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2,785 results for “genotyping”
Genotyping-By-Sequencing and Reference Genome Enabled Variant Discovery in Octoploid Strawberry
<p>(P0652) Genotyping-By-Sequencing and Reference Genome Enabled Variant Discovery in Octoploid Strawberry</p> <p>Genotyping-by-sequencing (GBS) approaches have enabled routine high-density genome-wide DNA variant discovery in numerous agriculturally important species. Applications of GBS in octoploid (2n = 8x = 56) strawberry (Fragaria × ananassa) have been hindered by the absence of a reference genome for physically mapping DNA sequences; for discovering variants with sub-genome resolution, or effectively distinguishing homologous from homeologous variation. High-quality reference genome assemblies have recently emerged, supplying the foundation for this study, which focused on demonstrating the utility of GBS for calling sub-genome specific DNA variants in octoploid strawberry. To reduce genomic DNA complexity, double-digest protocols were tested on diverse accessions with two restriction enzyme combinations (PstI-MseI and HindIII-MseI). GBS libraries were sequenced on an Illumina HiSeq 4000 using a 150 bp paired-end protocol. For the purpose of this study, we describe the deployment of a flexible bioinformatic pipeline for GBS-facilitated variant discovery in octoploid strawberry. The percentage of uniquely mapped reads ranged from 51.41% for PstI-MseI to 55.56% for HindIII- MseI resulting in 1,591,764 and 2,362,556 unique locations, respectively. The number of discovered variants was 2.5-fold greater for HindIII-MseI (491,811) than PstI-MseI (199,486). The GBS protocols uncovered a dense genome-wide landscape of DNA variants for high- precision genetic mapping, identification of DNA variants associated with agriculturally important phenotypes, genomic-enabled breeding, and other applications in octoploid strawberry.</p> <p>Poster: PDF of poster and abstract for PAG 2018 (P0652)</p> <p>Figures: PNGs of figures on the poster</p> <p>Scrips: Txt files of SLURM scripts used to generate the follow .vcf files.</p> <p>- 8x_GBS_0_index: Uses BWA to index the reference genome (Edger et al 2019) for later use.</p> <p>- 8x_GBS_1_Demultiplex: Used Sabre to demultiplex fastq.gz files. Demultiplex_key_PE links individuals to their unique barcode.</p> <p>- 8x_GBS_2_Main: adapter removal, sequence alignment, and individual variant calling as a SLURM array. results in a .gvcf file for individuals.</p> <p>- 8x_GBS_3_Variant: population-level variant calling to a final .vcf file</p> <p>VCF: Two VCF files from the two enzyme experiments. H = HindIII-MseI; P = PstI-MseI</p>
Gel-electrophoresis of subjects' BDNF genotyping PCR
<p>Supplementary Figure of BDNF genotyping</p>
Comparative evaluation of band-based genotyping methods for Mycobacterium intracellulare and its application for epidemiological analysis
<p><em>Mycobacterium intracellulare</em> is a leading cause of nontuberculous mycobacterial pulmonary disease, with a rapidly increasing prevalence worldwide. This bacterium, commonly distributed in soil and water, is known to be transmitted through the environment rather than between people. Therefore, it is imperative to establish distinguishable genotyping methods to understand the clinical outcome, disease relapses, and epidemiology. Therefore, the present study comprised two steps. First, variable number tandem repetition (VNTR), VNTR-mycobacterial interspersed repetitive units (VNTR-MIRU), repetitive sequence based-PCR (rep-PCR) and pulsed field gel electrophoresis (PFGE) as band-based genotyping methods were performed using 19 <em>M. intracellualre</em> isolated from patients with PD. The comparative results of genotyping techniques and geographical characteristics in this study may provide fundamental information for the epidemiology of <em>M. intracellulare</em>.</p>
Host genotype and stable differences in algal symbiont communities explain patterns of thermal stress response of Montipora capitata following thermal pre-exposure and across multiple bleaching events
<p>Data and script supporting "Stable symbiont communities and host genotype underpin complex differences in thermal stress response in <em>Montipora capitata</em>".</p> <p>"Data_MASTER.xlsx" contains raw water temperature, PAM fluorometry F<sub>v</sub>/F<sub>M</sub>, and qPCR data, as well as fragment identification information.</p> <p>"data_processing.R" contains the R script used to clean up, analyze, and visualize the data.</p> <p><strong>Abstract:</strong></p> <p>As sea surface temperatures increase worldwide due to climate change, coral bleaching events are becoming more frequent and severe, resulting in reef degradation. Leveraging the inherent ability of reef-building corals to acclimatize to thermal stress via pre-exposure to protective temperature treatments may become an important tool in improving the resilience of coral reefs to rapid environmental change. We investigated whether historical bleaching phenotype, coral host genotype, and exposure to protective temperature treatments would affect the response of the Hawaiian coral <em>Montipora capitata</em> to natural thermal stress. Fragments were collected from colonies that demonstrated different bleaching responses during the 2014-2015 event in Kāne‘ohe Bay (O‘ahu, Hawai‘i) and exposed to four different artificial temperature pre-treatments (and a control at ambient temperature). After recovery, fragments experienced a natural thermal stress event either in laboratory conditions or their native reef environment. Response to thermal stress was quantified by measuring changes in the algal symbionts’ photochemical efficiency, community composition, and relative density. Historical bleaching phenotype was reflected in stable differences in symbiont community composition, with historically bleached corals containing only <em>Cladocopium</em> symbionts and historically non-bleached corals having mixed symbiont communities dominated by <em>Durusdinium</em>. Mixed-community corals lost more <em>Cladocopium</em> than <em>Cladocopium</em>-only corals during the natural thermal stress event, and preferentially recovered with <em>Durusdinium</em>. Laboratory pre-treatments exposed corals to more thermal stress than anticipated, causing photochemical damage that varied significantly by genotype. While none of the treatments had a protective effect, temperature variation during treatments had a significant detrimental effect on photochemical efficiency during the thermal stress event. These results show that acclimatization potential is affected by fine-scale differences in temperature regime, host genotype, and relatively stable differences in symbiont community composition that underpin historical bleaching phenotypes in <em>M. capitata</em>.</p> <p> </p>
Data from: Temperature-dependent development and survival of an invasive genotype of wheat curl mite, Aceria tosichella
<p><strong>Filename: Development.xlsx</strong></p> <p>Variables:</p> <p>1. id_spec - specimen ID<br> 2. temp - temperature of incubation<br> 3. trial - replication ID<br> 4. larv - number of days needed to reach larva stage <br> 5. q_larv - number of days needed to reach quiescent larva stage <br> 6. nymph - number of days needed to reach nymph stage <br> 7. q_nymph - number of days needed to reach quiescent nymph stage <br> 8. adult - number of days needed to reach adult stage <br> 9. egg - number of days needed to oviposit egg of next generation </p> <p><strong>Filename: Survival.xlsx</strong></p> <p>Variables:</p> <p>1. id_spec - specimen ID<br> 2. temp - temperature of incubation<br> 3. time - number of days when individual was observed alive<br> 4. stage - developmental stage which individual reached before death<br> 5. sex - sex of an individual (F - female; M - male; NA - unknown)<br> 6. status - 0 - censored observation; 1 - observed event of death</p>
Genotype_data_NBPGR
<p><strong>Genotyping for the manuscript entitled "Identification of QTLs/defense genes effective at seedling stage against prevailing races of wheat stripe rust in India."</strong></p>
Data from: Interaction of serum vitamin B12 and folate with MTHFR genotypes on risk of ischemic stroke
<p>Abstract Objective We evaluated the interaction of serum folate and vitamin B12 (B12) with methylenetetrahydrofolate reductase (MTHFR) C677T genotypes, on the risk of first ischemic stroke, and on the efficacy of folic acid (FA) treatment in prevention of first ischemic stroke. Methods A total of 20,702 hypertensive adults were randomized to a double-blind treatment of daily enalapril 10mg and FA 0.8mg or enalapril 10mg alone. Participants were followed-up every three months. Results Median values of folate and B12 concentrations at baseline were 8.1 ng/mL and 280.2 pmol/L, respectively. Over a median of 4.5 years, among those not receiving FA, participants with baseline serum B12 and/or serum folate above the median had a significantly lower risk of first ischemic stroke (HR, 0.74; 95%CI: 0.57-0.96), especially in those with MTHFR 677 CC genotype (wild type) (HR, 0.49; 95%CI: 0.31-0.78). FA treatment significantly reduced the risk of first ischemic stroke in participants with both folate and B12 below the median (2.3% in enalapril-folic acid group vs. 3.6% in enalapril-only group; HR, 0.62; 95%CI: 0.46-0.86), particularly in MTHFR 677 CC carriers (1.6% vs. 4.9%; HR, 0.24; 95%CI: 0.11-0.55). However, carriers of TT responded better with both folate and B12 levels above the median (HR, 0.28; 95%CI: 0.10-0.75). Conclusions The risk of first ischemic stroke was significantly higher in hypertensive patients with low levels of both folate and B12. Effect of FA treatment was greatest in patients with low folate and B12 with the CC genotype, and with high folate and B12 with the TT genotype.</p>
Parentage analysis: Maternal, paternal, and offspring genotypes
<p>Males pursuing alternative reproductive tactics (ARTs) face uneven sperm competition risk and often invest differently into ejaculates and mate acquisition. In loliginid squids, the existence of two fertilization sites in females (buccal membrane vs. oviduct opening), associated with ARTs, might even raise such asymmetries. By using a privileged site, consorts are predicted to monopolize paternity, making it difficult to understand how sneakers persist along generations. By controlling spermatophore attachment sites used by males, we empirically evidence that fertilization sites indeed influence male reproductive success, with consorts monopolizing paternity when competing with sneakers. However, we also show that females store sperm from several sneakers, which are often used to fertilize part of their progeny, even after recent mating with a consort. Our results not only highlight the importance of the buccal sperm storage organ for sperm provision and offspring genetic diversity but also explain how sneakers might persevere in a system dominated by consorts. Together, these results indicate that loliginid ARTs reflect complex fertilization dynamics, with consorts displaying agonistic behaviors to control paternity, and sneakers mating promiscuously to assure cumulative reproductive success – enhanced by long-term sperm storage. Ultimately, these results highlight the importance of considering fertilization environments when studying ARTs evolution.</p>
Data from: Estimating genotyping errors from genotype and reconstructed pedigree data
1. Genotyping errors are rules rather than exceptions in reality, and are found in virtually all but very small datasets. These errors, even when occurring at an extremely low rate, can derail many genetic analyses such as parentage/sibship assignments and linkage/association studies. 2. Nonetheless, few robust and accurate methods are available for estimating the rate of occurrence of genotyping errors and for identifying individual erroneous genotypes at a locus. Methods based on duplicate genotyping are expensive, and estimate genotype inconsistency rather than error rate at a locus. Methods based on Hardy-Weinberg equilibrium tests have low robustness and low power, and apply only to those particular errors that cause excessive homozygosity. Methods based on pedigrees are powerful, robust and accurate. However, they rely on known and complete pedigrees that are unfortunately rarely available from natural populations in the wild. 3. I proposed a maximum likelihood method to reconstruct pedigrees from genotype data with errors occurring at a roughly estimated (presumed) rate. In this paper, I describe how to use the method and inferred pedigree in estimating allelic dropout (or null allele) rate and false allele rate jointly at each marker locus, in identifying the erroneous genotypes, and in inferring the most likely genotypes at each locus of each individual. I examine the power, accuracy and robustness of the method by extensive simulations, and demonstrate the usefulness of the method by analysing three empirical datasets. 4. It is concluded that, both pedigrees and the rates of genotyping errors at each locus can be reliably estimated from the same genotype data by the same likelihood method, when marker information is sufficient and some sampled individuals are first-degree relatives. The erroneous genotypes are however inferred conservatively, and are reliably detected only when they occur in large families and/or at highly polymorphic loci. Estimation of genotyping error rates per locus and identification of erroneous genotypes of each individual at each locus should be routinely conducted to assess and improve data quality, to highlight markers for optimization of genotyping protocols or for replacement, and to enable the integration of genotyping errors in a robust statistical analysis.
Data from: Using partial genotyping to estimate the genetic and maternal determinants of adaptive traits in a progeny trial of Fagus sylvatica
Understanding the determinants of phenotypic variation is critical to evaluate the ability of traits to evolve in a changing environment. In trees, the genetic component of the phenotypic variance is most often estimated based on maternal progeny tests. However, the lack of knowledge about the paternal relatedness hampers the accurate estimation of additive genetic and maternal effects. Here, we investigate how different methods accounting for paternal relatedness allow the estimation of heritability and maternal determinants of adaptive traits in a natural population of Fagus sylvatica L., presenting non-random mating. Twelve potentially adaptive functional traits were measured in 60 maternal families in a nursery. We genotyped a subset of offspring and of all the potentially reproductive adults in the population at 13 microsatellite markers to infer paternal relationships and to estimate average relatedness within and between maternal families. This relatedness information was then used in family and animal models to estimate the components of phenotypic variance. All the studied traits displayed significant genetic variance and moderate heritability. Maternal effects were detected for the diameter increment, stem volume and bud burst. Comparison of family and animal models showed that unbalanced mating system led to only slight departures from maternal family assumptions in the progeny trial. However, neglecting the significant maternal effects led to an overestimation of the heritability. Overall, we highlighted the usefulness of relatedness pattern analyses using polymorphic molecular markers to accurately analyse tree sibling designs.
Illumina SNP Chip and Sequenom MassARRAY genotype data of Swedish Giant Schnauzers with and without hypothyroidism
<p>In this study, we sought to identify the genetic risk factors potentially involved in the susceptibility to hypothyroidism in the high-risk Giant Schnauzer dog breed. The genotype data generated in the study (Illumina 170k CanineHD Bead Chip, Sequenom MassARRAY high-throughput re-genotyping) proved to be essential for the identification and fine-mapping of a locus associated with protection against canine hypothyroidism.</p>
Data and R scripts for: Variation in phenotypic plasticity across age-at-maturity genotypes in wild Atlantic salmon
<p>Data and R-scripts underlying the statistical analyses of the study. </p>
Database of MSTN gene multi-loci genotypes of samples of the 1st trial (A22) of sheep breeds of Latvia within the framework of the project of the Latvian Council of Science LZP-2021/1-0489 project
<p><span>Project of The Latvian Council of Science (LCS) - LZP-2021/1-0489 project: “<strong>Development of an innovative approach to identify biological determinants involved in the between-animal variation in feed efficiency in sheep farming</strong>”.</span></p> <p><span>The <strong>aim of the project</strong> is</span><span> to determine whether the feed efficiency status of <span>Latvian meat sheep breeds</span> could be predicted using a panel of genetic and molecular markers previously found to be associated with divergent FE status in a training population of lambs when fed the same diet.</span></p> <p><strong><span>Novelty</span></strong><span>: to determine the parameters predicting the most productive result of lamb rearing, we set out to develop the cheapest and most effective method for determining markers of feed efficiency - based on molecular and genetic markers obtained from the blood of live lambs. </span></p> <p><strong><span>About the project:</span></strong></p> <p><span>The costs associated with lambing (buying or keeping sheep) and preparing or purchasing feed are the two most significant components of variable costs in sheep raising. Feed costs are high due to poor grain growing conditions in major producing countries, the use of feed grains in ethanol production, and increased competition for land in crop production compared to urban development<span>.</span> <span>Feed efficiency </span>in growing lambs (i.e., the animal’s ability to reach a market or adult body weight (BW) with the least feed intake) is a critical factor in the sheep industry. <span>Improving FE reduces production costs. Improving FE by 5% can bring economic benefits up to four times higher than a 5% increase in average daily gain (ADG).</span></span></p> <p><span>Traditionally, meat breeding programs have focused on outputs due mainly to the routine availability of phenotypic data on outputs or correlated traits. Currently, no marker has successfully explained enough of the variability in <span>feed efficiency </span>that they were used as part of a routine improvement program. According to our data, no genetic parameters for performance and feed efficiency traits are available for sheep. <span>The physiological determinants of feed efficiency or putative biomarkers used to analyse animal-to-animal variation in live lambs could be a cost-effective and rapid tool for genetic selection or management decisions.</span></span></p> <p><span>Myostatin (MSTN), a highly conserved member of the transforming growth factor-beta (TGF-b) superfamily, also known as growth/differentiation factor 8 (GDF8), the major regulator of myogenesis, functions as a negative regulator of muscle growth and development in mammals. Myostatin is a transforming growth factor (TGF)-β superfamily member and cannot be classified into the existing TGF-β subfamilies, such as inhibins or bone morphogenic proteins.<span> Mutations <em><span>MSTN</span></em> produce a “double-muscle” phenotype, making it commercially invaluable for improving livestock meat production and providing high-quality human protein. However, mutations at different loci of the <em><span>MSTN</span></em> often produce a variety of different phenotypes.</span></span></p> <p><strong><span>About the data of the project:</span></strong></p> <p><span>LZP-2021/1-0489 project data on lamb samples of the year 2022, or the A22 group, which consists of 76 intensively fattened lambs from six breeds.</span></p> <p><span><span>The whole MSTN gene was sequenced using Illumina NGS technology (AmpliSeq).</span></span><span><span> </span></span><span><span>The MSTN gene has been fully sequenced in lambs of Latvia (in sheep research in Latvia) for the first time. Information about 23 loci (</span></span><span><a href="https://doi.org/10.5281/zenodo.8146724"><span>https://doi.org/10.5281/zenodo.8146724</span></a></span><u><span>)</span></u><span><span> <span>compared with the last </span></span></span><span>reference sequences <span>ARS_UI_Ramb_v2.0.</span></span></p> <p><span>All variable SNPs in the MSTN gene were constructed by combining 24 distinct multi-loci genotypes. Reducing the number of loci to 16 by excluding those variables in only one sample or complete linkage disequilibrium did not decrease the number of genotypes. Among these 16 loci, 12 multi-locus genotypes were found in only one sample. To streamline the association analysis, the MSTN gene was divided into four regions: the promoter and exon 1, intron 1, intron 2, and the 3′UTR. This division helped reduce the number of multilocus genotypes.</span></p> <p><span>The database contains information on multiloci genotypes for four regions of the MSTN gene. </span><span>The multi-locus genotypes are presented using standard IUB/IUPAC nucleic acid codes, representing the genotype of two alleles at a single locus with a single letter.</span></p> <p> </p> <p><span><span>The data is the<strong><span> joint property</span></strong> of the participants of the LCS project: the University of Latvia and the Latvian University of Life Sciences and Technologies</span></span></p>
Database of genotypes of significant SNPs of samples of the 2nd trial (A23) of sheep breeds in Latvia within the framework of the project of the Latvian Council of Science LZP-2021/1-0489
<p><span>Project of The Latvian Council of Science (LCS) - LZP-2021/1-0489 project: “<strong>Development of an innovative approach to identify biological determinants involved in the between-animal variation in feed efficiency in sheep farming</strong>”.</span></p> <p><span>The <strong>aim of the project</strong> is</span><span> to determine whether the feed efficiency status of <span>Latvian meat sheep breeds</span> could be predicted using a panel of genetic and molecular markers previously found to be associated with divergent FE status in a training population of lambs when fed the same diet.</span></p> <p><strong><span>Novelty</span></strong><span>: to determine the parameters predicting the most productive result of lamb rearing, we set out to develop the cheapest and most effective method for determining markers of feed efficiency - based on molecular and genetic markers obtained from the blood of live lambs. </span></p> <p><strong><span>About the project:</span></strong></p> <p><span>The costs associated with lambing (buying or keeping sheep) and preparing or purchasing feed are the two most significant components of variable costs in sheep raising. Feed costs are high due to poor grain growing conditions in major producing countries, the use of feed grains in ethanol production, and increased competition for land in crop production compared to urban development<span>.</span> <span>Feed efficiency </span>in growing lambs (i.e., the animal’s ability to reach a market or adult body weight (BW) with the least feed intake) is a critical factor in the sheep industry. <span>Improving FE reduces production costs. Improving FE by 5% can bring economic benefits up to four times higher than a 5% increase in average daily gain (ADG).</span></span></p> <p><span>Traditionally, meat breeding programs have focused on outputs due mainly to the routine availability of phenotypic data on outputs or correlated traits. Currently, no marker has successfully explained enough of the variability in <span>feed efficiency </span>that they were used as part of a routine improvement program. According to our data, no genetic parameters for performance and feed efficiency traits are available for sheep. <span>The physiological determinants of feed efficiency or putative biomarkers used to analyse animal-to-animal variation in live lambs could be a cost-effective and rapid tool for genetic selection or management decisions.</span></span></p> <p><strong><span>About the data of the project:</span></strong></p> <p><span>LZP-2021/1-0489 project data on lamb samples of the second year: 2023, or A23 group, which consists of 92 intensively fattened lambs from eight breeds, including LT breed, which were raised in the meadow and are semi-sibi lambs within the scope of the study.</span></p> <p><span>The database contains genotyping results for 57 SNPs, for which a statistically significant association with one of the feed digestion indicators was found in the project's first group (A22). A laboratory-based genotyping method was developed for each selected SNP, which was tested using samples from the A22 group; the results were obtained using the NGS methodology.</span></p> <p><span>In the database, SNPs are coded with a laboratory code and an rs ID number. The gene in which the SNP is located is also indicated. The genotypes of each SNP are presented using standard IUB/IUPAC nucleic acid codes, representing the genotype of two alleles at a single locus with a single letter. </span></p> <p><strong><span> </span></strong></p> <p><span>The data is the<strong><span> joint property</span></strong> of the participants of the LCS project: the University of Latvia and the Latvian University of Life Sciences and Technologies.</span></p>
Database of genotypes of significant SNPs of samples of the 1st trial (A22) of sheep breeds inLatvia within the framework of the project of the Latvian Louncil of Lcience LZP-2021/1-0489
<p><span>Project of The Latvian Council of Science (LCS) - LZP-2021/1-0489 project: “<strong>Development of an innovative approach to identify biological determinants involved in the between-animal variation in feed efficiency in sheep farming</strong>”.</span></p> <p><span>The <strong>aim of the project</strong> is</span><span> to determine whether the feed efficiency status of <span>Latvian meat sheep breeds</span> could be predicted using a panel of genetic and molecular markers previously found to be associated with divergent FE status in a training population of lambs when fed the same diet.</span></p> <p><strong><span>Novelty</span></strong><span>: to determine the parameters predicting the most productive result of lamb rearing, we set out to develop the cheapest and most effective method for determining markers of feed efficiency - based on molecular and genetic markers obtained from the blood of live lambs. </span></p> <p><strong><span>About the project:</span></strong></p> <p><span>The costs associated with lambing (buying or keeping sheep) and preparing or purchasing feed are the two most significant components of variable costs in sheep raising. Feed costs are high due to poor grain growing conditions in major producing countries, the use of feed grains in ethanol production, and increased competition for land in crop production compared to urban development<span>.</span> <span>Feed efficiency </span>in growing lambs (i.e., the animal’s ability to reach a market or adult body weight (BW) with the least feed intake) is a critical factor in the sheep industry. <span>Improving FE reduces production costs. Improving FE by 5% can bring economic benefits up to four times higher than a 5% increase in average daily gain (ADG).</span></span></p> <p><span>Traditionally, meat breeding programs have focused on outputs due mainly to the routine availability of phenotypic data on outputs or correlated traits. Currently, no marker has successfully explained enough of the variability in <span>feed efficiency </span>that they were used as part of a routine improvement program. According to our data, no genetic parameters for performance and feed efficiency traits are available for sheep. <span>The physiological determinants of feed efficiency or putative biomarkers used to analyse animal-to-animal variation in live lambs could be a cost-effective and rapid tool for genetic selection or management decisions.</span></span></p> <p><strong><span>About the data of the project:</span></strong></p> <p><span>LZP-2021/1-0489 project data on lamb samples of the year 2022, or the A22 group, which consists of 76 intensively fattened lambs from six breeds.</span></p> <p><span>The database contains genotyping results for 57 SNPs, for which a statistically significant association with one of the feed efficiency indicators was established within the project, using NGS methodology and association statistical methods. The specific SNPs were selected for further work as the first DNA molecular markers for future sheep breeding programs in Latvia.</span></p> <p><span>In the database, SNPs are coded with a laboratory code and an rs ID number. The gene in which the SNP is located is also indicated. The genotypes of each SNP are presented using standard IUB/IUPAC nucleic acid codes, representing the genotype of two alleles at a single locus with a single letter. </span></p> <p><strong><span> </span></strong></p> <p><span>The data is the<strong><span> joint property</span></strong> of the participants of the LCS project: the University of Latvia and the Latvian University of Life Sciences and Technologies.</span></p>
Summary Statistics - Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations
<p>Summary Statistics - Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations</p> <p>Files contain imputation quality and allele frequency for each imputed variant. A file exists for each method and add-on tag selection setting (Setting 1 or Setting 2)</p>
Genotype data for 91 Braunvieh and 161 Fleckvieh individuals
<h2>Context and methodology </h2> <p>This dataset was created as part of a research project focusing on investigating recombination rates and genomic features for two Swiss cattle breeds and it offers genotypic data for 91 Braunvieh and 161 Fleckvieh individuals, specifically focusing on chromosome 25. </p> <p>Through this dataset, researchers gain insight into genetic variations, including single nucleotide polymorphism (SNPs) and insertions and deletions (INDELs), enabling deeper investigations into breed-specific characteristics.</p> <p>The genotypic data was generated via high-throughput sequencing and genotyping techniques, involving blood sample collection, DNA extraction, and sequencing using Illumina HiSeq X platform. Analysis pipelines, starting with data preprocessing and alignment, followed by variant calling and quality filtering, were employed. The resulting VCF files contain detailed genotype information, serving as a foundation for population genetics studies. These genotype data serve as the foundation for downstream analyses, including the estimation of recombination rates and the investigation of genomic features such as SNP density and GC content in the respective cattle breeds.</p> <h2>Technical details </h2> <p>The dataset consists of four VCF files, each representing genotypic information for a specific subset of individuals within the Braunvieh and Fleckvieh cattle breeds. The VCF files are named according to the breed (Braunvieh or Fleckvieh) and the part number, along with the date of creation (e.g., braunvieh_part1_20072019.vcf). Furthermore, there is a README file describing the VCF files. </p> <p>The VCF files can be opened and viewed using standard text editors, such as Notepad on Windows or TextEdit on macOS. This allows researchers to inspect the contents of the files and understand the structure of the genetic variant data. </p> <p>For more advanced analysis and manipulation of the genotype data, researchers may require bioinformatics software capable of handling VCF files, such as Genome Analysis Toolkit (GATK), SAMtools, or Variant Call Format (VCF) tools. </p> <p>Additionally, software for statistical analysis and visualization, such as R or Python with relevant libraries, may be needed for downstream analysis of the genotype data. </p> <h2>Further details </h2> <p>Please note that the dataset is restricted, and access must be requested for data reuse. </p>
Figure 1 in Prevalence and new genotypes of Enterocytozoon bieneusi in sheltered dogs and cats in Sichuan province, southwestern China
Figure 1. Geographical distribution of the sampled cities (filled red dot) in Sichuan Province.
Microsatellites raw genotypes of Aedes koreicus mosquitoes
<p>Genotypes of single mosquito of the species <em>Aedes koreicus</em>; genotyping was performed using capillary electrophoresis (Fragment Length Analysis) by Eurofins Genomics at 10 loci specific for <em>Ae. koreicus</em>.</p>
Rapid phenotypic and genotypic change in a laboratory schistosome population
<p>The present dataset contains all phenotype data and input files, as well as shell and R scripts used for data analysis and generation of figures (1-5, S1-S2) present in the manuscript entitled "Rapid phenotypic and genotypic change in a laboratory schistosome population."</p> <p><strong><span>Abstract</span></strong></p> <p><strong><span>Background:</span></strong><span> Genomic analysis has revealed extensive contamination among laboratory-maintained microbes including malaria parasites, <em>Mycobacterium tuberculosis</em> and <em>Salmonella </em>spp. Here, we provide direct evidence for recent contamination of a laboratory schistosome parasite population, and we investigate its genomic consequences. The Brazilian <em>Schistosoma mansoni</em> population SmBRE has several distinctive phenotypes, showing poor infectivity, reduced sporocysts number, low levels of cercarial shedding and low virulence in the intermediate snail host, and low worm burden and low fecundity in the vertebrate rodent host. In 2021 we observed a rapid change in SmBRE parasite phenotypes, with a ~10x increase in cercarial production and ~4x increase in worm burden. </span></p> <p><strong><span>Methods:</span></strong><span> To determine the underlying genomic cause of these changes, </span><span>we sequenced pools of SmBRE adults collected during parasite maintenance between 2015 and 2023. We also sequenced another parasite population (SmLE) maintained alongside </span><span>SmBRE without phenotypic changes. </span></p> <p><strong><span>Results:</span></strong><span> While SmLE allele frequencies remained stable over the eight-year period, we observed sudden changes in allele frequency across the genome in SmBRE between July 2021 and February 2023, consistent with expectations of laboratory contamination. (i) SmLE-specific alleles rose in the SmBRE population from 0 to 41-46% across the genome between </span><span>September and October 2021, documenting the timing and magnitude of the contamination event.</span><span> (ii) After contamination, strong selection (<em>s</em> = ~0.23) drove replacement of low fitness SmBRE with high fitness SmLE alleles. (iii) Allele frequency changed rapidly across the whole genome, except for a region on chromosome 4 where SmBRE alleles remained at high frequency. </span></p> <p><strong><span>Conclusions:</span></strong><span> We were able to detect contamination in this case because SmBRE shows distinctive phenotypes. However, this would likely have been missed with phenotypically similar parasites. These results provide a cautionary tale about the importance of tracking the identity of parasite populations, but also showcase a simple approach to monitor changes within populations using molecular profiling of pooled population samples to characterize fixed single nucleotide polymorphisms. We also show that genetic drift results in continuous change even in the absence of contamination, causing parasites maintained in different labs (or sampled from the same lab at different times) to diverge.</span></p>
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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.