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19 results for “genomic boundaries”
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.
Data from: Repetitive DNA profiles reveal evidence of rapid genome evolution and reflect species boundaries in ground beetles
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CTCF BINDING PATTERNS DEFINE TADS AND BOUNDARY ELEMENTS IN HUMAN AND MOUSE GENOMES
<p><em><strong>Msci thesis from Industrial Placement at Politecnico di Milano</strong></em></p> <p> </p> <p><strong>Abstract</strong></p> <p>In eukaryotes, the genome is highly packaged inside the nucleus. This hierarchical structure requires complex compartmentation and organization. Topologically associating domains (TADs) serve as architectural units in the 3D genome, functioning to regulate and constrain gene interaction. TAD boundaries are enriched in the CCCTC-binding factor (CTCF). Due to the asymmetric nature of the CTCF motif, it exhibits differing orientations based on the strand it is localized. Motif orientation is crucial for loop formation, which is facilitated in a convergent orientation. While the relationship between TADs and CTCF motif patterns has been described in humans, the model remained to be corroborated in other mammals. </p> <p>We conducted a comparative analysis by applying the research conducted in humans to the mouse genome. By integrating ChIP-seq data, we examined the CTCF sites based on ChIP-seq peak consolidation, signal value, and motif p-value. This analysis aimed to comprehend the binding profile of CTCF and elucidate its complexity in terms of binding strength and cross-tissue conservation. Mouse genome CTCF motifs were categorized into cluster patterns based on their relative orientation. Following this classification, the distribution of each pattern was studied using ChIP-seq-related descriptors. We then built a TAD boundary collection based on the insulation score. Boundary consolidation and length, insulation score, and CTCF number were used to reconcile CTCF to TAD boundary function. The cluster patterns were then mapped to TAD and TAD boundaries to elucidate their structure based on the spatial arrangement of CTCF.</p> <p>The distribution of ChIP-seq-validated CTCF sites within TAD boundaries revealed a well-defined structure, characterized by an abundance of the divergent pattern. Boundaries with the highest insulation scores exhibited both a high consolidation and CTCF enrichment. This set of boundaries was used to study TAD structure. An increment of the convergent pattern was observed inside TADs. The individual CTCF sites on the interior of the TAD were further organized into left and right sections, corresponding to an opposing directional arrangement to TAD boundaries. Significantly, the ChIP-seq data contained many unannotated peaks and non-signal motifs. These were associated with a high motif p-value, low ChIP-seq signal, low consolidation, and a less structured arrangement of CTCF clustering. Moreover, non-signal motifs were underrepresented within TAD boundaries and displayed a disorderly distribution.</p> <p>The human model of CTCF-dependent TAD structure was confirmed in mice. The model suggested the inherent alternation between convergent and divergent patterns, with these CTCF sites conferring characteristic properties upon TADs and their boundaries. These traits encompass the change of preferential genomic interaction and boundary insulation capability. Thus, the orientation-based clustering of CTCF sites was further validated as a good method to define TADs in a precise organized manner.</p>
Data from: Preserving wild pears: Using genomic data to assess species boundaries, interspecific hybridization, and genetic diversity to inform conservation
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Data from: Species delimitation with gene flow: a methodological comparison and population genomics approach to elucidate cryptic species boundaries in Malaysian Torrent Frogs
Accurately delimiting species boundaries is a non-trivial undertaking that can have significant effects on downstream inferences. We compared the efficacy of commonly-used species delimitation methods (SDMs) and a population genomics approach based on genome-wide single nucleotide polymorphisms (SNPs) to assess lineage separation in the Malaysian Torrent Frog Complex currently recognized as a single species (Amolops larutensis). First, we used morphological, mitochondrial DNA and genome-wide SNPs to identify putative species boundaries by implementing non-coalescent and coalescent-based SDMs (mPTP, iBPP, BFD*). We then tested the validity of putative boundaries by estimating spatiotemporal gene flow (fastsimcoal2, ABBA-BABA) to assess the extent of genetic isolation among putative species. Our results show that the A. larutensis complex runs the gamut of the speciation continuum from highly divergent, genetically isolated lineages (mean Fst = 0.9) to differentiating populations involving recent gene flow (mean Fst = 0.05; Nm > 5). As expected, SDMs were effective at delimiting divergent lineages in the absence of gene flow but overestimated species in the presence of marked population structure and gene flow. However, using a population genomics approach and the concept of species as separately evolving metapopulation lineages as the only necessary property of a species, we were able to objectively elucidate cryptic species boundaries in the presence of past and present gene flow. This study does not discount the utility of SDMs but highlights the danger of violating model assumptions and the importance of carefully considering methods that appropriately fit the diversification history of a particular system.
Data from: Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation
Although population genomic studies using next generation sequencing (NGS) data are becoming increasingly common, studies focusing on phylogenetic inference using these data are in their infancy. Here, we use NGS data generated from reduced representation genomic libraries of restriction-site-associated DNA (RAD) markers to infer phylogenetic relationships among 16 species of cichlid fishes from a single rocky island community within Lake Victoria's cichlid adaptive radiation. Previous attempts at sequence-based phylogenetic analyses in Victoria cichlids have shown extensive sharing of genetic variation among species and no resolution of species or higher-level relationships. These patterns have generally been attributed to the very recent origin (<15 000 years) of the radiation, and ongoing hybridization between species. We show that as we increase the amount of sequence data used in phylogenetic analyses, we produce phylogenetic trees with unprecedented resolution for this group. In trees derived from our largest data supermatrices (3 to >5.8 million base pairs in width), species are reciprocally monophyletic with high bootstrap support, and the majority of internal branches on the tree have high support. Given the difficulty of the phylogenetic problem that the Lake Victoria cichlid adaptive radiation represents, these results are striking. The strict interpretation of the topologies we present here warrants caution because many questions remain about phylogenetic inference with very large genomic data set and because we can with the current analysis not distinguish between effects of shared ancestry and post-speciation gene flow. However, these results provide the first conclusive evidence for the monophyly of species in the Lake Victoria cichlid radiation and demonstrate the power that NGS data sets hold to resolve even the most difficult of phylogenetic challenges.
Data from: Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation
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Data from: Genome-wide admixture and ecological niche modeling reveal the maintenance of species boundaries despite long history of interspecific gene flow
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Data from: Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary
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Data from: Species delimitation with gene flow: a methodological comparison and population genomics approach to elucidate cryptic species boundaries in Malaysian Torrent Frogs
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In situ dissection of domain boundaries affects genome topology and gene transcription in Drosophila [Hi-C]
GEO Series GSE136104. Drosophila melanogaster. 13 samples. Type: Other.
In situ dissection of domain boundaries affects genome topology and gene transcription in Drosophila [RNA-seq]
GEO Series GSE136136. Drosophila melanogaster. 4 samples. Type: Expression profiling by high throughput sequencing.
In situ dissection of domain boundaries affects genome topology and gene transcription in Drosophila
GEO Series GSE136137. Drosophila melanogaster. 17 samples. Type: Expression profiling by high throughput sequencing; Other.
Topologically Associating Domain Boundaries are Required for Normal Genome Function
GEO Series GSE172089. Mus musculus. 89 samples. Type: Expression profiling by high throughput sequencing; Other.
Evolution of heterochromatin and heterochromatin genes in the Oryza genomes reveals a new heterochromatin-euchromatin boundary [ChIP-Seq]
GEO Series GSE126436. Oryza glaberrima; Oryza sativa Japonica Group; Oryza punctata; Sorghum bicolor; Oryza brachyantha; Leersia perrieri. 38 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Evolution of heterochromatin and heterochromatin genes in the Oryza genomes reveals a new heterochromatin-euchromatin boundary
GEO Series GSE126444. Leersia perrieri; Oryza sativa; Oryza brachyantha; Oryza punctata; Sorghum bicolor; Oryza sativa Japonica Group; Oryza glaberrima. 47 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
Evolution of heterochromatin and heterochromatin genes in the Oryza genomes reveals a new heterochromatin-euchromatin boundary [RNA-Seq]
GEO Series GSE126431. Oryza brachyantha; Oryza punctata; Oryza glaberrima; Leersia perrieri; Sorghum bicolor; Oryza sativa Japonica Group. 6 samples. Type: Expression profiling by high throughput sequencing.
Evolution of heterochromatin and heterochromatin genes in the Oryza genomes reveals a new heterochromatin-euchromatin boundary [bisulfite-Seq]
GEO Series GSE126432. Oryza brachyantha. 1 samples. Type: Methylation profiling by high throughput sequencing.
Evolution of heterochromatin and heterochromatin genes in the Oryza genomes reveals a new heterochromatin-euchromatin boundary [ncRNA-Seq]
GEO Series GSE127665. Oryza sativa; Oryza brachyantha. 2 samples. Type: Non-coding RNA profiling by high throughput sequencing.
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Allen Brain Atlas
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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.