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Dataset results
21 results for “genome mosaic”
Population genomic and morphological datasets from: An evolutionary mosaic challenges traditional monitoring of a foundation species in a coastal environment - the Baltic Fucus vesiculosus
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Population genomic consequences of life history and mating system adaptation to a geothermal soil mosaic in yellow monkeyflowers (common garden phenotype data)
<p>Local selection can promote phenotypic divergence despite gene flow across habitat mosaics, but adaptation itself may generate substantial barriers to genetic exchange. In plants, life-history, phenology, and mating system divergence have been proposed to promote genetic differentiation in sympatry. In this study, we investigate phenotypic and genetic variation in <em>Mimulus guttatus</em> (yellow monkeyflowers) across a geothermal soil mosaic in Yellowstone National Park (YNP). Plants from thermal annual and nonthermal perennial habitats were heritably differentiated for life history and mating system traits, consistent with local adaptation to the ephemeral thermal-soil growing season. However, genome-wide genetic variation primarily clustered plants by geographic region, with little variation sorting by habitat. The one exception was an extreme thermal population also isolated by a 200m geographical gap of no intermediate habitat. Individual inbreeding coefficients (F<sub>IS</sub>) were higher (and predicted by trait variation) in annual plants and annual pairs showed greater isolation by distance at local (<1km) scales. Finally, YNP adaptation does not re-use a widespread inversion that underlies <em>M. guttatus</em> life-history ecotypes range-wide, suggesting a novel genetic mechanism. Overall, this work suggests that life history and mating system adaptation strong enough to shape individual mating patterns does not necessarily generate incipient speciation without geographical barriers.</p>
GeMo : a web-based platform for the visualization and curation of mosaic genomes
<p>Dataset that will be used by TraceAncestor or by VCFHunter.</p> <p><strong>Reference for dataset</strong></p> <ul> <li> <p><a href="https://doi.org/10.1093/molbev/msy199">Baurens,F.-C. et al.(2019) Recombination and Large Structural Variations Shape Interspecific Edible Bananas Genomes. Mol Biol Evol, 36, 97–111.</a></p> </li> <li> <p><a href="https://doi.org/10.1111/tpj.14683">Martin et al., 2020a. Martin G, Cardi C, Sarah G, Ricci S, Jenny C, Fondi E, Perrier X, Glaszmann J-C, D’Hont A, Yahiaoui N. 2020. Genome ancestry mosaics reveal multiple and cryptic contributors to cultivated banana. Plant J. 102:1008–1025.</a></p> </li> <li> <p><a href="https://doi.org/10.1093/aob/mcz029">Ahmed,D. et al. (2019) Genotyping by sequencing can reveal the complex mosaic genomes in gene pools resulting from reticulate evolution: a case study in diploid and polyploid citrus. Annals of Botany, 123, 1231–1251.</a></p> </li> </ul>
Data for "Mixed viral infection constrains the genome formula of multipartite cucumber mosaic virus"
<p>We performed a study to assess the effect of mixed infection on the genome formula of multipartite virus CMV. We used qPCR to determine genome formulas and titer. Additionally, simulation models were developed to describe mechanisms for genome formula change under mixed infection. </p>
Population genomic consequences of life history and mating system adaptation to a geothermal soil mosaic in yellow monkeyflowers (common garden phenotype data)
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Data from: Patterns of genomic heterogeneity in a classic field cricket mosaic hybrid zone
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Risk of Recurrence of de Novo Mutations: Research and Quantification of Paternal Germinal Mosaicism by the Combined Use of Genomic Tools
ClinicalTrials.gov study NCT04564235. IPD Sharing: NO. Countries: 1. Publications: 0.
Data from: Identifying targets of selection in mosaic genomes with machine learning: applications in Anopheles gambiae for detecting sites within locally adapted chromosomal inversions
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Data from: Parallel pattern of differentiation at a genomic island shared between clinal and mosaic hybrid zones in a complex of cryptic seahorse lineages
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Data from: Chlamydomonas genome resource for laboratory strains reveals a mosaic of sequence variation, identifies true strain histories, and enables strain-specific studies
Chlamydomonas reinhardtii is a widely used reference organism in studies of photosynthesis, cilia, and biofuels. Most research in this field uses a few dozen standard laboratory strains that are reported to share a common ancestry, but exhibit substantial phenotypic differences. In order to facilitate ongoing Chlamydomonas research and explain the phenotypic variation, we mapped the genetic diversity within these strains using whole-genome resequencing. We identified 524,640 single nucleotide variants and 4812 structural variants among 39 commonly used laboratory strains. Nearly all (98.2%) of the total observed genetic diversity was attributable to the presence of two, previously unrecognized, alternate haplotypes that are distributed in a mosaic pattern among the extant laboratory strains. We propose that these two haplotypes are the remnants of an ancestral cross between two strains with ∼2% relative divergence. These haplotype patterns create a fingerprint for each strain that facilitates the positive identification of that strain and reveals its relatedness to other strains. The presence of these alternate haplotype regions affects phenotype scoring and gene expression measurements. Here, we present a rich set of genetic differences as a community resource to allow researchers to more accurately conduct and interpret their experiments with Chlamydomonas.
Data from: Untangling the hybrid nature of modern pig genomes: a mosaic derived from biogeographically distinct and highly divergent Sus scrofa populations
The merging of populations after an extended period of isolation and divergence is a common phenomenon, in natural settings as well as due to human interference. Individuals with such hybrid origins contain genomes that essentially form a mosaic of different histories and demographies. Pigs are an excellent model species to study hybridization because European and Asian wild boars diverged ~1.2 Mya and pigs were domesticated independently in Europe and Asia. During the Industrial Revolution in England, pigs were imported from China to improve the local pigs. This study utilizes the latest genomics tools to identify the origin of haplotypes in European domesticated pigs that are descendant from Asian and European populations. Our results reveal fine-scale haplotype structure representing different ancient demographic events, as well as a mosaic composition of those distinct histories due to recently introgressed haplotypes in the pig genome. As a consequence, nucleotide diversity in the genome of European domesticated pigs is higher when at least one haplotype of Asian origin is present, and haplotype length correlates negatively with recombination frequency and nucleotide diversity. Another consequence is that the inference of past effective population size is influenced by the background of the haplotypes in an individual, but we demonstrate that by careful sorting based on the origin of haplotypes both distinct demographic histories can be reconstructed. Future detailed mapping of the genomic distribution of variation will enable a targeted approach to increase genetic diversity of captive and wild populations, thus facilitating conservation efforts in the near future.
Data from: Genome divergence and diversification within a geographic mosaic of coevolution
Despite substantial interest in coevolution's role in diversification, examples of coevolution contributing to speciation have been elusive. Here, we build upon past studies that have shown both coevolution between South Hills crossbills and lodgepole pine (Pinus contorta), and high levels of reproductive isolation between South Hills crossbills and other ecotypes in the North American red crossbill (Loxia curvirostra) complex. We used genotyping by sequencing to generate population genomic data and applied phylogenetic and population genetic analyses to characterize the genetic structure within and among nine of the ecotypes. Although genome-wide divergence was slight between ecotypes (FST = 0.011–0.035), we found evidence of relative genetic differentiation (as measured by FST) between and genetic cohesiveness within many of them. As expected for nomadic and opportunistic breeders, we detected no evidence of isolation by distance. The one sedentary ecotype, the South Hills crossbill, was genetically most distinct because of elevated divergence at a small number of loci rather than pronounced overall genome-wide divergence. These findings suggest that mechanisms related to recent local coevolution between South Hills crossbills and lodgepole pine (e.g. strong resource-based density dependence limiting gene flow) have been associated with genome divergence in the face of gene flow. Our results further characterize a striking example of coevolution driving speciation within perhaps as little as 6000 years.
Data from: Untangling the hybrid nature of modern pig genomes: a mosaic derived from biogeographically distinct and highly divergent Sus scrofa populations
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Data from: Genome divergence and diversification within a geographic mosaic of coevolution
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Data from: Chlamydomonas genome resource for laboratory strains reveals a mosaic of sequence variation, identifies true strain histories, and enables strain-specific studies
Open the record for dataset details and reuse information.
Babaco Mosaic Virus (BabMV) induces genome-wide transcriptomic reprogramming in Carica papaya.
GEO Series GSE266643. Carica papaya. 32 samples. Type: Expression profiling by high throughput sequencing.
Characterization of the complete genome sequence of Barley yellow striate mosaic virus reveals an overprinted ancillary gene encoding a small hydrophobic protein
GEO Series GSE61565. Triticum aestivum. 2 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Genome-wide transcriptional Responses to Fusarium oxysporum and Tomato mosaic virus in Tomato
GEO Series GSE52336. Solanum lycopersicum. 8 samples. Type: Expression profiling by array.
Implications of Maternal 45,X Mosaicism as a Secondary Genomic Finding Following Cell-Free DNA Sequencing During Pregnancy: A Deep Phenotype Study
ClinicalTrials.gov study NCT05548881. IPD Sharing: NO. Countries: 1. Publications: 0.
Genome-wide investigation using sRNA-seq, degradome-seq and transcriptome-seq reveals regulatory networks of microRNAs and their target genes in soybean during Soybean mosaic virus infection
GEO Series GSE76636. Glycine max. 12 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
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.