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.
521
datasets available to search
ShareScore release 0.9.0
Dataset results
521 results for “DNA sequence data”
FIGURES 3–8 in Sporolithon indopacificum sp. nov. (Sporolithales, Rhodophyta) from tropical western Indian and western Pacific oceans: First report, confirmed by DNA sequence data, of a widely distributed species of Sporolithon
FIGURES 3–8. Vegetative anatomy of the holotype of Sporolithon indopacificum (L 3964509). 3. Holotype specimen showing lumpy growth form with swollen, crowded protuberances (scale bar = 10 mm). 4. Magnified view of the protuberances showing their contiguously fused nature and numerous superficial sori (white arrowheads) scattered across the protuberances. Note that sori are often abraded or shed from the surface (black arrowheads) (scale bar = 2 mm). 5. Vertical section showing layers of S. indopacificum crusts (L) overgrowing itself in a superimposed manner (scale bar = 200 μm). 6. Vertical section through the monomerous thallus showing the epithallus (arrowhead) and a predominantly thick cortex (C) subtended by a thin medulla (M) (scale bar = 100 μm). 7. Vertical section of the ventral region of the thallus showing a plumose medulla (M) and cortical filaments (C) joined primarily by secondary pit connections (arrowheads) (scale bar = 50 μm). 8. Vertical section of the dorsal region of the thallus showing a single layer of flared epithallial cells (arrow) subtended by a layer of subepithallial initials (i). Note the layer of senescent epithallial cells (e) being shed, the primary pit connections between adjacent cortical filaments (black arrowheads) and a single, rare cell fusion (white arrowhead) (scale bar = 20 μm).
FIGURE 1 in Sporolithon indopacificum sp. nov. (Sporolithales, Rhodophyta) from tropical western Indian and western Pacific oceans: First report, confirmed by DNA sequence data, of a widely distributed species of Sporolithon
FIGURE 1. Phylogram of Sporolithon species inferred by maximum likelihood analysis of psbA sequences; Heydrichia species were the outgroup; sequences identified by GenBank accession number. Bolded scientific names are type specimens, topotype specimens, or specimens linked to type specimens by DNA sequence. Bootstrap support values (in %) are provided for nodes where> 50%. Scale bar refers to substitutions per site.
FIGURE 2 in Sporolithon indopacificum sp. nov. (Sporolithales, Rhodophyta) from tropical western Indian and western Pacific oceans: First report, confirmed by DNA sequence data, of a widely distributed species of Sporolithon
FIGURE 2. Phylogram of Sporolithon species inferred by maximum likelihood analysis of rbcL sequences; Heydrichia species were the outgroup; sequences identified by GenBank accession number. Bolded scientific names are type specimens, topotype specimens, or specimens linked to type specimens by DNA sequence. Bootstrap support values (in %) are provided for nodes where> 50%. Scale bar refers to substitutions per site.
FIGURE 3 in Sansevieria (Asparagaceae, Nolinoideae) is a herbaceous clade within Dracaena: inference from non-coding plastid and nuclear DNA sequence data
FIGURE 3. Bayesian maximum clade reliability trees based on combined nuclear At103 and chloroplast rps16, trnL-F datasets for Dracaena, Sansevieria, and selected outgroups. The values above the branch represent the maximum parsimony bootstrap percentage (BS), and the ones below are the Bayesian posterior probability (PP). Bold branches indicate strong support, interpreted as ≥ 70 BS and ≥ 95 PP. Long branches were shortened by half their length (indicated by \\).
FIGURE 2 in Sansevieria (Asparagaceae, Nolinoideae) is a herbaceous clade within Dracaena: inference from non-coding plastid and nuclear DNA sequence data
FIGURE 2. Bayesian maximum clade credibility trees based on nuclear At103 (A) and chloroplast rps16, trnL-F (B) datasets for Dracaena and Sansevieria. Outgroups were trimmed from the Figure. The values above the branch represent the maximum parsimony bootstrap percentage (BS), and the ones below are the Bayesian posterior probability (PP). Bold branches indicate strong support, interpreted as ≥ 70 BS and ≥ 95 PP.
FIGURE 1 in Sansevieria (Asparagaceae, Nolinoideae) is a herbaceous clade within Dracaena: inference from non-coding plastid and nuclear DNA sequence data
FIGURE 1. Representative morphological diversity in the dracaenoid genera, Dracaena and Sansevieria. A, Dracaena draco subsp. draco, Spain, Canary Islands, Tenerife, Icod de los Vinos; B, D. konaensis, origin: USA, Hawai'i, Big Island, Kona coast, in cultivation at Kew (Acc. No. 2008-239); C, D. arborea, Gabon, Woleu-Ntem Rd, Mitzic to Njole; D, D. laxissima, São Tomé and Príncipe, São Nicolau; E, D. goldieana, origin: Gabon, in cultivation at Kew (Acc. No. 1990-2300); F, D. aubryana, Gabon, Woleu-Ntem Rd Mitzic to Njole; G, Sansevieria frequens, Kenya, Laikipia District, Ngare Ndare Farm (type locality); H, S. aethiopica, Namibia, 74 km from Windhoek, on road to Walvis Bay; I, S. fischeri, Kenya, Munda, 18.9 km NE of Mwatate on Taveta road; J, S. pinguicula, Kenya, by Kowi airstrip, north bank of Tiva Lugga; K, S. ascendens, Kenya, Coast Province, Kwale District, around base of Taru Hill (type locality); L, S. kirkii var. pulchra, in cultivation (private collection, Miami, FL). Photographs by A, L. Mucina; B, I. Willey; C, E–F, T.H.J. Damen; D, J.J.F.E. de Wilde; G-K, L. E. Newton; L, S. Zona.
Data from: The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing
Understanding how genetic variation is partitioned across genomes within and among populations is a fundamental problem in ecological and evolutionary genetics. To address this problem, we studied the threespine stickleback fish, which has repeatedly undergone parallel phenotypic and genetic differentiation when oceanic fish have invaded freshwater habitats. While significant evolutionary genetic research has been performed using stickleback from geographic regions that have been deglaciated in the last 20 000 years, less research has focused on freshwater populations that predate the last glacial maximum. We performed restriction-site associated DNA-sequencing (RAD-seq) based population genomic analyses on stickleback from across Oregon, which was not glaciated during the last maximum. We sampled stickleback from coastal, Willamette Basin and central Oregon sites, analysed their genetic diversity using RAD-seq, performed structure analyses, reconstructed their phylogeographic history and tested the hypothesis of recent stickleback introduction into central Oregon, where incidence of this species was only recently documented. Our results showed a clear phylogeographic break between coastal and inland populations, with oceanic populations exhibiting the lowest levels of divergence from one another. Willamette Basin and central Oregon populations formed a clade of closely related populations, a finding consistent with a recent introduction of stickleback into central Oregon. Finally, genome-wide analysis of genetic diversity (π) and correlations of alleles within individuals in subpopulations (FIS) supported a role for introgressive hybridization in coastal populations and a recent expansion in central Oregon. Our results exhibit the power of next-generation sequencing genomic approaches such as RAD-seq to identify both historical population structure and recent colonization history.
Data from: Skin swabbing of amphibian larvae yields sufficient DNA for efficient sequencing and reliable microsatellite genotyping
Skin swabbing, a minimally invasive DNA sampling method recently developed on adult amphibians, was tested on larvae of fire salamanders (Salamandra salamandra). The quality and quantity of the sampled DNA was evaluated by (i) measuring DNA concentration in DNA extracts, (ii) sequencing part of the mtDNA cytochrome b gene (692 bp) and (iii) genotyping eight polymorphic nuclear microsatellite loci. The multiple-tubes approach was used for calculating allelic dropout (ADO) and false allele (FA) rates to evaluate the reliability of the genotypes. DNA extracts from tissue samples of road-killed individuals were included in the study as positive controls. Our results showed that skin swabs of fire salamander larvae can provide DNA in sufficient quantity and quality, as sequencing was successful and no allelic dropouts or false alleles were detected. This method, tested for the first time on amphibian larvae, has proven to be an efficient and reliable alternative to the controversial tail fin clipping procedure.
Data from: Genotyping-in-Thousands by sequencing (GT-seq) panel development and application to minimally-invasive DNA samples to support studies in molecular ecology
Minimally-invasive sampling (MIS) is widespread in wildlife studies; however, its utility for massively parallel DNA sequencing (MPS) is limited. Poor sample quality and contamination by exogenous DNA can make MIS challenging to use with modern genotyping-by-sequencing approaches, which have been traditionally developed for high-quality DNA sources. Given that MIS is often more appropriate in many contexts, there is a need to make such samples practical for harnessing MPS. Here, we test the ability for Genotyping-in-Thousands by sequencing (GT-seq), a multiplex amplicon sequencing approach, to effectively genotype minimally-invasive cloacal DNA samples collected from the Western Rattlesnake (Crotalus oreganus), a threatened species in British Columbia, Canada. As there was no previous genetic information for this species, an optimized panel of 362 SNPs was selected for use with GT-seq from a de novo restriction-site associated DNA sequencing (RADseq) assembly. Comparisons of genotypes generated within and among RADseq and GT-seq for the same individuals found low rates of genotyping error (GT-seq: 0.50%; RADseq: 0.80%) and discordance (2.57%), the latter likely due to the different genotype calling models employed. GT-seq mean genotype discordance between blood and cloacal swab samples collected from the same individuals was also minimal (1.37%). Estimates of population diversity parameters were similar across GT-seq and RADseq datasets, as were inferred patterns of population structure. Overall, GT-seq can be effectively applied to low quality DNA samples, minimizing the inefficiencies presented by exogenous DNA typically found in minimally-invasive samples and continuing the expansion of molecular ecology and conservation genetics in the genomics era.
Figure 6 in The species of the varius group of Coccophagus (Hymenoptera: Aphelinidae) from China, with description of a new species, DNA sequence data, and a new country record
Figure 6. Maximum likelihood (ML) tree inferred using IQ-TREE, version 1.6. Bootstrap support values indicated on branches; scale bar represents the number of nucleotide substitutions per site.
Figure 5 in The species of the varius group of Coccophagus (Hymenoptera: Aphelinidae) from China, with description of a new species, DNA sequence data, and a new country record
Figure 5. Coccophagus yunnana sp.nov. female. (a) antenna; (b) fore wing; (c) F3 and clubs; (d) stigma vein of fore wing.
Figure 4 in The species of the varius group of Coccophagus (Hymenoptera: Aphelinidae) from China, with description of a new species, DNA sequence data, and a new country record
Figure 4. Coccophagus yunnana sp. nov. female. (a) head and mesosoma; (b) head in face view; (c) mesosoma; (d) ovipositor.
Figure 1 in The species of the varius group of Coccophagus (Hymenoptera: Aphelinidae) from China, with description of a new species, DNA sequence data, and a new country record
Figure 1. Coccophagus anchoroides (Huang), female. (a) antenna; (b) fore wing; (c) mesosoma and metasoma; (d) ovipositor, mid-tibia and tarsus. Scale bars = μm (from Huang 1994).
Figure 2 in The species of the varius group of Coccophagus (Hymenoptera: Aphelinidae) from China, with description of a new species, DNA sequence data, and a new country record
Figure 2. Coccophagus fumadus Hayat, female. (a) meso- and metasoma (gaster); (b) antenna; (c) fore wing; (d) dorsal mesosoma; (e) head.
Figure 3 in The species of the varius group of Coccophagus (Hymenoptera: Aphelinidae) from China, with description of a new species, DNA sequence data, and a new country record
Figure 3. Coccophagus yunnana sp. nov. female. (a) coccid scale host with C. yunnana pupa and meconia visible; (b) pupa in dorsal view; (c) pupa in ventral view; (d) body in dorsal view; (e) body in ventral view.
Data from: HyRAD-X, a versatile method combining exome capture and RAD sequencing to extract genomic information from ancient DNA
Over the last decade, protocols aimed at reproducibly sequencing reduced-genome subsets in non-model organisms have been widely developed. Their use is however limited to DNA of relatively high molecular weight. During the last year, several methods exploiting hybridization capture using probes based on RAD-sequencing loci have circumvented this limitation and opened avenues to the study of samples characterized by degraded DNA, such as historical specimens. Here, we present a major update to those methods, namely Hybridization capture from RAD-derived probes obtained from a reduced eXome template (hyRAD-X), a technique applying RAD-sequencing to messenger RNA from one or few fresh specimens to elaborate bench-top produced probes, i.e., a reduced representation of the exome, further used to capture homologous DNA from a samples set. In contrast to previous hybridization-capture methods, the reference catalog on which reads are aligned does not rely on de novo assembly of anonymous RAD-sequencing loci, but on an assembled transcriptome obtained from RNAseq data, thus increasing the accuracy of loci definition and Single-Nucleotide-Polmorphisms (SNP) call, and targeting, specifically, expressed genes. Finally, the capture step of hyRAD-X relies on RNA probes, increasing stringency of hybridization, making it well suited for low-content DNA samples. As a proof of concept, we applied hyRAD-X to subfossil needles from the coniferous tree Abies alba, collected in lake sediments (Origlio, Switzerland) and dating back from 7200-5800 years before present (BP). More specifically we investigated genetic variation before, during, and after an anthropogenic perturbation that caused an abrupt decrease in Abies alba population size, 6500-6200 years BP. HyRAD-X produced a matrix encompassing 524 exome-derived SNPs. Despite a lower observed heterozygosity was observed during the 6.500-6.200 years BP time slice, genetic composition was nearly identical before and after the perturbation, indicating that re-expansion of the population after the decline was driven by autochthonous specimens. To the best of our knowledge, this is the first time a population genomic study incorporating ancient DNA samples of tree subfossils is conducted at a moderate cost using reproducible exome-reduced complexity.
Data for morphometric analysis and DNA barcode sequence for the new fish species Polymixia hollisterae
<p>Two datasets are provided to support the journal article (https://doi.org/10.1643/i2020112) by T. C. Grande and M. V. H. Wilson naming the new Bermuda fish species <em>Polymixia hollisterae</em>. The first dataset is for 2-D multivariate morphometric comparisons of selected specimens and species of the fish genus <em>Polymixia</em>. The file is in TPS format, as a plain text file, for use in the application MorphoJ. The data are for 27 specimens with pixel coordinates for 34 landmarks digitized in ImageJ and used to generate Fig. 13 in the referenced publication. The second dataset, published here courtesy of Dr. R. Eytan, is a mitochondrial DNA barcode sequence in fasta format for the second paratype specimen, a small juvenile of the new species. The specimen is only the third one known of the new species and the only one not from Bermuda. It was collected in the north-central Gulf of Mexico and is now deposited in the Harvard University MCZ fish collection as catalog number MCZ 174218. The fasta file can be used as input to the barcode identification function at boldsystems.org, although its original identification in BOLD was incorrect.</p>
Analysis of RNA-seq, DNA target enrichment, and Sanger nucleotide sequence data resolves deep splits in the phylogeny of cuckoo wasps (Hymenoptera: Chrysididae)
<p>The wasp family Chrysididae (cuckoo wasps, gold wasps) comprises exclusively parasitoid and kleptoparasitic species, many of which feature a stunning iridescent coloration and phenotypic adaptations to their parasitic life style. Previous attempts to infer phylogenetic relationships among the family's major lineages (subfamilies, tribes, genera) based on Sanger sequence data were insufficient to statistically resolve the monophyly and the phylogenetic position of the subfamily Amiseginae and the phylogenetic relationships among the tribes Allocoeliini, Chrysidini, Elampini, and Parnopini (Chrysidinae). Here, we present a phylogeny inferred from nucleotide sequence data of 492 nuclear single-copy genes (230,915 aligned amino acid sites) from 94 species of Chrysidoidea (representing Bethylidae, Chrysididae, Dryinidae, Plumariidae) and 45 outgroup species by combining RNA-seq and DNA target enrichment data. We find support for Amiseginae being more closely related to Cleptinae than to Chrysidinae. Furthermore, we find strong support for Allocoeliini being the sister lineage of all remaining Chrysidinae, while Elampini represent the sister lineage of Chrysidini and Parnopini. Our study corroborates results from a recent phylogenomic investigation which revealed Chrysidoidea as likely paraphyletic</p>
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>
Figure 9 in Systematic revision of Sabellariidae (Polychaeta) and their relationships with other polychaetes using morphological and DNA sequence data
Figure 9. Photographs of preserved specimens: A, nuchal spines (hooks), I. australiensis; B, thoracic segments with lateral lobes, I. australiensis; C, thoracic segments with lateral lobes, L. giardi; D, abdominal segments with 'proventricle', dorsal view, Sabellaria sp. nov. 2; E, abdominal segments with 'proventricle', ventral view, Sabellaria sp. nov. 2; F, posterior abdominal segments and cauda, Idanthyrsus australiensis. Abbreviations: b, branchia; ca, cauda; ll, lateral lobes; nh, nuchal spines (hooks); pv, proventricle.
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.