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899 results for “allele”
Training data for "Identification of allelic variants in SARS-CoV-2 from deep sequencing reads"
<p>Effectively monitoring global infectious disease crises, such as the COVID-19 pandemic, requires capacity to generate and analyze large volumes of sequencing data in near real time. These data have proven essential for monitoring the emergence and spread of new variants, and for understanding the evolutionary dynamics of the virus.</p> <p>Two sequencing platforms in combination with several established library preparation strategies are predominantly used to generate SARS-CoV-2 sequence data. However, data alone do not equal knowledge: they need to be analyzed. The Galaxy community developed analysis workflows to support the <strong>identification of allelic variants (AVs) in SARS-CoV-2 from deep sequencing reads</strong>.</p> <p>These workflows allow one to identify AVs and lineages in SARS-CoV-2 genomes with variant allele frequencies ranging from 5% to 100% (i.e., they detect variants with intermediate frequencies as well.</p> <p>In this tutorial we will see how to run these workflows for the different types of input data:</p> <ul> <li>Single end data derived from Illumina-based RNAseq experiments</li> <li>Paired end data derived from Illumina-based RNAseq experiments</li> <li>Paired-end data generated with Illumina-based Ampliconic (ARTIC) protocols</li> <li>ONT fastq files generated with Oxford nanopore (ONT)-based Ampliconic (ARTIC) protocols</li> </ul> <p>To illustrate the tutorial, we took some example datasets (paired-end data generated with Illumina-based Ampliconic (ARTIC) protocols) from COG-UK, the COVID-19 Genomics UK Consortium.</p>
Data from: CHIIMP: an automated high-throughput microsatellite genotyping approach reveals greater allelic diversity in wild chimpanzees
Short tandem repeats (STRs), also known as microsatellites, are commonly used to non-invasively genotype wild-living endangered species, including African apes. Until recently, capillary electrophoresis has been the method of choice to determine the length of polymorphic STR loci. However, this technique is labor intensive, difficult to compare across platforms, and notoriously imprecise. Here we developed a MiSeq-based approach and tested its performance using previously genotyped fecal samples from long-term studied chimpanzees in Gombe National Park, Tanzania. Using data from eight microsatellite loci as a reference, we designed a bioinformatics platform that converts raw MiSeq reads into locus-specific files and automatically calls alleles after filtering stutter sequences and other PCR artifacts. Applying this method to the entire Gombe population, we confirmed previously reported genotypes, but also identified 31 new alleles that had been missed due to sequence differences and size homoplasy. The new genotypes, which increased the allelic diversity and heterozygosity in Gombe by 61% and 8%, respectively, were validated by replicate amplification and pedigree analyses. This demonstrated inheritance and resolved one case of an ambiguous paternity. Using both singleplex and multiplex locus amplification, we also genotyped fecal samples from chimpanzees in the Greater Mahale Ecosystem in Tanzania, demonstrating the utility of the MiSeq-based approach for genotyping non-habituated populations and performing comparative analyses across field sites. The new automated high-throughput analysis platform (available at https://github.com/ShawHahnLab/chiimp) will allow biologists to more accurately and effectively determine wildlife population size and structure, and thus obtain information critical for conservation efforts.
Borrelia infection in bank voles Myodes glareolus is associated with specific DQB haplotypes which affect allelic divergence within individuals
<p>The high polymorphism of Major Histocompatibility Complex (MHC) genes is generally considered to be a result of pathogen-mediated balancing selection. Such selection may operate in the form of heterozygote advantage, and/or through specific MHC allele–pathogen interactions. Specific MHC allele–pathogen interactions may promote polymorphism via negative frequency-dependent selection (NFDS), or selection that varies in time and/or space because of variability in the composition of the pathogen community (fluctuating selection; FS). In addition, divergent allele advantage (DAA) may act on top of these forms of balancing selection, explaining the high sequence divergence between MHC alleles. DAA has primarily been thought of as an extension of heterozygote advantage. However, DAA could also work in concert with NFDS though this is yet to be tested explicitly. To evaluate the importance of DAA in pathogen-mediated balancing selection, we surveyed allelic polymorphism of MHC class II DQB genes in wild bank voles (<i>Myodes glareolus</i>) and tested for associations between DQB haplotypes and infection by <i>Borrelia afzelii</i>, a tick-transmitted bacterium causing Lyme disease in humans. We found two significant associations between DQB haplotypes and infection status: one haplotype was associated with lower risk of infection (resistance), while another was associated with higher risk of infection (susceptibility). Interestingly, allelic divergence within individuals was higher for voles with the resistance haplotype compared to other voles. In contrast, allelic divergence was lower for voles with the susceptibility haplotype than other voles. The pattern of higher allelic divergence in individuals with the resistance haplotype is consistent with NFDS favouring divergent alleles in a natural population, hence selection where DAA works in concert with NFDS. </p>
Improved library preparation protocols for amplicon sequencing-based noninvasive fetal genotyping for RHD-positive D antigen-negative alleles
<p>We aimed to simplify our fetal <i>RHD</i> genotyping protocol by changing the method to attach Illumina's sequencing adaptors to PCR products from the ligation-based method to a PCR-based method, and to improve its quantitative accuracy by introducing unique molecular indexes, which allow us to count the numbers of DNA fragments used as PCR templates and to minimize the effects of PCR and sequencing errors. Both of the newly established protocols reduced time and cost compared with our conventional protocol. Removal of PCR duplicates using UMIs reduced the frequencies of erroneously mapped sequences reads likely generated by PCR and sequencing errors. The modified protocols will help us facilitate implementing fetal <i>RHD</i> genotyping for East Asian populations into clinical practice.</p>
Allele‐specific cis‐regulatory methylation of the gene for vasoactive intestinal peptide in white‐throated sparrows
<p>White-throated sparrows (<em>Zonotrichia albicollis</em>) offer a unique opportunity to connect genotype with behavioral phenotype. In this species, a rearrangement of the second chromosome is linked with territorial aggression; birds with a copy of this "supergene" rearrangement are more aggressive than those without it. The supergene has captured the gene <em>VIP</em>, which encodes vasoactive intestinal peptide, a neuromodulator that causes aggression in other songbirds. In white-throated sparrows, <em>VIP</em> expression is higher in the anterior hypothalamus of birds with the supergene than those without it, and expression of <em>VIP</em> in this region predicts the level of territorial aggression regardless of genotype. Here, we aimed to identify epigenetic mechanisms that could contribute to differential expression of <em>VIP</em> both in breeding adults, which exhibit morph differences in territorial aggression, and in nestlings, before territorial behavior develops. We extracted and bisulfite-converted DNA from samples of the hypothalamus in wild-caught adults and nestlings and used high-throughput sequencing to measure DNA methylation of a region upstream of the <em>VIP</em> start site. We found that the allele inside the supergene was less methylated than the alternative allele in both adults and nestlings. The differential methylation was attributed primarily to CpG sites that were shared between the alleles, not to polymorphic sites, which suggests that epigenetic regulation is occurring independently of the genetic differentiation within the supergene. This work represents an initial step toward understanding how epigenetic differentiation inside chromosomal inversions leads to the development of alternative behavioral phenotypes.</p>
Asymmetric allelic introgression across a hybrid zone of the coal tit (Periparus ater) in the central Himalayas
<p>In the Himalayas, a number of secondary contact zones have been described for vicariant vertebrate taxa. However, analyses of genetic divergence and admixture are missing for most of these examples. In this study, we provide a population genetic analysis for the coal tit (<i>Periparus ater</i>) hybrid zone in Nepal. Intermediate phenotypes between the distinctive western 'spot-winged tit' (<i>P. a. melanolophus</i>) and e<span class="msoDel">E</span>astern Himalayan coal tits (<i>P. a. aemodius</i>) occur across a narrow range of less than 100 km in western Nepal. As a peculiarity, another distinctive cinnamon-bellied form is known from a single population so far. Genetic admixture of western and eastern mitochondrial lineages was restricted to the narrow zone of phenotypically intermediate populations. The cline width was estimated 46 km only with a center close to the population of the cinnamon-bellied phenotype. In contrast, allelic introgression of microsatellite loci was asymmetrical from eastern <i>P. a. aemodius</i> into far western populations of phenotypic <i>P. a. melanolophus</i> but not vice versa. Accordingly, the microsatellite cline was about 3.7 times wider than the mitochondrial one.</p>
Allele-specific collateral and fitness effects determine the dynamics of fluoroquinolone-resistance evolution
<p>Collateral sensitivity (CS), which arises when resistance to one antibiotic increases sensitivity towards other antibiotics, offers novel treatment opportunities to constrain or reverse the evolution of antibiotic resistance. The applicability of CS-informed treatments remains uncertain, in part because we lack an understanding of the generality of CS effects for different resistance mutations, singly or in combination. Here we address this issue in the Gram-positive pathogen <em>Streptococcus</em> <em>pneumoniae</em> by measuring collateral and fitness effects of clinically relevant <em>gyrA</em> and <em>parC</em> alleles, and their combinations, that confer resistance to fluoroquinolones. We integrated these results in a mathematical model which allowed us to evaluate how different <em>in</em> <em>silico</em> combination treatments impact the dynamics of resistance evolution. We identified common and conserved CS effects of different <em>gyrA</em> and <em>parC</em> alleles; however, the spectrum of collateral effects was unique for each allele or allelic pair. This indicated that allelic identity can impact the evolutionary dynamics of resistance evolution during monotreatment and combination treatment. Our model simulations, which included the experimentally derived antibiotic susceptibilities and fitness effects, and antibiotic-specific pharmacodynamics, revealed that both collateral and fitness effects impact the population dynamics of resistance evolution. Overall, we provide evidence that allelic identity and interactions can have a pronounced impact on collateral effects of different antibiotics and suggest that these need to be considered in models examining CS-based therapies.</p>
Data for: DRD4 allele frequencies in greylag geese vary between urban and rural sites
<p>With the increasing urbanisation of the last decades, more and more bird species occur in urban habitats. Birds which thrive in urban habitats often have a higher tolerance towards human disturbance and show behaviours which differ from their rural counterparts. There is increasing evidence that many behaviours have a genetic basis. One candidate gene is the dopamine receptor D4 (DRD4), which has been associated with fear and thus, flight initiation distance (FID). In this study, we analysed a segment of DRD4 in greylag geese <em>Anser anser</em>, describing the variability of this gene across several geographically distant populations, and comparing its variability between an urban and a rural site in south-west Germany. We additionally measured FIDs of urban and rural geese to test for a possible correlation with DRD4 genotypes. We found a high variation of DRD4, with 10 variable sites leading to 11 alleles and 35 genotypes. Two genotypes occurred in 60% of all geese and were thus defined as common genotypes versus 33 rare genotypes. Population differentiation was very low between the urban and rural sites in Germany but common genotypes occurred more often in the urban area and rare genotypes more often in the rural area. FID was significantly higher at the rural site, but no significant correlation between FID and DRD4 genotypes could be detected. Nevertheless, our results suggest that local site selection may be related to DRD4 genotypes.</p>
Prevalence of Borrelia burgdorferi and diversity of its outer surface protein C (ospC) alleles in blacklegged ticks (Ixodes scapularis) in Delaware
<p>Characterizing the diversity of genes associated with virulence and transmission of a pathogen across the pathogen's distribution can inform our understanding of host infection risk. <em>Borrelia burgdorferi</em> is a vector-borne bacterium that causes Lyme disease in humans and is common in the United States. The outer surface protein C (<em>ospC</em>) gene of <em>B</em>. <em>burgdorferi</em> exhibits substantial genetic variation across the pathogen's distribution and plays a critical role in virulence and transmission in vertebrate hosts. In fact, <em>B. burgdorferi </em>infections that disseminate across host tissues in humans are associated with only a subset of <em>ospC</em> alleles. Delaware has a high incidence of Lyme disease, but the diversity of <em>ospC</em> in <em>B. burgdorferi</em> in the state has not been evaluated. We used PCR to amplify <em>ospC</em> in <em>B. burgdorferi</em>-infected blacklegged ticks (<em>Ixodes</em> <em>scapularis</em>) in sites statewide and used short-read sequencing to identify <em>ospC</em> alleles. <em>B. burgdorferi</em> prevalence in blacklegged ticks varied across sites, but not significantly so. We identified 15 previously characterized <em>ospC</em> alleles accounting for nearly all of the expected diversity of alleles across the sites as estimated using the Chao1 index. Nearly 40% of sequenced infections (23/58) had more than one <em>ospC</em> allele present suggesting mixed strain infections and the relative frequencies of alleles in single infections were positively correlated with their relative frequencies in mixed infections. Turnover of ospC alleles was positively related to distance between sites with closer sites having more similar allele compositions than more distant sites. This suggests a degree of <em>B. burgdorferi</em> dispersal limitation or habitat specialization. <em>OspC</em> alleles known to cause disseminated infections in humans were found at the highest frequencies across sites, corresponding to Delaware's high incidence of Lyme disease.</p>
Raw GBIF data used in the article "Climate-induced range shifts drive adaptive response via spatio-temporal sieving of alleles"
<p>This table contains the raw (unfiltered) species occurrence data for Dianthus sylvestris complied from GBIF. A filtered subset of this data was combined with other data sources to define the input for the species distribution models used in the article "Climate-induced range shifts drive adaptive response via spatio-temporal sieving of alleles".</p>
Simulations on environmental fluctuations and the maintenance of sexually antagonistic alleles
<p>In this project, we investigate how environmental fluctuations impact the maintenance of sexually antagonistic alleles using the modelling framework of ecological coexistence theory.</p> <p>The simulations uploaded here can be used to reproduce the figures in the paper associated with this dataset. </p> <p> </p> <p>Please direct any queries about the project to <a href="https://github.com/stoufferlab/coexistence_alleles/blob/master/spflanagan.phd@gmail.com">spflanagan.phd@gmail.com</a>.</p>
Microsatellite alleles of two species of Tetramorium ants in their native and invasive ranges
<p>Microsatellite alleles at 16 loci, for 80 individuals of <em>Tetramorium immigrans</em> and 84 individuals of <em>T. tsushimae</em> from both their native and invasive ranges.</p>
Fixed allele differences associated with the centromere reveal chromosome morphology and rearrangements in a reptile (Varanus acanthurus Boulenger)
<p>Chromosome rearrangements are often implicated with genomic divergence and are proposed to be associated with species evolution. Rearrangements alter the genomic structure and interfere with homologous recombination by isolating a portion of the genome. Integration of multi-platform next generation DNA sequencing technologies has enabled putative identification of chromosome rearrangements in many taxa, however, integrating these data sets with cytogenetics is still uncommon beyond model genetic organisms. Therefore, to achieve the ultimate goal for the genomic classification of eukaryotic organisms, physical chromosome mapping remains critical. The ridge-tailed goannas (<em>Varanus</em> <em>acanthurus</em> BOULENGER) are a group of dwarf monitor lizards comprised of several species found throughout Northern Australia. These lizards exhibit extreme divergence at both the genic and chromosomal levels. The chromosome polymorphisms are widespread extending across much of their distribution, raising the question if these polymorphisms are homologous within the <em>V. acanthurus</em> complex. We used a combined genomic and cytogenetic approach to test for homology across divergent populations with morphologically similar chromosome rearrangements. We showed that more than one chromosome pair was involved with the widespread rearrangements. This finding provides evidence to support <em>de novo</em> chromosome rearrangements have occurred within populations. These chromosome rearrangements are characterised by fixed allele differences originating in the vicinity of the centromeric region. We then compared this region with several other assembled genomes of reptiles, chicken and the platypus. We demonstrated that the synteny of genes in chordates remains conserved despite centromere repositioning across these taxa.</p>
Allele surfing causes maladaptation in a Pacific salmon of conservation concern
<p>How different factors including demography, recombination or genome duplication may impact selection efficacy and the burden of deleterious mutations in different populations is a central question of evolutionary biology and genetics. Here we show that key evolutionary processes, including variation in effective population size through postglacial change in demography and recombination rates have affected the efficacy of selection and impacted the genetic load in Coho salmon (<em>Oncorhynchus kisutch</em>), a widely distributed salmonid species on the west coast of North America. Using whole genome resequencing data from 14 populations at different travelled migratory distances from their southern glacial refugium, we found support for postglacial gene surfing, with reduced <em>N</em><sub><em>e</em></sub> at the range recolonization front, thus inducing both a reduction in the efficacy of selection and a surf of deleterious alleles in populations evolving at low <em>N</em><sub><em>e</em></sub>. This inference was robust to various proxies of the load. In addition, comparing residual tetrasomic and re-diploidizing regions of the salmon genome, we found support for a prime role of recombination rates in shaping the within-genome variation of the load. Overall, our empirical results are remarkably consistent with expectations under the nearly neutral theory of molecular evolution. We discuss the fundamental and applied implications of these findings for evolutionary and conservation genomics.</p> <p> </p>
Genomic Answers for Kids pangenome graph and allele definitions
<p>This publication contains the Genomic Answer for Kids genome graph, the observes alleles and their frequencies.</p> <p>Included is a short document describing how to generate the graph, genotype samples, merge genotypes and identify singleton SVs.</p> <p>Related information such as assembly contig sizes, assembly intervals validated with Flagger, sequencing depth and repeat masking results are also included.</p> <p>Miscellaneous scripts that process and generate some of this data is also included.</p> <p>However, the assemblies and the genotypes, of each assembly, or any combination of identifying information cannot be included.</p>
Severe inbreeding depression is predicted by the “rare allele load” in Mimulus guttatus
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Asymmetric allelic introgression across a hybrid zone of the coal tit (Periparus ater) in the central Himalayas
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Raw data from: Natural alleles at the Doa locus underpin evolutionary changes in Drosophila lifespan and fecundity
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Revisiting the number of self‐incompatibility alleles in finite populations: From old models to new results
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Complete allele-specific silencing of the gain-of-function mutation of Huntington's disease
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ScienceDex guides
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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.