Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
6
datasets available to search
ShareScore release 0.9.0
Dataset results
6 results for “ddRAD-seq”
Genome-wide SNP discovery in native American and Hungarian Robinia pseudoacacia genotypes using next-generation double-digest restriction-site-associated DNA sequencing (ddRAD-Seq)
<p>Initial filtered ddRADseq dataset with highly variable SNP markers from native American and Hungarian <em>Robinia pseudoacacia</em> L. individuals</p>
Key triggers of adaptive genetic variability of sessile oak [Q. petraea (Matt.) Liebl.] from the Balkan refugia: outlier detection and association of SNP loci from ddRAD-seq data
<p>Knowledge on the genetic composition of <em>Quercus petraea</em> in south-eastern Europe is limited despite the species' significant role in the re-colonisation of Europe during the Holocene, and the diverse climate and physical geography of the region. Therefore, it is imperative to conduct research on adaptation in sessile oak to better understand its ecological significance in the region. While large sets of SNPs have been developed for the species, there is a continued need for smaller sets of SNPs that are highly informative about the possible adaptation to this varied landscape. By using double digest restriction site associated DNA sequencing data from our previous study, we mapped RAD-tag sequences to the <em>Quercus robur</em> reference genome and identified a set of SNPs putatively related to drought stress-response. A total of 179 individuals from eighteen natural populations at sites covering heterogeneous climatic conditions in the southeastern natural distribution range of <em>Q. petraea</em> were genotyped. The detected highly polymorphic variant sites revealed three genetic clusters with a generally low level of genetic differentiation and balanced diversity among them but showed a north–southeast gradient. Selection tests showed nine outlier SNPs positioned in different functional regions. Genotype-environment association analysis of these markers yielded a total of 53 significant associations, explaining 2.4–16.6% of the total genetic variation. Our work exemplifies that adaptation to drought may be under natural selection in the examined <em>Q. petraea</em> populations.</p>
<em>Scutellaria floridana</em> ddRAD-Seq vcf files
Open the record for dataset details and reuse information.
ddRAD-seq alignment data for Unionid mussels
<p><span><span><span><span><span><span><span><span><span><span><span><span><span>North American watersheds contain the world's highest diversity of freshwater mussels (Unionoida), and up to 40 species can co-occur in a single riffle. They collectively exhibit little evidence for ecological differentiation during the long-lived, benthic phase of their life cycle. In contrast, their brief parasitic larval phase involves the infection of a wide diversity of fish hosts. Gravid female mussels have evolved multiple methods for increasing the probability of infecting a host fish. Some species use a passive broadcast strategy: placing high numbers of larvae in the water column and relying on chance encounters with potential hosts for infection. Most species have a proactive strategy that entails the use of prey-mimetic lures to change the behavior of the hosts, <i>i.e.</i>, eliciting a feeding response through which they become infected. Gravid females collectively produce two main lure types: a mantle tissue lure (on the female's body) and a brood lure, containing infective larvae, that she releases into the external environment. In this study, we used a phylogenomic approach (ddRAD-seq) to place the diversity of infection strategies used by 54 North American lampsiline mussels into an evolutionary context. Ancestral state reconstruction recovered evidence for the early evolution of mantle lures in this clade, with brood lures and broadcast infection strategies both being independently derived twice. The most common infection strategy, occurring in our largest ingroup clade, is a mixed one in which mimetic mantle lures are apparently the predominant infection mechanism, but gravid females also release simple, non-mimetic brood lures at the end of the season. This mixed infection strategy clade shows some evidence of an increase in diversification rate and most members use bass (<i>Micropterus</i> & <i>Ambloplites spp</i>.) as their predominant fish hosts. Broad linkage between infection strategies and predominant fish host genera is also seen in other lampsiline clades: worm-like mantle lures of <i>Toxolasma spp. </i>with sunfish (<i>Lepomis spp.</i>); insect larvae-like brood lures (<i>Ptychobranchus spp.</i>), or mantle lures (<i>Medionidus</i> spp., <i>Obivaria</i>spp.), or mantle lures combined with host capture (<i>Epioblasma</i> spp.) with a spectrum of darter (<i>Etheostoma </i>& <i>Percina</i><i>spp.</i>) and sculpin (<i>Cottus spp.</i>) hosts, and tethered brood lures (<i>Hamiota</i> spp.) with bass (<i>Micropterus</i> & <i>Ambloplites spp</i>.). Our phylogenetic results confirm that discrete lampsiline mussel clades exhibit considerable specialization in the primary fish host clades their larvae parasitize, and in the host infection strategies they employ to do so. They are also consistent with the hypothesis that larval resource partitioning of fish hosts is an important factor in maintaining species diversity in mussel assemblages. We conclude that taking their larval ecology and host-infection mechanisms into account, lampsiline mussels may be legitimately viewed as a cryptic adaptive radiation.</span></span></span></span></span></span></span></span></span></span></span></span></span></p>
ddRAD-seq alignment data for Unionid mussels
Open the record for dataset details and reuse information.
ddRAD-seq generated genomic SNP dataset of Central and Southeast European Turkey oak (Quercus cerris L.) populations
<p>Turkey oak (<em>Quercus cerris</em> L.) is one of the most ecologically and economically significant deciduous tree species in the Central and Southeast European regions. The species has long been known to exhibit high levels of genetic and phenotypic variation. Recent climate response predictions for Turkey oak suggest a significant distribution extension in Europe under climate change. Since Turkey oak has relative drought-tolerant behavior, it is regarded as a potential alternative for other forest tree species during forestry climate adaptation efforts, not only in its native regions but also in Western Europe. For this reason, the survey of existing genetic variability, genetic resources, and adaptability of this species has great significance. Next-generation sequencing approaches, such as ddRAD-seq (Double digest restriction-site associated DNA sequencing), allow the attainment of high-resolution genome-wide simple nucleotide polymorphisms (SNPs). This study provides the first highly variable genome-wide SNP data for Turkey oak generated by ddRAD-seq. The dataset comprises 17 607 <em>de novo</em> and 26 059 reference-mapped SNPs for 88 individuals from eight populations, two from Bulgaria, one from Kosovo, and five from Hungary. Reference mapping was carried out by using cork oak’s reference genome. The obtained high-resolution genome-wide markers are suitable for investigating selection and local adaptation and inferring genetic diversity, differentiation, and population structure. The dataset is accessible at: <a href="https://doi.org/10.5281/zenodo.8091252">https://doi.org/10.5281/zenodo.8091252</a></p>
ScienceDex guides
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.