Find research datasets worth reusing

opencc-by-4.0Sep 2021View details →

Drug sensitive and multidrug-resistant Mycobacterium tuberculosis genotypes from Bulgaria

Dataset of drug sensitive and multidrug-resistant Mycobacteium tuberculosis spoligo- and MIRU-VNTR genotypes from Bulgaria collected between 2008 till 2019.

opencc-zeroDec 2021View details →

Microsatellite genotype data from: Male-biased dispersal in a fungus-gardening ant symbiosis (Matthews et al, Ecology and Evolution)

For nearly all organisms, dispersal is a fundamental life history trait that can shape their ecology and evolution. Variation in dispersal capabilities within a species exists and can influence population genetic structure and ecological interactions. In fungus-gardening (attine) ants, co-dispersal of ants and mutualistic fungi is crucial to the success of this obligate symbiosis. Female-biased dispersal (and gene flow) may be favored in attines because virgin queens carry the responsibility of dispersing the fungi, but a paucity of research has made this conclusion difficult. Here, we investigate dispersal of the fungus-gardening ant Trachymyrmex septentrionalis using a combination of maternally- (mitochondrial DNA) and biparentally-inherited (microsatellites) markers. We found three distinct, spatially isolated mitochondrial DNA haplotypes; two were found in the Florida panhandle and the other in the Florida peninsula. In contrast, biparental markers illustrated significant gene flow across this region and minimal spatial structure. The differential patterns uncovered from mitochondrial DNA and microsatellite markers suggest that most long-distance ant dispersal is male-biased and that females (and concomitantly the fungus) have more limited dispersal capabilities. Consequently, the limited female dispersal is likely an important bottleneck for the fungal symbiont. This bottleneck could slow fungal genetic diversification, which has significant implications for both ant hosts and fungal symbionts regarding population genetics, species distributions, adaptive responses to environmental change, and coevolutionary patterns.

opencc-zeroJan 2022View details →

C porosus genotype data

We collected 714 tissue samples of non-captive saltwater crocodiles Crocodylus porosus from Australia and its neighbouring countries and got them genotyped by Diversity Arrays Technology (Canberra, Australia) between 2016 and 2019. The folder contains two files named 'Report_DCroc19-4196_4_moreOrders_SNP_mapping_2.csv' and 'IDpop_sample_data_.csv'. The former contains the single-nucleotide polymorphism (SNP) data and latter has attributes (population ID, GPS coordinates, species, country) of each sample.

opencc-by-4.0Nov 2021View details →

Individual multilocus genotypes of adults and seed progeny from eight natural populations of Campanula glomerata

Individual multilocus genotypes based on 15 microsatellite loci of adults and seed progeny from eight natural populations of Campanula glomerata. For more details see Van Rossum et al. (2022) in Frontiers in Conservation Science

opencc-by-4.0Jan 2022View details →

Model-based analysis of tuberculosis genotype clusters in the United States reveals high degree of heterogeneity in transmission, and state-level differences across California, Florida, New York, and Texas.

Data and codes for the publication

opencc-zeroFeb 2022View details →

Data from: Location, but not defensive genotype, determines ectomycorrhizal community composition in Scots pine (Pinus sylvestris L.) seedlings

1. For successful colonisation of host roots, ectomycorrhizal (EM) fungi must overcome host defence systems, and defensive phenotypes have previously been shown to affect the community composition of EM fungi associated with hosts. Secondary metabolites, such as terpenes, form a core part of these defence systems, but it is not yet understood whether variation in these constitutive defences can result in variation in colonisation of hosts by specific fungal species. 2. We planted seedlings from twelve maternal families of Scots pine (Pinus sylvestris) of known terpene genotype reciprocally in the field in each of six sites. After three months we characterised the mycorrhizal fungal community of each seedling using a combination of morphological categorisation and molecular barcoding, and assessed the terpene chemodiversity for a subset of the seedlings. We examined whether parental genotype or terpene chemodiversity affected the diversity or composition of a seedling's mycorrhizal community. 3. While we found that terpene chemodiversity was highly heritable, we found no evidence that parental defensive genotypeor defensive phenoytpeaffected associations with EM fungi. Instead, we found that the location of seedlings, both within and between sites, was the only determinant of the diversity and makeup of EM communities. 4. These results suggest that while EM community composition varies within Scotland at both large and small scales, variation in constitutive defensive compounds does not determine the EM communities of closely cohabiting pine seedlings. Patchy distributions of EM fungi at small scales may render any genetic variation in associations with different species unrealisable in field conditions. The case for selection on traits mediating associations with specific fungal species may thus be overstated, at least in seedlings.

opencc-by-4.0Mar 2022View details →

TagSeq gene expression data from Acropora cervicornis genotypes exhibiting above or below average heat tolerance

TagSeq data taken from Acropora cervicornis genotypes taken from nurseries in the Florida Reef tract and subjected to thermal stress.

opencc-zeroMar 2022View details →

Genomics of humic adaptation in Eurasian perch (Perca fluviatilis): SNP genotypes of 32 perch individuals, supplementary figures and tables

Extreme environments are inhospitable to the majority of species, but some organisms are able to survive in such hostile conditions due to evolutionary adaptations. For example, modern bony fishes have colonized various aquatic environments, including perpetually dark, hypoxic, hypersaline and toxic habitats. Eurasian perch (Perca fluviatilis) is among the few fish species of northern latitudes that is able to live in very acidic humic lakes. Such lakes represent almost "nocturnal" environments; they contain high levels of dissolved organic matter, which in addition to creating a challenging visual environment, also affects a large number of other habitat parameters and biotic interactions. To reveal the genomic targets of humic-associated selection, we performed whole-genome sequencing of perch originating from 16 humic and 16 clear-water lakes in northern Europe. We identified over 800,000 SNPs, of which >10,000 were identified as potential candidates under selection (associated with >3,000 genes) using multiple outlier approaches. Our findings suggest that adaptation to the humic environment may involve hundreds of regions scattered across the genome. Putative signals of adaptation were detected in genes and gene families with diverse functions, including organism development and ion transportation. The observed excess of variants under selection in regulatory regions highlights the importance of adaptive evolution via regulatory elements, rather than via protein sequence modification. Our study demonstrates the power of whole-genome analysis to illuminate multifaceted nature of humic adaptation and provides the foundation for further investigation of causal mutations underlying phenotypic traits of ecological and evolutionary importance.

opencc-zeroMar 2022View details →

Genotype data of 970 Pedunculate oak trees (Quercus robur L.) in Russia and neighbouring countries at 385 gene loci covering the nuclear and organelle genome

The data set is the result of genetic inventory on 970 Pedunculate oak trees from 97 locations in Russia, Belarus, Ukraine and Latvia representing the eastern part of the natural species range. The data set includes the sample IDs, geographic coordinates of each sampled tree (longitude and latitude in decimal degrees) and the genotype data. All samples were screened with a set of 385 gene markers covering the nuclear (n=364) and the organelle genomes (chloroplast: n=14, mitochondria: n=7) by use of a genotyping by sequencing approach. With exception of three INDELs (Insert and Deletion mutations) all gene markers are SNPs (Single nucleotide Polymorphism).

Phenotypic and genotypic divergence of plant-herbivore interactions along an urbanization gradient

Urban environments provide challenging conditions for species survival, including increased temperatures, drought, and pollution. Species can deal with these conditions through evolution across generations or the immediate expression of phenotypic plasticity. The resulting phenotypic changes are key to the performance of species and their interactions with other species in the community. We here document patterns of herbivory in Arabidopsis thaliana along a rural-urban gradient, and tested the genetic background and ecological consequences of traits related to herbivore resistance. Aphid densities increased with urbanization levels along the gradient while plant size did not change. Offspring of urban mothers, raised under common garden conditions, were larger and had a decreased trichome density and seed set but a higher caterpillar (Pieris brassicae) tolerance. In contrast, no urban evolution was detected for defenses against aphids (Myzus persicae). Aphids reduced seed set more strongly in urban offspring, but this effect disappeared in second-generation plants. In general, urban adaptations as expressed in size and caterpillar tolerance were found, but these adaptations were associated with smaller inflorescences. The maternal effect on the response of seed set to aphid feeding demonstrates the relevance of intergenerational plasticity as a direct ecological consequence of herbivory. Our study demonstrates that the urban environment interacts with the plant's genotype and the extended phenotype as determined by ecological interactions.

Data from: Targeted genome-wide SNP genotyping in feral horses using non-invasive fecal swabs

The development of high-throughput sequencing has prompted a transition in wildlife genetics from using microsatellites toward sets of Single Nucleotide Polymorphisms (SNPs). However, genotyping large numbers of targeted SNPs using non-invasive samples remains challenging due to relatively large DNA input requirements. Recently, target enrichment has emerged as a promising approach requiring little template DNA. We assessed the efficacy of Tecan Genomics' Allegro Targeted Genotyping (ATG) for generating genome-wide SNP data in feral horses using DNA isolated from fecal swabs. Total and host-specific DNA were quantified for 989 samples collected as part of a long-term individual-based study of feral horses on Sable Island, Nova Scotia, Canada, using dsDNA fluorescence and a host-specific qPCR assay, respectively. Forty-eight samples representing 44 individuals containing at least 10ng of host DNA (ATG's recommended minimum input) were genotyped using a custom multiplex panel targeting 279 SNPs. Genotyping accuracy and consistency were assessed by contrasting ATG genotypes with those obtained from the same individuals with SNP microarrays, and from multiple samples from the same horse, respectively. 62% of swabs yielded the minimum recommended amount of host DNA for ATG. Ignoring samples that failed to amplify, ATG recovered an average of 86.7% targeted sites per sample, while genotype concordance between ATG and SNP microarrays was 98.5%. The repeatability of genotypes from the same individual approached unity with an average of 99.9%. This study demonstrates the suitability of ATG for genome-wide, non-invasive targeted SNP genotyping, and will facilitate further ecological and conservation genetics research in equids and related species.

Complex feline disease mapping using a dense genotyping array

The current feline genotyping array of 63k single nucleotide polymorphisms has proven its utility within breeds, and its use has led to the identification of variants associated with Mendelian traits in purebred cats. However, compared to single gene disorders, association studies of complex diseases, especially with the inclusion of random bred cats with relatively low linkage disequilibrium, require a denser genotyping array and an increased sample size to provide statistically significant associations. Here, we undertook a multi-breed study of 1,122 cats, most of which were admitted and phenotyped for nine common complex feline diseases at the Cornell University Hospital for Animals. Using a proprietary 340k single nucleotide polymorphism mapping array, we identified significant genome-wide associations with hyperthyroidism, diabetes mellitus, and eosinophilic keratoconjunctivitis. These results provide genomic locations for variant discovery and candidate gene screening for these important complex feline diseases, which are relevant not only to feline health, but also to the development of disease models for comparative studies.

Microsatellite genotypes of A. chlorotica parentage analysis

Historical events of population fragmentation, expansion and admixture over geological time may result in complex patterns of reproductive isolation and may explain why, for some taxa, the study of mitochondrial (mt) and nuclear (nu) genetic data results in discordant evolutionary patterns. Complex patterns of taxonomic diversity were recently revealed in earthworms for which distribution is largely the result of paleogeographical events. Here, we investigated reproductive isolation patterns in a complex of cryptic species of earthworms in which discordant patterns between mt and nu genetic lineages were previously revealed, the Allolobophora chlorotica aggregate. Using four nu microsatellite markers and a fragment of the cytochrome c oxidase subunit I mt gene we carried out a parentage analysis to investigate the mating patterns (i) between individuals belonging to two divergent mt lineages that cannot be distinguished with nu markers and (ii) between individuals belonging to lineages that are differentiated both at the mt and nu levels. Among the 157 field collected individuals, 66 adults were used in cross-breeding experiments to form 22 trios based on their assignment to a mt lineage, and 453 obtained juveniles were genotyped. We showed that adults that mated with both their potential mates in the trio produced significantly more juveniles. In crosses between lineages that diverged exclusively at the mt level, a sex-specific pattern of reproduction characteristic to each lineage was observed, suggesting a possible conflict of interest concerning the use of male/female function between mating partners. In crosses between lineages that diverged both at the mt and nu level, a high production of cocoons was counterbalanced by a low hatching rate, suggesting a post-zygotic reproductive isolation. Different degrees of reproductive isolation, from differential sex allocation to post-zygotic isolation, were thus revealed. Lineages appear to be at different stages in the speciation process, which likely explain the observed opposite patterns of mito-nuclear congruence.

Quantitative assessment of trace and macro element compositions of Cassava (Manihot esculenta) storage roots enriched with Β-Carotene as influenced by genotypes and growing locations

Cassava's important mineral contents depends on some factors, including genetic and growing locational factors. The study aimed to evaluate the influence of genotype and growing locations on the mineral concentrations in yellow-fleshed cassava root genotypes. Twenty-five pipeline yellow-fleshed cassava genotypes and three white-fleshed varieties (check samples) were planted at five different experimental fields for two seasons, each representing the major agroecological zones in Nigeria. Standard laboratory protocols were employed in the sampling to ensure zero contamination, and the trace and macro elements were determined using the inductively coupled plasma optical emission spectroscopic method (ICPOES). The trace and macro elements identified in all the genotypes and varieties investigated were Fe, Mn, B, Cu, Mo, Co, Ni, Zn, and Al; Ca, Mg, Na, K. P, and S respectively. Genotype and growing location had a highly significant (p < 0.05) effect on all the trace elements except Ti and Cr. However, there was no interactive effect between genotype and growing location on all the trace elements except for Pb and Zn. Among the explanatory variables, the variable growing location was the most influential on macro and trace elements. Conclusively, genotypes 01/1442 and 01/1273 have outstanding trace and macro element concentrations.

Unraveling the roles of genotype and environment in the expression of plant defense phenotypes

1. Phenotypic variability results from interactions between genotype and environment and is a major driver of ecological and evolutionary interactions. Measuring the relative contributions of genetic variation, the environment, and their interaction to phenotypic variation remains a fundamental goal of evolutionary ecology. 2. In this study, we assess the question: How do genetic variation and local environmental conditions interact to influence phenotype within a single population? We explored this question using seed from a single population of common milkweed, Asclepias syriaca, in northern Michigan. We first measured resistance and resistance traits of 14 maternal lines in two common garden experiments (field and greenhouse) to detect genetic variation within the population. We carried out a reciprocal transplant experiment with three of these maternal lines to assess effects of local environment on phenotype. Finally, we compared the phenotypic traits measured in our experiments with the phenotypic traits of the naturally-growing maternal genets to be able to compare relative effect of genetic and environmental variation on naturally-occurring phenotypic variation. We measured defoliation levels, arthropod abundances, foliar cardenolide concentrations, foliar latex exudation, foliar carbon and nitrogen concentrations, and plant growth. 3. We found a striking lack of correlation in trait expression of the maternal lines between the common gardens, or between the common gardens and the naturally-growing maternal genets, suggesting that environment plays a larger role in phenotypic trait variation of this population. We found evidence of significant genotype-by-environment interactions for all traits except foliar concentrations of nitrogen and cardenolide. Milkweed resistance to chewing herbivores was associated more strongly with the growing environment. We observed no variation in foliar cardenolide concentrations among maternal lines but did observe variation among maternal lines in foliar latex exudation. 4. Overall, our data reveal powerful genotype-by-environment interactions on the expression of most resistance traits in milkweed.

Genotyping-by-sequencing of Canada's Apple Biodiversity Collection

Canada's Apple Biodiversity Collection (ABC) is one of the most diverse collections of apples in the world, which was designed to enable genetic mapping. The ABC is located at the Agriculture and Agri-Food Canada (AAFC) Kentville Research and Development Centre in Nova Scotia, Canada. In addition to phenotypic descriptions of the ABC, sequencing the accessions in the collection provides a valuable resource not only for researchers working on the collection, but for those studying apples more broadly. With this in mind, we report and make publicly available genotyping-by-sequencing (GBS) data for over 1,000 apple accessions from the ABC. By using three SNP callers and imputation, we were able to genotype 278,231 SNPs from 1,175 diverse apple accessions from the ABC.

Elevated O3 inhibited isoprene emission of a diploid and a triploid genotype of Populus tomentosa by different mechanisms

Ozone (O3) pollution affects plant growth and isoprene (ISO) emission. However, the response mechanism of isoprene emission rate (ISOrate) to elevated O3 (EO3) remains poorly understood. ISOrate was investigated in two genotypes (diploid and triploid) of Chinese white poplar (Populus tomentosa Carr.) exposed to EO3 in an open top chamber (OTC) system. The triploid genotype had higher photosynthesis rate (A) and stomatal conductance (gs) than the diploid one. EO3 significantly decreased A, gs, and ISOrate of middle and lower leaf positions in both genotypes. In the diploid genotype, the reduction of ISOrate was caused by a systematic decrease related to ISO synthesis capacity, as indicated by decreased contents of isoprene precursor dimethylallyl diphosphate (DMADP) and isoprene synthase (ISPS) protein and activity of ISPS. On the other hand, the negative effect of O3 on ISOrate of the triploid genotype did not result from inhibited ISO synthesis capacity, but from increased ISO oxidative loss within the leaf. Our findings will be useful for breeding poplar genotypes with high-yield and lower ISOrate, depending on local atmospheric VOC/NOx ratio, to cope with both the rising O3 concentrations and increasing biomass demand. They can also enlighten the incorporation of O3 effects into process-based models of isoprene emission.

opencc-zeroDec 2021View details →

Data from: A genotyping-in-thousands by sequencing panel to inform invasive deer management using non-invasive fecal and hair samples

Studies in ecology, evolution, and conservation often rely on non-invasive samples, making it challenging to generate large amounts of high-quality genetic data for many elusive and at-risk species. We developed and optimized a Genotyping-in-Thousands by sequencing (GT-seq) panel using non-invasive samples to inform the management of invasive Sitka black-tailed deer (Odocoileus hemionus sitkensis) in Haida Gwaii (Canada). We validated our panel using paired high-quality tissue and non-invasive fecal and hair samples to simultaneously distinguish individuals, identify sex and reconstruct kinship among deer sampled across the archipelago, then provided a proof-of-concept application using field-collected feces on SGang Gwaay, an island of high ecological and cultural value. Genotyping success across 244 loci was high (90.3%) and comparable to that of high-quality tissue samples genotyped using restriction-site associated DNA sequencing (92.4%), while genotyping discordance between paired high-quality tissue and non-invasive samples was low (0.50%). The panel will be used to inform future invasive species operations (culls or eradications) in Haida Gwaii by providing individual and population information to inform management. More broadly, our GT-seq workflow that includes quality control analyses for targeted SNP selection and a modified protocol may be of wider utility for other studies and systems where non-invasive genetic sampling is employed.

opencc-by-4.0Jun 2022View details →

Documentation and code for reproducing analyses presented in: vcferr: Development, Validation, and Application of a SNP Genotyping Error Simulation Framework

Documentation and code for reproducing analyses presented in: vcferr: Development, Validation, and Application of a SNP Genotyping Error Simulation Framework. Please see the README.pdf for step-by-step instructions for reproducing the entire analysis described in the paper.