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84 results for “genetic resources”
Data from: Genome-wide SNP discovery in the annual herb, Lasthenia fremontii (Asteraceae): genetic resources for the conservation and restoration of a California vernal pool endemic
California vernal pool (VP) ecosystems support a diverse community of endemic plants that are threatened by multiple anthropogenic pressures, generating a need for molecular tools to quantify the extent and distribution of genetic variation in native populations. Here, we used RADseq to discover single nucleotide polymorphisms (SNPs) for a widespread VP endemic plant species, Lasthenia fremontii. We discovered nuclear-based SNPs using a RAD-tag library of 12 individuals from different VP complexes using SbfI, a restriction enzyme that does not cleave the chloroplast genome in Lasthenia. A total of 316,106 catalog loci were obtained across all twelve individuals in the library. Of these, 713 loci were polymorphic, yielding 3918 candidate SNPs. Next, we genotyped an additional 285 additional plants to validate and characterize 71 of the candidate SNPs. Of these, 44 were polymorphic among VP complexes. A preliminary analysis of the distribution of genetic variation using these loci revealed significant isolation-by-distance across the species' geographic range. Weaker, but in some cases significant, genetic differentiation was detected among subpopulations from different pools within a single VP complex. Thus, in this study, RADseq allowed the discovery of SNP markers that can characterize patterns of genetic variation at multiple spatial scales in L. fremontii, which can be used to inform the conservation and mitigation of VP populations.
Data from: A Mesoamerican origin of cherimoya (Annona cherimola Mill.). Implications for the conservation of plant genetic resources
Knowledge on the structure and distribution of genetic diversity is a key aspect in order to plan and execute an efficient conservation and utilization of the genetic resources of any crop as well as for determining historical demographic inferences. In this work, a large data set of 1765 accessions of cherimoya (Annona cherimola Mill, Annonaceae), an underutilized fruit tree crop native to the neotropics and used as a food source by pre-Columbian cultures, was collected from 6 different countries across the American continent and amplified with 9 highly informative microsatellite markers. The structure analyses, fine representation of the genetic diversity and an ABC approach suggest a Mesoamerican origin of the crop, contrary to previous reports, with clear implications for the dispersion of plant germplasm between Central and South America in pre-Columbian times. These results together with the potential distribution of the species in a climatic change context using two different climate models provide new insights for the history and conservation of extant genetic resources of cherimoya that can be applied to other currently underutilized woody perennial crops.
Data underlying RSOS-210474: Mitochondrial DNA sequencing of a wet-collection syntype demonstrates the importance of type material as genetic resource for Lantern Shark taxonomy (Chondrichthyes: Etmopteridae)
<p>After initial detection of target archival DNA of a 116 year old syntype specimen of the Smooth Lanternshark, <i>Etmopterus pusillus</i> in a single stranded DNA library, we shotgun-sequenced additional 9 million reads from this same DNA library. Sequencing reads were used for extracting mitochondrial sequence information for analyses of mitochondrial DNA characteristics and reconstruction of the mitochondrial genome. The archival DNA is highly fragmented. A total of 4,599 mitochondrial reads were available for the genome reconstruction using an iterative mapping approach. The resulting genome sequence has a 12 times coverage and a length of 16,741 basepairs. All 37 vertebrate mitochondrial loci plus the control region were identified and annotated. The mitochondrial NADH2 gene was subsequently used to place the syntype haplotype in a network comprising multiple <i>E. pusillus</i> samples from various distant localities as well as sequences from a morphological similar species, the Shortfin Smooth Lantern Shark <i>Etmopterus joungi</i>. Results confirm the almost global distribution of <i>E. pusillus</i> and suggest <i>E. joungi </i>to be a junior synonym of <i>E. pusillus</i>. As mitochondrial DNA often represents the only available reference information in non-model organisms, this study illustrates the importance of mitochondrial DNA from an aged, wet-collection type specimen for taxonomy.</p>
Citrus genomic resources unravel putative genetic determinants of Huanglongbing pathogenicity
<p>Citrus HLB caused by Candidatus Liberibacter asiaticus is a pathogen-triggered</p> <p>immune disease. Here, we identified putative genetic determinants of HLB</p> <p>pathogenicity by integrating citrus genomic resources to characterize the pan</p> <p>genome of accessions that differ in their response to HLB. Genome-wide associ</p> <p>ation mapping and analysis of allele-specific expression between susceptible,</p> <p>tolerant, and resistant accessions further refined candidates underlying the</p> <p>response to HLB. We first developed a phased diploid assembly of Citrus sinensis</p> <p>‘Newhall’ genome and produced resequencing data for 91 citrus accessions that</p> <p>differ in their response to HLB. These data were combined with previous rese</p> <p>quencing data from 356 accessions for genome-wide association mapping of</p> <p>the HLB response. Genes determinants for HLB pathogenicity were associated</p> <p>with host immune response, ROS production, and antioxidants. Overall, this</p> <p>study has provided a significant resource of citrus genomic data and identified</p> <p>candidate genes to be further explored to understand the genetic determinants</p> <p>of HLB pathogenicity</p>
Data, Code and Computational Environment for: Wild olive tree genetic diversity in Greece: a diverse resource in danger of erosion
<p><strong>Data</strong></p> <p>The csv file "2023-06-27_data.csv" contains genetic profiles for all olive trees analyzed in the publication: Wild olive tree genetic diversity in Greece: a diverse resource in danger of erosion". The genotypes are provided in the GenAlEx format.</p> <p> </p> <p><strong>Code</strong></p> <p>Code is provided in the compressed folder "Tourvas_et_al_Olive". It is structured as a R project and can easily be opened, after decompressing, from the Rstudio interface. If you prefer to review and/or reuse code you can access it from the "analysis" folder inside the "Tourvas_et_al_Olive" folder.</p> <p> </p> <p><strong>Computational Environment</strong></p> <p>A tarball for the Docker image "tourvas_et_al_olive" is also provided. This is the recommended way to reproduce the results of the publication: "Wild olive tree genetic diversity in Greece: a diverse resource in danger of erosion".</p> <p>It is assumed that you already have Docker installed on your system. If not, please visit <a href="https://docs.docker.com/get-started/">https://docs.docker.com/get-started/</a></p> <p>To use it:</p> <ul> <li>download the image file tourvas_et_al_olive.tar</li> <li>load it with docker with the command:</li> </ul> <pre><code class="language-bash">docker load --input tourvas_et_al_olive.tar</code></pre> <ul> <li>then launch the Docker container with the command:</li> </ul> <pre><code class="language-bash">docker run --name popgen --rm -dp 8787:8787 -e ROOT=TRUE -e DISABLE_AUTH=true -v "`pwd`":/home/rstudio/working nikostourvas/tourvas_et_al_olive</code></pre> <ul> <li>start your favorite web browser and go to: http://localhost:8787/</li> <li>from the bottomright pane of the Rstudio server click on the directory "Tourvas_et_al_Olive" and open the project by clicking on the "Tourvas_et_al_Olive.Rproj" file</li> <li>launch the scripts inside the "analysis" directory and run them to reproduce results</li> </ul>
Creation of a Prospective Cohort of Healthy and Sick Subjects and of a Collection of Associated Biological Resources, for the Study of the Immune System and of Its Genetic and Environmental Determinan
ClinicalTrials.gov study NCT03925272. IPD Sharing: NO. Countries: 1. Publications: 16.
Data from: A Mesoamerican origin of cherimoya (Annona cherimola Mill.). Implications for the conservation of plant genetic resources
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Data from: Does local adaptation to resources explain genetic differentiation among Daphnia populations?
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Data from: Complex genetic effects on early vegetative development shape resource allocation differences between Arabidopsis lyrata populations
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Data from: Genome-wide SNP discovery in the annual herb, Lasthenia fremontii (Asteraceae): genetic resources for the conservation and restoration of a California vernal pool endemic
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Data from: Genetic resources of teak (Tectona grandis Linn. f.) – strong genetic structure among natural populations
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Data from: Study of genetic variability in Vitis vinifera L. germplasm by high-throughput Vitis18kSNP array: the case of Georgian genetic resources
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Data from: Phylogeny of Morella rubra and its relatives (Myricaceae) and genetic resources of Chinese bayberry using RAD sequencing
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Leveraging genetic resources and genomic prediction to enhance flavonol content in cranberry fruit
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Data from: New resources for genetic studies in Populus nigra: genome wide SNP discovery and development of a 12k Infinium array
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Data from: Multi-objective optimization for plant germplasm collection conservation of genetic resources based on molecular variability
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Data from: Resource allocation during ontogeny is influenced by genetic, developmental, and ecological factors in the horned beetle, Onthophagus taurus
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A genomics resource for genetics, physiology, and breeding of West African sorghum
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Resource quality determines the evolution of resistance and its genetic basis
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Data underlying RSOS-210474: Mitochondrial DNA sequencing of a wet-collection syntype demonstrates the importance of type material as genetic resource for Lantern Shark taxonomy (Chondrichthyes: Etmopteridae)
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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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.