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Figure 3 in Genome-wide characterization of microsatellites and development of polymorphic markers shared between two weevils of Eucryptorrhynchus (Coleoptera: Curculionidae)
Figure 3. Genetic structure of Eucryptorrhynchus brandti (a) and E. scrobiculatus (b) populations based on 14 microsatellite markers inferred using the software STRUCTURE. Each bin indicates an individual. Different colors show the identified clusters. The best number of clusters (K) is 3. Abbreviations: BJHD—Haidian District, Beijing; NXZW—Zhongwei, Ningxia; SDTA—Tai'an, Shandong; SXYL—Yangling, Shaanxi.
Figure 2 in Genome-wide characterization of microsatellites and development of polymorphic markers shared between two weevils of Eucryptorrhynchus (Coleoptera: Curculionidae)
Figure 2. Frequency distribution of microsatellites among different motifs in the Eucryptorrhynchus brandti and E. scrobiculatus. The "others" category represents summed motifs with counts below 100.
Figure 1 in Genome-wide characterization of microsatellites and development of polymorphic markers shared between two weevils of Eucryptorrhynchus (Coleoptera: Curculionidae)
Figure 1. Collection sites for specimens of Eucryptorrhynchus brandti (red) and E. scrobiculatus (green). Abbreviations: BJHD— Haidian District, Beijing (116.22°E, 40.04°N); NXZW—Zhongwei, Ningxia (105.12°E, 37.50°N); SDTA—Tai'an, Shandong (116.72°E, 36.27°N); SXYL—Yangling, Shaanxi (108.07°E, 34.26°N).
Development of twenty-four microsatellite markers for Afrotropical Ornithodoros ticks
<p><strong>Background: </strong>Soft ticks of the genus <em>Ornithodoros</em> are responsible for the maintenance and transmission of the <em>African swine fever </em>(ASF)<em> virus</em> in the sylvatic and domestic viral cycles in Southern Africa. They are also the main vectors of <em>Borrelia</em> species causing relapsing fevers. Currently, no genetic markers are available for Afrotropical <em>Ornithodoros </em>ticks. As ASF spreads globally, such markers are needed to assess the role of ticks in the emergence of new outbreaks. The aim of this study was to design microsatellite markers that could be used for ticks of the <em>Ornithodoros moubata</em> complex, particularly <em>Ornithodoros phacochoerus</em>, to assess population structure and tick movements in ASF endemic areas.</p> <p><strong>Methods: </strong>One hundred and fifty-one markers were designed using the <em>O. moubata </em>and <em>O. porcinus</em> genomes after elimination of repeated sequences in the genomes. All designed markers were tested on <em>O. phacochoerus </em>and <em>O. porcinus </em>DNA to select the best markers.</p> <p><strong>Results:</strong> Twenty-four microsatellite markers were genotyped on two populations of <em>O. phacochoerus</em> and on few individuals from four other <em>Ornithodoros</em> species. Nineteen markers were selected to be as robust as possible for population genetic studies on <em>O. phacochoerus</em>.</p> <p><strong>Conclusions:</strong> The microsatellite markers developed here represent the first genetic tool to study nidicolous populations of Afrotropical <em>Ornithodoros</em>. This dataset contains the genotyping results obtained for all twenty-four markers tested.</p>
Characterization and microsatellite marker development for Geosmithia obscura, a common bark and ambrosia beetle associate
<p class="MsoNormal"><strong><span>Background. </span></strong><span>S</span><span>ymbioses between <em>Geosmithia</em> fungi and </span><span>wood-boring and bark beetles</span><span> seldom result in disease induction within the plant host. Yet exceptions exist such as <em>Geosmithia</em> <em>morbida</em>, the causal agent of Thousand Cankers Disease (TCD) of walnuts and wingnuts and <em>Geosmithia</em> sp. 41, the causal agent of Foamy Bark Canker disease of oaks. Isolates of<em> G. obscura </em>were recovered from black walnut trees in eastern Tennessee and<em> </em>at least one isolate induced cankers following artificial inoculation. Due to the putative pathogenicity and lack of recovery of <em>G. obscura </em>from natural lesions, a molecular diagnostic screening tool was developed using microsatellite markers mined from the <em>G. obscura </em>genome.</span></p> <p class="MsoNormal"><strong><span>Results. </span></strong><span>A total of 3,256 candidate microsatellite markers were identified (2236, 789, 137 di-, tri-, and tetra- motifs were identified, respectively), with 2011, 703, 101 di-, tri-, and tetra- motifs containing markers with primers. From these, 75 microsatellite markers were randomly selected, screened, and optimized, resulting in 28 polymorphic markers that yielded single, consistently recovered bands which were used in downstream analyses. Five of these microsatellite markers were found to be specific to <em>G. obscura </em>and did not cross-amplify into other, closely related species. Although the remaining tested markers could be useful, they cross-amplified within different <em>Geosmithia</em> species, making them not reliable for <em>G. obscura </em>detection.</span></p> <p class="MsoNormal"><strong><span>Conclusion.</span></strong><span> Five novel microsatellite markers (GOBS9, GOBS10, GOBS41, GOBS43, GOBS50) were developed based on <em>G. obscura</em> genome. These species-specific microsatellite markers are available as a tool for use in molecular diagnostics and can assist future surveillance studies.</span></p>
De novo developed microsatellite markers in gill parasites of the genus Dactylogyrus (Monogenea)
<p class="MsoBodyText">Approaches using microsatellite markers are considered the gold standard for modern population-genetic studies. However, though they have found application in research into various platyhelminth taxa, they remained substantially underutilized in the study of monogeneans. In the present study, a newly-developed set of 24 microsatellite markers was used to investigate the genetic diversity of the generalist monogenean species <i>Dactylogyrus vistulae</i>. The analyzed parasite specimens were collected from 13 cyprinoid species from 11 sites in the Apennine and Balkan peninsulas. A total of 159 specimens were genotyped at each of the loci and the number of alleles per locus ranged from 2 to 16, with a mean number of 6.958 alleles per locus. Exceptionally high genetic diversity was observed among <i>D. vistulae </i>individuals in the southern Balkans (mean N<sub>A </sub>per locus = 3.917), suggesting that generalist <i>D. vistulae </i>expanded from the south to the north in the Balkans and later putatively into central Europe. The initial clustering analysis divided all investigated specimens into three major clusters; however, the results of the subsequent analyses revealed the existence of various subpopulations, suggesting that the population structure of <i>D. vistulae </i>is associated with the diversification of their cyprinoid hosts. In addition, the partition of the parasite population was observed in regions of the sympatric occurrence of two host species, indicating that these hosts may represent a barrier to gene flow, even for generalist parasite species.</p>
Dataset for: Utilizing high-resolution genetic markers to track population-level exposure of migratory birds to renewable energy development
<p class="MsoNormal"><span>With new motivation to increase the proportion of energy demands met by zero-carbon sources, there is a greater focus on efforts to assess and mitigate the impacts of renewable energy development on sensitive ecosystems and wildlife, of which birds are of particular interest. One challenge for researchers, due in part to a lack of appropriate tools, has been estimating the effects from such development on individual breeding populations of migratory birds. To help address this, we utilize a newly developed, high-resolution genetic tagging method to rapidly identify the breeding population of origin of carcasses recovered from renewable energy facilities and combine them with maps of genetic variation across geographic space (called 'genoscapes') for five species of migratory birds known to be exposed to energy development, to assess the extent of population-level effects on migratory birds. We demonstrate that most avian remains collected were from the largest populations of a given species. In contrast, those remains from smaller, declining populations made up a smaller percentage of the total number of birds assayed. Results suggest that application of this genetic tagging method can successfully define population-level exposure to renewable energy development and may be a powerful tool to inform future siting and mitigation activities associated with renewable energy programs.</span></p>
Data from: genetic resources of macroalgae: development of an efficient method using microsatellite markers in non-model organisms
<p><span>Red and brown seaweeds are species with high ecological and economic importance. Here we report the feasibility of cost-effective molecular marker development in 6 species from different clades. Microsatellites markers of two brown seaweed species <em>Alaria esculenta</em>, <em>Pylaiella littoralis</em>, and of four red seaweed species <em>Calliblepharis jubata</em>, <em>Gracilaria gracilis</em>, <em>Gracilaria dura </em>and <em>Palmaria palmata</em> were identified and characterized using genomic sequences of Double-Digest Restriction site Associated DNA (ddRAD). A total of 64,623,186 reads were generated from two runs of multiplexed Illumina Miseq sequencing for which 30,636 reads containing microsatellites and 15,443 microsatellite loci with primers pairs were found. Five hundred seventy-six primers pairs were selected for amplification trials and levels of polymorphism. From the 338 that gave a positive amplification, 142 primers pairs were polymorphic. For genetic analyses two or three populations per species from 13 different geographic locations were used. A total of 28 usable polymorphic markers for <em>A. esculenta</em>, 18 for <em>P. littoralis</em>, 11 for <em>C. jubata</em>, 14 for <em>G. gracilis</em>, 21 for <em>G. dura </em>and 13 for <em>P. palmata </em>were developed. The overall number of alleles per locus ranged from 2 to 22. These 105 new microsatellite markers will be useful for further studies of population genetics, breeding programs and conservation genetics of these species. Compared with traditional approaches, our study yielded thousands of microsatellite loci in a short tim</span><span>e with affordable costs in six different species. This study based on ddRAD-sequencing for the development of microsatellite markers provides preliminary data u</span><span>sing a few individuals from two distinct populations on the genetic structure and reproduction mode of a non-model species as shown </span>with the detection of clonality for the two red algae, <em>C. jubata </em>and <em>G. dura</em> and the detection of highly genetically divergent populations corresponding probably to different cryptic species under the name of<em> P. littoralis</em>.</p>
De novo developed microsatellite markers in gill parasites of the genus Dactylogyrus (Monogenea)
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Data from: genetic resources of macroalgae: development of an efficient method using microsatellite markers in non-model organisms
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Dataset for: Utilizing high-resolution genetic markers to track population-level exposure of migratory birds to renewable energy development
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Development of twenty-four microsatellite markers for Afrotropical Ornithodoros ticks
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Data from: Haploid gynogens facilitate disomic marker development in paleotetraploid sturgeons
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Characterization and microsatellite marker development for Geosmithia obscura, a common bark and ambrosia beetle associate
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QTL mapping and marker development for tolerance to sulfur phytotoxicity in melon (Cucumis Melo)
<p><span>Elemental sulfur is an effective, inexpensive fungicide for many foliar pathogens, but severe phytotoxicity prohibits its use on many melon varieties. Sulfur phytotoxicity causes chlorosis and necrosis of leaf tissue, leading to plant death in the most sensitive lines, while other varieties have little to no damage. A high-density, genotyping-by-sequencing (GBS)-based genetic map of a recombinant inbred line (RIL) population segregating for sulfur tolerance was used for a quantitative trait loci (QTL) mapping study of sulfur phytotoxicity in melon. One major (qSulf-1) and two minor (qSulf-8 and qSulf-12) QTL were associated with sulfur tolerance in the population. <a name="_Hlk40443716">The development of Kompetitive Allele-Specific PCR (KASP) markers developed across qSulf-1 decreased the QTL interval from 239 kb (cotyledons) and 157 kb (leaves) to 97 kb (both tissues). </a>The markers were validated for linkage to sulfur tolerance in a set of melon cultivars. These KASP markers can be incorporated into melon breeding programs for introgression of sulfur tolerance into elite melon germplasm.</span></p> <p> </p> <p> </p>
SNPs markers of Trypoxylus dichotomus developed by using specific‐locus amplified fragment sequencing (SLAF‐seq) techniques
<p>The Japanese rhinoceros beetle Trypoxylus dichotomus is one of the largest beetle species in the world and is commonly used in traditional chinese medicine. Ten subspecies of T. dichotomus and a related Trypoxylus species (T. kanamorii) have been described throughout Asia, but their taxonomic delimitations remain problematic. To clarify issues such as taxonomy, and the degree of genetic differentiation of Trypoxylus populations, we investigated the genetic structure, genetic variability and phylogeography of 53 specimens of Trypoxylus species from 44 locations in five Asian countries (China, Japan, Korea, Thailand, and Myanmar). Using specific‐locus amplified fragment sequencing (SLAF‐seq) techniques, we developed 330,799 SLAFs over 114.16M reads, in turn yielding 46,939 high-resolution single nucleotide polymorphisms (SNPs) for genotyping.</p>
Data from: Development of Diversity Arrays Technology markers as a tool for rapid genomic assessment in Nile tilapia, Oreochromis niloticus
The development of genomic markers is described for Nile tilapia, Oreochromis niloticus, using the Diversity Arrays Technology (DArT) genotype-by-sequencing platform. A total of 13 215 single nucleotide polymorphism (SNP) markers and 12 490 silicoDArT (dominant) markers were identified from broodstock of two selective breeding programs [Genetically Improved Farmed Tilapia (GIFT) strain from Malaysia and the Abbassa strain from Egypt]. Over 10 000 SNPs were polymorphic in either strain, and 2985 and 3087 showed strain-specific polymorphisms for the GIFT and Abbassa strains respectively. We demonstrate the potential utility of these markers for rapid genomic screening and use in breeding programs.
Data from: High-throughput microsatellite marker development in two sparid species and verification of their transferability in the family Sparidae
Recently, 454 sequencing has emerged as a popular method for isolating microsatellites owing to cost-effectiveness and time saving. In this study, repeat-enriched libraries from two southern African endemic sparids (Pachymetopon blochii and Lithognathus lithognathus) were 454 GS-FLX sequenced. From these, 7370 sequences containing repeats (SCRs) were identified. A brief survey of 23 studies showed a significant difference between the number of SCRs when enrichment was performed first before 454 sequencing. We designed primers for 302 unique fragments containing more than five repeat units and suitable flanking regions. A fraction (<11%) of these loci were characterized with 18 polymorphic microsatellite loci (nine in each of the focal species) being described. Sanger sequencing of alleles confirmed that size variation was because of differences in the number of tandem repeats. However, a case of homoplasy and sequencing errors in the 454 sequencing were identified. These newly developed and four previously isolated loci were successfully used to identify polymorphic markers in nine other economically important species, representative of sparid diversity. The combination of newly developed markers with data from previous sparid cross-species studies showed a significant negative correlation between genetic divergence to focal species and microsatellite transferability. The high level of transferability we described (48% amplification success and 32% polymorphism) suggests that the 302 microsatellite loci identified represent an excellent resource for future studies on sparids. Microsatellite marker development should commonly include tests of transferability to reduce costs and increase feasibility of population genetics studies in nonmodel organisms.
Data from: Development of genomic tools in a widespread tropical tree, Symphonia globulifera L.f.: a new low-coverage draft genome, SNP and SSR markers
Population genetic studies in tropical plants are often challenging because of limited information on taxonomy, phylogenetic relationships and distribution ranges, scarce genomic information and logistic challenges in sampling. We describe a strategy to develop robust and widely applicable genetic markers based on a modest development of genomic resources in the ancient tropical tree species Symphonia globulifera L.f. (Clusiaceae), a keystone species in African and Neotropical rainforests. We provide the first low-coverage (11X) fragmented draft genome sequenced on an individual from Cameroon, covering 1.027 Gbp or 67.5% of the estimated genome size. Annotation of 565 scaffolds (7.57 Mbp) resulted in the prediction of 1046 putative genes (231 of them containing a complete open reading frame) and 1523 exact simple sequence repeats (SSRs, microsatellites). Aligning a published transcriptome of a French Guiana population against this draft genome produced 923 high-quality single nucleotide polymorphisms. We also preselected genic SSRs in silico that were conserved and polymorphic across a wide geographical range, thus reducing marker development tests on rare DNA samples. Of 23 SSRs tested, 19 amplified and 18 were successfully genotyped in four S. globulifera populations from South America (Brazil and French Guiana) and Africa (Cameroon and São Tomé island, FST = 0.34). Most loci showed only population-specific deviations from Hardy–Weinberg proportions, pointing to local population effects (e.g. null alleles). The described genomic resources are valuable for evolutionary studies in Symphonia and for comparative studies in plants. The methods are especially interesting for widespread tropical or endangered taxa with limited DNA availability.
Development of novel, Exon-Primed Intron-Crossing (EPIC) markers from EST databases and evaluation of their phylogenetic utility in Commiphora (Burseraceae)
Premise of the study: Novel nuclear exon-primed intron-crossing (EPIC) markers were developed to increase phylogenetic resolution among recently diverged lineages in the frankincense and myrrh family, Burseraceae, using Citrus, Arabidopsis, and Oryza genome resources. Methods and Results: Primer pairs for 48 nuclear introns were developed using the genome resource IntrEST and were screened using species of Commiphora and other Burseraceae taxa. Four putative intron regions (RPT6A, BXL2, mtATP Synthase D, and Rab6) sequenced successfully for multiple taxa and recovered phylogenies consistent with those of existing studies. In some cases, these regions yielded informative sequence variation on par with that of the nrDNA internal transcribed spacer. Conclusions: The combination of freely available genome resources and our design criteria have uncovered four, single-copy nuclear intron regions that are useful for phylogenetic reconstruction of Burseraceae taxa. Because our EPIC primers also amplify Arabidopsis, we recommend their trial in other rosid and eudicot lineages.
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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.