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.
54
datasets available to search
ShareScore release 0.9.0
Dataset results
54 results for “immunogenetics”
Data for: The immunogenetics of sexual parasitism
<p>Aligned amino acid sequences of 946 orthologous exon loci that were used to obtain a phylogeny of 13 anglerfish species. The locus sequences were obtained using a best hit search using TBLASTN v2.9.0 with the consensus amino acid sequences of the exons from Hughes et al. (PNAS 2013) as queries against databases of whole-genome shotgun sequencing reads (published with the study by Swann et al. (2020) that this dataset belongs to). The sequences for each locus were then aligned using MAFFT v7.464 with the L-INS-i strategy.</p>
Data from: The genome sequence and insights into the immunogenetics of the bananaquit (Passeriformes: Coereba flaveola)
Avian genomics, especially of non-model species, is in its infancy relative to mammalian genomics. Here, we describe the sequencing, assembly, and annotation of a new avian genome, that of the bananaquit Coereba flaveola (Passeriformes: Thraupidae). We produced ∼30-fold coverage of the genome with an assembly size of ca. 1.2 Gb, including approximately 16,500 annotated genes. Passerine birds, such as the bananaquit, are commonly infected by avian malarial parasites (Haemosporida), which presumably drive adaptive evolution of immunogenetic loci within the host genome. In the context of our research on the distribution of avian Haemosporida, we specifically characterized immune loci, including toll-like receptor (TLR) and major histocompatibility complex (MHC) genes. Additionally, we identified novel molecular markers in the form of single nucleotide polymorphisms (SNPs), both genome-wide and within identified immune loci. We discovered nine TLR genes and four MHC genes and identified five other TLR- or MHC- associated genes. Genome-wide, over 6 million high-quality SNPs were annotated, including 568 within TLR genes and 102 in MHC genes. This newly described genome and immune characterization expands the knowledge base for avian genomics and phylogenetics and allows for immune genotyping in the bananaquit, providing tools for the investigation of host-parasite coevolution.
Data from: Influence of immunogenetics, sex, and body condition on the cutaneous microbial communities of two giant salamanders
Open the record for dataset details and reuse information.
Data from: The genome sequence and insights into the immunogenetics of the bananaquit (Passeriformes: Coereba flaveola)
Open the record for dataset details and reuse information.
Data from: Parasite-mediated selection drives an immunogenetic tradeoff in plains zebras (Equus quagga)
Open the record for dataset details and reuse information.
Data from: Weak link between dispersal and parasite community differentiation or immunogenetic divergence in two sympatric cichlid fishes
Geographical isolation, habitat variation and trophic specialization have contributed to a large extent to the astonishing diversity of cichlid fishes in the Great East African lakes. Because parasite communities often vary across space and environments, parasites can accompany and potentially enhance cichlid species diversification. However, host dispersal may reduce opportunities for parasite-driven evolution by homogenizing parasite communities and allele frequencies of immunity genes. To test for the relationships between parasite community variation, host dispersal and parasite-induced host evolution, we studied two sympatric cichlid species with contrasting dispersal capacities along the shores of southern Lake Tanganyika. Whereas the philopatric Tropheus moorii evolved into several genetically differentiated colour morphs, Simochromis diagramma is phenotypically rather uniform across its distribution range and shows only weak population structure. Populations of both species were infected with divergent parasite communities and harbour differentiated variant pools of an important set of immune genes, the major histocompatibility complex (MHC). The overall extent of geographical variation of parasites and MHC genes was similar between host species. This indicates that immunogenetic divergence among populations of Lake Tanganyika cichlids can occur even in species that are strongly dispersing. However, because this also includes species that are phenotypically uniform, parasite-induced evolution may not represent a key factor underlying species diversification in this system.
Data from: Linking innate immunogenetic variation with phenotypic traits in a wild population of tree swallows, Tachycineta bicolor
Unravelling the genetic basis of phenotypic variation among individuals is an important step in our understanding of evolution. Recent studies of innate immune genes, such as β -defensins, revealed that these genes had high levels of polymorphism. However, researchers have yet to quantify the effects of such variability on immune responses and fitness-related traits in wild populations. In this study, we assessed how the variability at six avian β -defensin (AvBD) genes was linked to an immune function and reproductive success in adult tree swallows (Tachycineta bicolor). We investigated the links between genetic variations using single nucleotide polymorphisms at AvBD genes, immune function as the bacterial killing ability (BKA) and fledging success. We assessed how female immunogenetics were linked to the presence of eggshell bacteria in their clutches and hatching success. We found weak associations between the presence of AvBD genes, BKA and eggshell bacteria. Our results suggested that homozygosity at some loci may be advantageous for defence against bacteria. Variability at β -defensin genes was not related to either hatching or fledging success. BKA of parents was positively linked with fledging success. More studies are needed to assess whether or not β -defensin genes are significantly affecting fitness-related traits in wild populations.
Data from: Prelude to a panzootic: gene flow and immunogenetic variation in northern little brown myotis vulnerable to bat white-nose syndrome
The fungus that causes bat white-nose syndrome (WNS) recently leaped from eastern North America to the Pacific Coast. The pathogen's spread is associated with the genetic population structure of a host (Myotis lucifugus). To understand the fine-scale neutral and immunogenetic variation among northern populations of M. lucifugus, we sampled 1142 individuals across the species' northern range. We used genotypes at 11 microsatellite loci to reveal the genetic structure of, and directional gene flow among, populations to predict the likely future spread of the pathogen in the northwest and to estimate effective population size (Ne). We also pyrosequenced the DRB1-like exon 2 of the class II major histocompatibility complex (MHC) in 160 individuals to explore immunogenetic selection by WNS. We identified three major neutral genetic clusters: Eastern, Montane Cordillera (and adjacent sampling areas), and Haida Gwaii, with admixture at intermediate areas and significant substructure west of the prairies. Estimates of Ne were unexpectedly low (289–16 000). Haida Gwaii may provide temporary refuge from WNS, but the western mountain ranges are not barriers to its dispersal in M. lucifugus and are unlikely to slow its spread. Our major histocompatibility complex (MHC) data suggest potential selection by WNS on the MHC, but gene duplication limited the immunogenetic analyses.
Data from: Development of a genotype-by-sequencing immunogenetic assay as exemplified by screening for variation in red fox with and without endemic rabies exposure
Pathogens are recognized as major drivers of local adaptation in wildlife systems. By determining which gene variants are favored in local interactions among populations with and without disease, spatially explicit adaptive responses to pathogens can be elucidated. Much of our current understanding of host responses to disease comes from a small number of genes associated with an immune response. High-throughput sequencing (HTS) technologies, such as genotype-by-sequencing (GBS), facilitate expanded explorations of genomic variation among populations. Hybridization-based GBS techniques can be leveraged in systems not well characterized for specific variants associated with disease outcome to "capture" specific genes and regulatory regions known to influence expression and disease outcome. We developed a multiplexed, sequence capture assay for red foxes to simultaneously assess ~300-kbp of genomic sequence from 116 adaptive, intrinsic, and innate immunity genes of predicted adaptive significance and their putative upstream regulatory regions along with 23 neutral microsatellite regions to control for demographic effects. The assay was applied to 45 fox DNA samples from Alaska, where three arctic rabies strains are geographically restricted and endemic to coastal tundra regions, yet absent from the boreal interior. The assay provided 61.5% on-target enrichment with relatively even sequence coverage across all targeted loci and samples (mean = 50×), which allowed us to elucidate genetic variation across introns, exons, and potential regulatory regions (4,819 SNPs). Challenges remained in accurately describing microsatellite variation using this technique; however, longer-read HTS technologies should overcome these issues. We used these data to conduct preliminary analyses and detected genetic structure in a subset of red fox immune-related genes between regions with and without endemic arctic rabies. This assay provides a template to assess immunogenetic variation in wildlife disease systems.
Data from: Transcriptomic characterization of the immunogenetic repertoires of heteromyid rodents
Background: When populations evolve under disparate environmental conditions, they experience different selective pressures that shape patterns of sequence evolution and gene expression. These may be manifested in genetic and phenotypic differences such as a diverse immunogenetic repertoire in species from tropical latitudes that have greater and/or different parasite burdens than more temperate species. To test this idea, we compared the transcriptomes of one tropical species (Heteromys desmarestianus) and two species from temperate latitudes (Dipodomys spectabilis and Chaetodipus baileyi) from the Heteromyidae. We did so in a search for positive selection on sequences and/or differential expression, while controlling for phylogenetic history in our choice of species. Results: We identified 127,812 contigs and annotated 34,878 of these, identifying immune genes associated with interleukins, cytokines, and the production of mast cells. We identified 632 genes that were upregulated in H. desmarestianus (8.7% of genes tested) and 492 (6.7%) that were downregulated. Gene ontology terms including "immune response" were associated with 31 (4.9%) of the 632 upregulated genes. We found preliminary evidence for positive selection on three genes (Palmitoyltransferase ZDHHC5 Ubiquitin-conjugating enzyme E2 N, Krueppel-like factor 10, and Spindle and kinetochore-associated protein 1) along the H. desmarestianus lineage. Conclusions: Overall our findings pinpoint genes in species from disparate environments that are on different evolutionary trajectories in terms of expression levels and/or nucleotide sequence. Our data indicate there are significant differences in the expression of genes among the spleen transcriptomes of these species and that a number of these differentially expressed genes do not show the same pattern of differential expression in another tissue type. This points to the possibility of expression differences between these species specific to the spleen transcriptome.
Data from: Immunogenetic response of the bananaquit in the face of malarial parasites
Background: In the arms race between hosts and parasites, genes involved in the immune response are targets for natural selection. Toll-Like Receptor (TLR) genes play a role in parasite detection as part of the innate immune system whereas Major Histocompatibility Complex (MHC) genes encode proteins that display antigens as part of the vertebrate adaptive immune system. Thus, both gene families are under selection pressure from pathogens. The bananaquit (Coereba flaveola) is a passerine bird that is a common host of avian malarial parasites (Plasmodium sp. and Haemoproteus sp.). We assessed molecular variation of TLR and MHC genes in a wild population of bananaquits and identified allelic associations with resistance/susceptibility to parasitic infection to address hypotheses of avian immune response to haemosporidian parasites. Results: We found that allele frequencies are associated with infection status at the immune loci studied. A consistent general trend showed the infected groups possessed more alleles at lower frequencies, and exhibited unique alleles, compared to the uninfected group. Conclusions: Our results support the theory of natural selection favoring particular alleles for resistance while maintaining overall genetic diversity in the population, a mechanism which has been demonstrated in some systems in MHC previously but understudied in TLRs.
Annotated transcriptome data from: Transcriptome annotation reveals minimal immunogenetic diversity among Wyoming toads, Anaxyrus baxteri
<p>Briefly considered extinct in the wild, the future of the wild population of the Wyoming toad (Anaxyrus baxteri) continues to rely on captive breeding to supplement the wild population. Given its small natural geographic range and history of rapid population decline at least partly due to fungal disease, investigation of the diversity of key receptor families involved in the host immune response represents an important conservation need. Population decline may have reduced immunogenetic diversity sufficiently to increase the vulnerability of the species to infectious diseases. Here we use comparative transcriptomics to examine the diversity of toll-like receptors and major histocompatibility complex (MHC) sequences across three individual Wyoming toads. We find reduced diversity at MHC genes compared to bufonid species with a similar history of bottleneck events. Our data provide a foundation for future studies that seek to evaluate the genetic diversity of Wyoming toads, identify biomarkers for infectious disease outcomes, and guide breeding strategies to increase genomic variability and wild release successes.</p>
Integrative genomics sheds light on the immunogenetics of tuberculosis in cattle
<p><em><span>Mycobacterium bovis</span></em><span> causes bovine tuberculosis (bTB), an infectious disease of cattle that represents a zoonotic threat to humans. Research has shown that the peripheral blood (PB) transcriptome is perturbed during bTB disease but the genomic architecture underpinning this transcriptional response remains poorly understood.</span> Here, we analyse PB transcriptomics data from 63 control and 60 confirmed <em>M. bovis </em>infected animals and detect 2,592 differently expressed genes perturbing multiple immune response pathways. Leveraging imputed genome-wide SNP data, we characterise thousands of <em>cis­</em>-expression quantitative trait loci (eQTLs) and show that the PB transcriptome is substantially impacted by intrapopulation genomic variation during <em>M. bovis</em> infection. Integrating our <em>cis-</em>eQTL data with bTB susceptibility GWAS summary statistics, we perform a transcriptome-wide association study and identify 132 functionally relevant genes (including <em>RGS10</em>, <em>GBP4</em>, <em>TREML2</em>, and <em>RELT</em>) and provide important new omics data for understanding the host response to mycobacterial infections that cause tuberculosis in mammals.</p> <p> </p>
Data from: Selection from parasites favors immunogenetic diversity but not divergence among locally adapted host populations
The unprecedented polymorphism in the major histocompatibility complex (MHC) genes is thought to be maintained by balancing selection from parasites. However, do parasites also drive divergence at MHC loci between host populations, or do the effects of balancing selection maintain similarities among populations? We examined MHC variation in populations of the livebearing fish Poecilia mexicana and characterized their parasite communities. Poecilia mexicana populations in the Cueva del Azufre system are locally adapted to darkness and the presence of toxic hydrogen sulfide, and represent highly divergent ecotypes or incipient species. Parasite communities differed significantly across populations, and populations with higher parasite loads had higher levels of diversity at class II MHC genes. However, despite different parasite communities, marked divergence in adaptive traits and in neutral genetic markers, we found MHC alleles to be remarkably similar among host populations. Our findings indicate that balancing selection from parasites maintains immunogenetic diversity of hosts, but this process does not promote MHC divergence in this system. On the contrary, we suggest that balancing selection on immunogenetic loci may outweigh divergent selection causing divergence, thereby hindering host divergence and speciation. Our findings support the hypothesis that balancing selection maintains MHC similarities among lineages during and after speciation (trans-species evolution).
Immunogenetics Predictors With COVID-19
ClinicalTrials.gov study NCT04390269. IPD Sharing: NO. Countries: 1. Publications: 7.
Immunogenetic Mechanisms in Behcet's Disease
ClinicalTrials.gov study NCT01109433. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Immunogenetic Modulators of Mucosal Protection From HIV-1
ClinicalTrials.gov study NCT03701802. IPD Sharing: UNDECIDED. Countries: 1. Publications: 13.
Immunogenetics of Visceral Leishmaniasis
ClinicalTrials.gov study NCT00342823. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Birdshot Chorioretinopathy : Prospective Follow-up and Immunogenetic Studies(CO-BIRD)
ClinicalTrials.gov study NCT05153057. IPD Sharing: YES. Countries: 1. Publications: 17.
Immunogenetic Profiling of Goeckerman Therapy in the Treatment of Psoriasis Vulgaris
ClinicalTrials.gov study NCT03662685. IPD Sharing: NO. Countries: 1. Publications: 8.
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.