Find research datasets worth reusing

opencc-by-4.0Mar 2023View details →

Supplemental material for the paper "Genotype-phenotype correlation, clinical presentation, and feminizing surgery in children with congenital adrenal hyperplasia - a nationwide study"

This dataset provides documentation for the translation between historical nomenclature for variants in the CYP21A2 gene to the Human genome variation society nomenclature.  Furthermore, it provides data on all Danish CYP21A2 variants included in the study and the translation into genotype groups: Null, A, B, C, and D.

opencc-zeroMar 2023View details →

Alamo x Kanlow genotypic and phenotypic data for biomass yield and yield-related traits in lowland switchgrass (Panicum virgatum L.) crosses

Switchgrass (Panicum virgatum L.) is a model herbaceous bioenergy crop in the USA. It is a native, perennial, warm-season grass, and has broad adaptability. Many breeding programs focus on the genetic improvement of switchgrass for increasing biomass yield. Significant genetic variation for biomass yield observed in lowland switchgrass hybrids. Due to the quantitative inheritance of biomass yield, varietal improvement for the trait through conventional breeding is slow. Therefore, quantitative trait loci (QTL) mapping is used to discover marker-trait associations and accelerate the breeding process through marker-assisted selection. To identify significant QTL, this study mapped seven biparental crosses and one combined cross of two biparental crosses (30 to 96 F1s) between lowland Alamo and Kanlow genotypes. The crosses were evaluated for biomass yield, plant height, and clonal mass scores in a simulated-sward plot with two replications at two locations in Tennessee from 2019 to 2021. The crosses were genotyped using 17,251 single nucleotide polymorphisms generated through genotyping-by-sequencing. QTL mapping was performed using a single-QTL model in R-QTL. The study identified major QTL for biomass yield, plant height, and clonal mass scores resided on chromosomes 7K, 4K, and 3K and had 0.47, 0.63, and 0.62 heritability, respectively. The dataset contains five files describing the phenotype and genotype of each individual used in the quantitative trait loci (QTL) analysis. <ul> <li>'File 1' contains biomass yield, plant height, and clonal mass data for each genotype and parents evaluated at two locations in Tennessee; the Plateau Research and Education Center (PREC), Crossville and East Tennessee Research and Education Center (ETREC), Knoxville from 2019 to 2021. Plant height and biomass yield were measured at maturity, and clonal mass scores were evaluated after harvesting biomass.</li> <li>'File 2' has the genotype name, library, index, total reads, bases, and the Phred quality score (Q30). Young leaf tissue was collected from each F1 progeny and parent, and DNA was extracted using the cetyltrimethylammonium bromide (CTAB) procedure. The extracted DNA was genotyped at the USDA-ARS Western Regional Research Center laboratory in Albany, CA. Genotyping by sequencing (GBS) was performed on 951 lines (F1s and their parents) using the PstI-MspI GBS protocol. The quality of these sequences showed that 94.4% of the bases were at or above Q30. Reads were mapped to version 5.0 of the switchgrass reference genome. Single nucleotide polymorphism (SNP) calling was performed, and redundant markers were filtered out for linkage map construction. 'File 3' has SNP ID numbers, SNP locations on chromosomes, map positions, and SNP scores. The cross was used as a four-way cross for QTL analysis, where the male parent Kanlow (K) was assigned as '1', and the female parent Alamo (A) was assigned as '2'.</li> <li>The phased output data from the four-way cross, i.e., 11, 12, 21, and 22, were represented by AC, BC, AD, and BD, respectively ('File 3').</li> <li>The progeny file ('File 4') contains the name of the parents used for making crosses and their progenies.</li> <li>A consensus linkage map ('File 5') was produced with Lep-Map3 software. The linkage map contains 18 linkage groups associated with 18 switchgrass chromosomes, marker size (bp), map position (cM) based on male and female maps, and map order.</li> </ul>

opencc-zeroMar 2023View details →

Intensified livestock farming increases antibiotic resistance genotypes and phenotypes in animal feces

Animal feces from livestock farming can be a major source of antibiotic resistance to the environment, but a clear gap exists on how the resistance reservoir in feces alters as farming activities intensify. Here, we sampled feces from eight Chinese farms, where yak, sheep, pig, and horse were reared under free-range to intensive conditions, and determined fecal resistance using both genotype and phenotype approaches. Animals reared intensively exhibited increased diversity of antibiotic resistance genes (ARGs) and greater resistance phenotypes in feces, which were cross-correlated. Furthermore, at the metagenome contig level, ARGs were co-located with mobile genetic elements at a higher frequency (27.38%) as farming intensified, with associated resistance phenotypes being less coupled with bacterial phylogeny. Intensified farming also expanded the multidrug resistance preferentially carried on pathogens in fecal microbiomes. Overall, farming intensification can increase antibiotic resistance genotypes and phenotypes in domestic animal feces, with implications for environmental health.

opencc-zeroApr 2023View details →

Genotype data for wild lupin populations from central Michigan

Habitat degradation can have significant effects on native species inhabiting natural ecosystems. Within oak barrens and oak-pine barrens ecosystems, there is a complex interspecies interaction between the federally endangered Karner blue butterfly (Lycaeides melissa samuelis) and its obligate host plant, wild lupine (Lupinus perennis L.). Recruitment of wild lupine is critical for maintaining butterfly populations; however, this recruitment can be impeded by habitat fragmentation. Reduced recruitment can result in low genetic diversity in isolated populations, limiting its adaptive potential to respond to environmental change. This study was aimed at understanding the genetic diversity and population structure of wild lupine populations throughout central and west Michigan. We identified significant population structure across most of the populations sampled, with only two sites not significantly different from each other. No sites within our study area displayed statistically significant levels of inbreeding. There are also at least two genetic clusters of wild lupine present within our study region, although there is significant overlap among these groups, indicating that genetic differentiation among clusters may be limited.

opencc-by-4.0Mar 2023View details →

Beneficial effects of exercise prior to development of hypertrophic cardiomyopathy in genotype positive mice

Supplementary data for research article titled "Beneficial effects of exercise initiated prior to development of hypertrophic cardiomyopathy in genotype positive mice"

opencc-by-4.0May 2023View details →

gapseq reconstructions for 124 prototrophic genotypes

The data set contains genome-scale metabolic network reconstructions for 124 bacterial genomes, that are phototrophic for all 20 proteinogenic amino acids (doi: <a href="https://doi.org/10.1038/s41559-022-01936-3">10.1038/s41559-022-01936-3</a>). Reconstructions were made using gapseq (development version: 1.2, commit 13d88a68; Sequence DB md5sum: bf8ba98 (2023-02-15, Bacteria). The models were reconstructed using the following workflow. <pre><code># Reaction & Pathway prediction ./gapseq find -b 200 -v 1 -p all -k -t Bacteria <genomeID>.fna.gz # Transporter prediction ./gapseq find-transport -b 200 -k <genomeID>.fna.gz # Draft network reconstruction ./gapseq draft -r <genomeID>-all-Reactions.tbl -t <genomeID>-Transporter.tbl -b Bacteria -c <genomeID>.fna.gz -p <genomeID>-all-Pathways.tbl -u 200 -l 100 # gapfill/growth medium prediction ./gapseq medium -m <genomeID>-draft.RDS -p <genomeID>-all-Pathways.tbl # Gap-filling # (If H2 is part of the medium) ./gapseq fill -m <genomeID>-draft.RDS -n <genomeID>-medium.csv -c <genomeID>-rxnWeights.RDS -g <genomeID>-rxnXgenes.RDS -b 100 -e highH2 # (If H2 is not part of the medium) ./gapseq fill -m <genomeID>-draft.RDS -n <genomeID>-medium.csv -c <genomeID>-rxnWeights.RDS -g <genomeID>-rxnXgenes.RDS -b 100</code></pre> Please note that the model collection is missing three genomes because they were not available (suppressed) on NCBI (GCF_000014265.1, GCF_000020545.1, GCF_9001188395.1).

opencc-by-4.0May 2023View details →

Comparative transcriptomic analysis reveals coordinated mechanisms of different genotypes of common vetch in response to Al stress

Supplementary Table

opencc-zeroMay 2023View details →

Data from: Maintenance and expansion of genetic and trait variation following domestication in a clonal crop: Enset tGBS individual genotype data

Clonal propagation enables favourable crop genotypes to be rapidly selected and multiplied. However, the absence of sexual propagation can lead to low genetic diversity and accumulation of deleterious mutations, which may eventually render crops less resilient to pathogens or environmental change. To better understand this trade-off, we characterise the domestication and contemporary genetic diversity of Enset (Ensete ventricosum), an indigenous African relative of bananas (Musa) and principal starch staple for 20 million Ethiopians. Wild enset is strictly sexually outcrossing, but in cultivation is propagated clonally and associated with diversification and specialisation into hundreds of named landraces. We applied tGBS sequencing to generate genome-wide genotypes for 192 accessions from across enset's cultivated distribution, and surveyed 1340 farmers on enset agronomic traits. Overall, reduced heterozygosity in the domesticated lineage was consistent with a domestication bottleneck that retained 37% of wild diversity. However, an excess of putatively deleterious missense mutations at low frequency present as heterozygotes suggested accumulation of mutational load in clonal domesticated lineages. Our evidence indicates that the major domesticated lineages initially arose through historic sexual recombination associated with a domestication bottleneck, followed by amplification of favourable genotypes through an extended period of clonal propagation. Among domesticated lineages we found significant phylogenetic signal for multiple farmer-identified food, nutrition and disease resistance traits and little evidence of contemporary recombination. Development of future-climate adapted genotypes may require crop breeding, but outcrossing risks exposing deleterious alleles as homozygotes. This trade-off may partly explain the ubiquity and persistence of clonal propagation over recent centuries of comparative climate stability.

opencc-zeroMay 2023View details →

Short-term fitness consequences of parasitism depend on host genotype and within-host parasite community

Multi-parasite communities inhabiting individual hosts are common and often consist of parasites from multiple taxa. The effects of parasite community composition and complexity on host fitness are critical for understanding how host-parasite coevolution is affected by parasite diversity. To test how naturally-occurring parasites affect host fitness of multiple host genotypes, we performed a common-garden experiment where we inoculated four genotypes of host plant Plantago lanceolata with six microbial parasite treatments: three single parasite treatments, a fungal mixture, a viral mixture, and a cross-kingdom treatment. Seed production was affected by both host genotype and parasite treatment, and their interaction jointly determined growth of the hosts. Fungal parasites had more consistent negative effects than viruses in both single mixed parasite treatments. These results demonstrate that parasite communities have the potential to affect the evolution and ecology of host populations through their effects on host growth and reproduction. Moreover, the results highlight the importance of accounting for the diversity of parasites as well as host genotypes when aiming to predict the consequences of parasites for epidemics as the effects of multi-parasitism are not necessarily additive of single parasite effects, nor uniform across all host genotypes.

opencc-zeroMay 2023View details →

Data from: A comparison of non-destructive visceral swab and tissue biopsy sampling methods for genotyping-by-sequencing in the freshwater mussel Fusconaia askewi

Limiting harm to organisms via genetic sampling is an important consideration for rare species. Nondestructive sampling techniques have been developed to address this issue in freshwater mussels. Two methods, visceral swabbing and tissue biopsies, have proven to be effective for DNA sampling, though it is unclear as to which method is preferable for genotyping-by-sequencing (GBS). Tissue biopsies may cause undue stress and damage to organisms, while visceral swabbing potentially reduces the chance of such harm. Our study compared the efficacy of these two DNA sampling methods for generating GBS data for the Unionid freshwater mussel, Texas Pigtoe (Fusconaia askewi). Our results find both methods generate quality sequence data, though some considerations are in order. Tissue biopsies produced significantly higher DNA concentrations and larger numbers of reads when compared to swabs, though there was no significant association between starting DNA concentration and number of reads generated. Swabbing produced greater sequence depth (more reads per sequence) while tissue biopsies revealed greater coverage across the genome (at lower sequence depth). Patterns of genomic variation as characterized in principal component analyses were similar regardless of the sampling method, suggesting that the less invasive swabbing is a viable option for producing quality GBS data in these organisms.

opencc-zeroJun 2023View details →

Ecological consequences of plant genotypic diversity within a foundation plant, Spartina alterniflora, are pervasive but not universal across multiple stress gradients

<ol> <li>Plant genotypic diversity can influence population- and community-level processes, yet we have a limited understanding of how these effects vary across environmental gradients that are ubiquitous in nature. </li> <li>We conducted a 2-year field experiment manipulating plant (Spartina alterniflora) genotypic diversity across a natural stress gradient in tidal elevation, both with and without the addition of nutrients. </li> <li> Spartina diversity increased stem production, but the magnitude of this effect was reduced at both the most stressful and most benign endpoints of the combined elevation and nutrient gradient, consistent with recent species diversity studies. Complementarity among individuals likely underpins the observed benefit of Spartina diversity. </li> <li> Spartina diversity also affected the associated marsh community, with higher consumer (Littoraria irrorata) abundance in more diverse plots, owing to both greater Spartina density and increased variation in Spartina traits.</li> <li> Synthesis: The positive effects of Spartina diversity on population- and community-level responses under most environmental conditions highlights the ecological importance of plant genotypic diversity for the maintenance of function across the marsh landscape. </li> </ol>

opencc-zeroDec 2021View details →

Data from: Reliable and fast genotyping protocol for galactosylceramidase (GALC) in the Twitcher (Twi) mouse

The Twitcher (Twi) mouse is a neurological Krabbe disease (KD, or globoid cell leukodystrophy) spontaneous mutant line. The genome of the Twi mouse presents a single nucleotide polymorphism (SNP), leading to an enzymatically inactive galactosylceramidase (GALC) protein and causing KD. In this context, mouse Twi genotyping is an essential step in KD research. To date, the genotyping method used is labor-intensive and often drives ambiguous results. Here, we evaluate a novel protocol for the genotype determination of GALC mutation status in Twi mice based on the allele-discrimination real-time polymerase chain reaction (PCR). DNA is extracted from Twi mice (n = 20, pilot study; n = 120, verification study) and control group (n = 10, pilot study; n = 30 verification study) and assessed by allele-discrimination real-time PCR to detect SNP c.355G>A. Using the allele-discrimination PCR, all the samples are identified correctly with the genotype GG (wild-type, WT), GA (heterozygote, HET), or AA (homozygote, HOM) by the first analysis and no animals were not genotyped. We demonstrated that this novel method can be used to distinguish timely, accurately and without ambiguity among HOM, WT, and HET animals. This protocol represents a great opportunity to increase accuracy and speed in KD research.

opencc-by-4.0May 2023View details →

Individual multilocus genotypes of F1 seed progeny and recruits from two translocated populations of Campanula glomerata

Individual multilocus genotypes for 15 microsatellite loci and spatial coordinates of F1 seed progeny and recruits from two translocated populations of Campanula glomerata from southern Belgium. For more information, see Van Rossum et al.(2023), Assessing spatial mating patterns in translocated populations of Campanula glomerata, in Gobal Ecology and Conservation.

opencc-zeroJun 2023View details →

Genotypes for yardstick population from the Nakai Plateau, Lao PDR at 25 loci

Conservation biologists often deal with species that have small, fragmented populations throughout their range, making it necessary to prioritize populations for management. Genetics provides tools to assist with prioritization according to the levels and distribution of genetic diversity and evolutionary distinctiveness. Many studies have used nuclear microsatellite loci to measure genetic diversity in disparate populations and mitochondrial DNA to assess genetic distinctiveness. However, comparing metrics based on microsatellite genotypes ascertained in different laboratories is complicated by the selection of different loci with distinct nucleotide repeat motifs. This issue may be resolved by comparing metrics to a well-characterized reference population with shared microsatellite markers. The Asian elephant, Elephas maximus, is an endangered species with 50–60% of populations in India and Sri Lanka, and small, fragmented populations throughout southeast and insular Asia. We assessed range-wide genetic diversity of the Asian elephant by directly comparing allelic diversity and heterozygosity estimates from 35 populations, overcoming marker selection bias by calibrating metrics to a large population on the Nakai Plateau, Lao PDR, genotyped at 25 loci. We coupled these results with mtDNA analysis to evaluate genetic distinctiveness and identify potential conservation management units. We found the greatest diversity in the populations of southeast Asia and the greatest genetic distinctiveness among the subspecies designations, particularly Borneo and Sumatra, and other southeast Asian populations. The populations of southeast Asia, albeit small, fragmented, and at high risk of extirpation, contain valuable diversity and distinctiveness and are thus of high priority for the preservation of the Asian elephant.

opencc-by-4.0Dec 2022View details →

Fig. 1 in Genotype diversity, phylogenetic analysis and seasonality of isolates of Acanthamoeba spp. in swimming pools in Kafrelsheikh, Egypt

Fig. 1. Fresh unstained trophozoites (A) and cysts (B–D) of Acanthamoeba spp.

GigaMUGA genotypes for 72 house mice collected in grain-growing regions of southeastern Australia

The management of invasive species has been greatly enhanced by population genetic analyses of multilocus single-nucleotide polymorphism (SNP) datasets that provide critical information regarding pest population structure, invasion pathways, and reproductive biology. For many applications, there is a need for protocols that offer rapid, robust, and efficient genotyping on the order of hundreds to thousands of SNPs, that can be tailored to specific study populations, and that are scalable for long-term monitoring schemes. Despite its status as a model laboratory species, there are few existing resources for studying wild populations of house mice (Mus musculus spp.) that strike this balance between data density and laboratory efficiency. Here we evaluate the utility of a custom-targeted capture genotyping-by-sequencing approach to support research on plaguing house mouse populations in Australia. This approach utilizes 3,651 hybridization capture probes targeting genome-wide SNPs identified from a sample of mice collected in grain-producing regions of southeastern Australia genotyped using a commercially available microarray platform. To assess performance of the custom panel, we genotyped wild caught mice (N=320) from two adjoining farms and demonstrate the ability to correctly assign individuals to source populations with high confidence (mean >95%), as well as robust kinship inference within sites. We discuss these results in the context of proposed applications for future genetic monitoring of house mice in Australia.

Asian elephant microsatellite genotypes: Nakai Plateau and Sepon mines region, Lao PDR

Habitat loss and fragmentation are leading contributors to the endangered status of species. In 2006, the Nakai Plateau contained the largest known Asian elephant (Elephas maximus) population in the Lao People's Democratic Republic (Lao PDR), and the population was among those with the highest genetic diversity reported for Asian elephants. In 2008, completion of the Nam Theun 2 hydroelectric dam inundated much of the Plateau, resulting in the loss of 40% of elephant habitat. We studied elephant presence, movements, and the incidence of human–elephant conflict (HEC) on the Nakai Plateau and surrounding areas from 2004-2020, before and for 12 years after dam completion. To examine contemporary population dynamics in the Nakai elephants, we used genetic sampling to compare minimum population numbers, demography, and levels of genetic diversity from the wet and dry seasons in 2018/2019, 10 years after dam completion, with those reported in a pre-dam-completion genetic survey. After dam completion, we found a major increase in HEC locally and the creation of new, serious, and persistent HEC problems as far as 100 km away. While we were unable to compare estimated population sizes before and after dam completion, our data revealed a decrease in genetic diversity, a male-biased sex ratio, and evidence of dispersal from the Plateau by breeding-age females. Our results raise concerns about the long-term viability of this important population as well as that of other species in this region. Given that hydropower projects are of economic importance throughout Laos and elsewhere in southeast Asia, this study has important implications for understanding and mitigating their impact.

Data for: Russian honey bee genotype identification through enhanced marker panel set

Russian honey bees (RHB) are a breeding population developed by USDA-ARS as an effort to provide Varroa-resistant honey bees to beekeepers. The selection strategy for this breeding population was the first in honey bees to incorporate genetic stock identification (GSI). The original GSI approach has been in use for over a decade, and though effective, novel technologies and analytical approaches recently developed provide an opportunity for improvement. Here we outline a novel genotyping assay that capitalizes on the markers used in the GSI as well as novel loci recently identified in a whole genome pooled study of commercial honey bee stocks. Our approach utilizes a microfluidic platform and machine learning analyses to arrive at an accurate, high throughput assay. This novel approach provides an improved tool that can be readily incorporated into breeding decisions towards healthier more productive bees.

Leukochimerism genotyping data

Twinning in cattle is infrequent, and also undesired. It can result in increased occurrence of abortion and dystocia, reduced calf survival, and a high likelihood of freemartinism in mixed-sex twins. Twin gestations also commonly are associated with the formation of placental vascular anastomoses (PVA) between twins. Through this, they share blood, hormones (leading to freemartinism in mixed-sex twins) and hematopoietic stem cells, which are the progenitors of white blood cells. The sharing of stem cells between twins can result in leukochimeric twinsets; these are twins that have white blood cells derived from both self and co-twin owing to the fetal migration of hematopoietic stem cells from the extraembryonic mesoderm of the yolk sac to final sites like bone marrow and thymus. This study examined the degree to which this leukochimerism changes over time. DNA was extracted from hair bulbs to determine the individual's true genotype and blood samples obtained at six time points from 1 week to 8 months of age to assess leukochimerism. Samples were genotyped using a medium-density SNP chip, and quantitative estimates of allele frequency were determined using SNPs for which members of a twin set had alternative homozygous genotypes. Results indicated statistically significant changes in proportion self and co-twin with age and suggest that by four months of age, the genotypic mix in white blood cells represents the hematopoietic cell population resident in the individual.

Red drum genotypes and raw fecundity data

Understanding the processes that drive reproductive success in marine fish stocks is critical to effective fisheries management. These processes can be difficult to investigate, especially in age-structured populations, because they occur at transgenerational scales. Reproductive success is often attributed to a small portion of the adult population (< 0.01%) and thought to be driven primarily by random external factors, consistent with the concept of sweepstakes reproductive success (SRS). A competing concept, the reproductive resilience paradigm, posits that fish have evolved complex spawner-recruit systems to achieve lifetime reproductive success and maintain population stability within highly variable environments. Here, we examine these two concepts. First, we analyze the popular sport fish red drum (Sciaenops ocellatus), drawing on genetic and reproductive data to estimate a plausible range for the Ne/NA ratio of effective population size (Ne) to adult abundance (NA) and to infer variance in lifetime reproductive success (V*k). Then, we synthesize available data and infer for two other fishes that have ratios reportedly > 0.10, the southern bluefin tuna (Thunnus maccoyii, Scombridae) and the silver seabream (Chrysophrys auratus, Sparidae). Although commonly regarded as an SRS species, red drum did not meet the SRS criterion. Overdispersed values were inferred for all three species, with those for red drum and silver seabream being dependent upon population-closure assumptions. Results are presented within the conceptual framework of reproductive resilience, considering the roles of random extrinsic forces versus evolved traits to achieve lifetime reproductive success and population stability in high and variable mortality environments.