging of genomic domains with a resolution limit of 4.9 kb. To target shorter elements, we developed a simple FISH method that uses only molecular beacon (MB) probes to facilitate the probe-target binding, while minimizing non-specific fluorescence. We used three-dimensional stochastic optical reconstruction microscopy (3D-STORM) and optimized the imaging conditions to efficiently distinguish sparsely distributed Alexa-647 from background cellular autofluorescence. Utilizing 3D-STORM and 29-34 individual MB probes, we observed 3D fine-scale nanostructures of 2.5 kb integrated or endogenous unique DNA in situ in the human or mouse genome, respectively, demonstrating the capability of MB-based FISH in visualizing a so far shortest and non-repetitive genomic sequence in 3D at super-resolution.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.