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.
505
datasets available to search
ShareScore release 0.9.0
Dataset results
505 results for “Complete genomes”
Fig. 1 in Complete mitochondrial genome of Nyctalus aviator and phylogenetic analysis of the family Vespertilionidae
Fig. 1. Neighbor Joining (NJ) phylogeny of Vespertilionidae was inferred from concatenated nucleotide sequences of 13 mitogenomic protein-coding genes. Node labels indicate the bootstrap values. GenBank accession numbers for the sequences are indicated next to species designations.
Repeat-masked <i>Strix occidentalis caurina</i> nuclear genome version 1.0 and complete mitochondrial genome
<p><strong>StrOccCau_1.0_nuc_finalMito_RepeatMasked.fa.bz2</strong> : This file is homology-based and <em>de novo</em> model-based repeat-masking of the reference <em>Strix occidentalis caurina</em> genome StrOccCau_1.0_nuc.fa from Hanna et al., 2017a,b) with the mitochondrial genome from Hanna et al. (2017c).</p> <p><strong>StrOccCau_1.0_nuc_finalMito_RepeatMasked.bed.bgz</strong> : This is a file in Browser Extensible Data (BED) format that provides the genomic intervals of the N-regions in the above masked assembly. The N-regions include hard-masked low complexity and repeat regions as well as N-regions that were gaps in the original assembly. I compressed the file using the bgzip tool from HTSlib version 1.7 (Davies et al. 2018).</p> <p>See full details of the creation of these files in section 2.1 of the materials and methods at protocols.io (http://dx.doi.org/10.17504/protocols.io.rmrd456).</p> <p>If you use these data, please cite the following:</p> <p>Hanna ZR. 2018. Repeat-masked <em>Strix occidentalis caurina</em> nuclear genome version 1.0 and complete mitochondrial genome. Version 1.0.0. <em>Zenodo.</em></p> <p> </p> <p><strong>References</strong></p> <p>Davies R, Randall JC, McCarthy SA, Bonfield J, Pollard MO, Marshall J, et al. 2018. HTSlib. Version 1.7. [Accessed 2018 Mar 19]. Available from: https://github.com/samtools/htslib</p> <p>Hanna ZR, Henderson JB, Wall JD, Emerling CA, Fuchs J, Runckel C, et al. 2017a. Northern Spotted Owl (<em>Strix occidentalis caurina</em>) Genome: Divergence with the Barred Owl (<em>Strix varia</em>) and Characterization of Light-Associated Genes. Genome Biology and Evolution. 9: 2522–2545. DOI: 10.1093/gbe/evx158</p> <p>Hanna ZR, Henderson JB, Wall JD, Emerling CA, Fuchs J, Runckel C, et al. 2017b. Supplemental dataset for Northern Spotted Owl (<em>Strix occidentalis caurina</em>) genome assembly version 1.0. <em>Zenodo</em>. DOI: 10.5281/zenodo.822859</p> <p>Hanna ZR, Henderson JB, Sellas AB, Fuchs J, Bowie RCK, Dumbacher JP. 2017c. Complete mitochondrial genome sequences of the northern spotted owl (<em>Strix occidentalis caurina</em>) and the barred owl (<em>Strix varia</em>; Aves: Strigiformes: Strigidae) confirm the presence of a duplicated control region. <em>PeerJ</em>. 5: e3901. DOI: 10.7717/peerj.3901</p> <p> </p>
Figure 3 in Complete mitochondrial genome of an Arctic Collared Lemming subspecies endemic to the Novaya Zemlya Archipelago, Russia
Figure 3. Bayesian Inference phylogenetic tree of the concatenated protein coding and rRNA genes based on available mitogenomes of Arctic Collared Lemming Dicrostonyx torquatus. The red font indicates the Novaya Zemlya subspecies D. torquatus ungulatus. The numbers near nodes represent Bayesian Posterior Probabilities (BPP) of MrBayes / Bootstrap Support (BS) values of IQ-Tree. The values above 95% for both BPP/BS are replaced with an asterisk. Outgroup taxa (Dicrostonyx hudsonius and D. groenlandicus) are not shown.
Figure 1 in Complete mitochondrial genome of an Arctic Collared Lemming subspecies endemic to the Novaya Zemlya Archipelago, Russia
Figure 1. Morphology of Novaya Zemlya Collared Lemming Dicrostonyx torquatus ungulatus (von Baer, 1841) from Novaya Zemlya Archipelago, Arctic Russia [topotype No. RMBH Lem16]: (A, B) specimen: (A) dorsal view, (B) ventral view; (C, D, E) crania: (C) dorsal view, (D) ventral view, (E) lateral view; (F, G) lower jaw: (F) outer lateral view, (G) inner lateral view; (H, I) molar rows: (H) maxillary, and (I) mandibular. Scale bars = 10 mm. (Photos: Elizaveta A. Spitsyna).
Fig. 1. Diplodiscus japonicus and Diplodiscus mehari mitochondrial genomes arrangement. All 22 in Characterization of the complete mitochondrial genomes of Diplodiscus japonicus and Diplodiscus mehari (Trematoda: Diplodiscidae): Comparison with the members of the superfamily Paramphistomoidea and phylogenetic implication
Fig. 1. Diplodiscus japonicus and Diplodiscus mehari mitochondrial genomes arrangement. All 22 tRNA genes are designated by the one-letter code with numbers differentiating each of the two tRNAs leucine and serine. All genes are coded by the same DNA strand and are transcribed clockwise. NCR refers to the non-coding region.
Fig. 5 in Characterization of the complete mitochondrial genomes of Diplodiscus japonicus and Diplodiscus mehari (Trematoda: Diplodiscidae): Comparison with the members of the superfamily Paramphistomoidea and phylogenetic implication
Fig. 5. Proportions between rates of non-synonymous (dN) and synonymous (dS) nucleotide substitutions (dN/dS). Bar chart for pairwise proportions of dN/dS for each of the mitochondrial subunits of the Diplodiscus spp.
Fig. 4 in Characterization of the complete mitochondrial genomes of Diplodiscus japonicus and Diplodiscus mehari (Trematoda: Diplodiscidae): Comparison with the members of the superfamily Paramphistomoidea and phylogenetic implication
Fig. 4. Sliding window analysis of the complete mt genome sequences of 11 Paramphistomoidea trematodes. A sliding window of 300 bp (in 10 bp overlapping steps) was used to estimate nucleotide diversity Pi (π) across the alignments. Nucleotide diversity was plotted against the mid-point positions of each window. Each gene boundary is identified.
Fig. 5 in The complete mitochondrial genome of Platygaster robiniae (Hymenoptera: Platygastridae): A novel tRNA secondary structure, gene rearrangements and phylogenetic implications
Fig. 5. Phylogenetic tree Note: (A): Maximum likelihood (ML) phylogenetic tree inferred from the mitochondrial genome based on the 13 PCGs dataset; (B): Bayesian inference (BI) phylogenetic tree inferred from the mitochondrial genome based on the 13 PCGs dataset.
Fig. 4 in The complete mitochondrial genome of Platygaster robiniae (Hymenoptera: Platygastridae): A novel tRNA secondary structure, gene rearrangements and phylogenetic implications
Fig. 4. Mitochondrial genome organization of Platygaster robiniae and 11 species of Platygastroidea, compared with the ancestral pancrustacean mt genome organization. Note: tRNA genes are indicated by single letter amino acid codes, L1, L2, S1 and S2 denote tRNALeu(CUN), tRNALeu(UUR), tRNASer(AGN) and tRNASer(UCN), respectively. Genes are transcribed from left to right except those indicated by underlining. Gene movements, relative to the ancestral organization, are indicated with arrows.
Fig. 3 in Characterization of the complete mitochondrial genomes of Diplodiscus japonicus and Diplodiscus mehari (Trematoda: Diplodiscidae): Comparison with the members of the superfamily Paramphistomoidea and phylogenetic implication
Fig. 3. Relative synonymous codon usage (RSCU) of 12 protein coding genes of Diplodiscus japonicus and Diplodiscus mehari. The termination codon is not given.
Fig. 2 in The complete mitochondrial genome of Platygaster robiniae (Hymenoptera: Platygastridae): A novel tRNA secondary structure, gene rearrangements and phylogenetic implications
Fig. 2. Amino acids (A) and relative synonymous codons (B) of protein-coding genes of the mitochondrial genome of Platygaster robiniae.
Fig. 2. A in Characterization of the complete mitochondrial genomes of Diplodiscus japonicus and Diplodiscus mehari (Trematoda: Diplodiscidae): Comparison with the members of the superfamily Paramphistomoidea and phylogenetic implication
Fig. 2. A + T content and nucleotide skew of genes, individual elements, and the complete mitogenome of 11 Paramphistomoidea trematodes.
Fig. 1 in The complete mitochondrial genome of Platygaster robiniae (Hymenoptera: Platygastridae): A novel tRNA secondary structure, gene rearrangements and phylogenetic implications
Fig. 1. Genetic map of the complete mitochondrial genome of Platygaster robiniae. Notes: the blue arrow represents the direction of gene transcription; the black peak represents the deviation of GC%; the purple and green peaks represent the deviation in GC skew; green refers to positive skew, and purple indicates negative skew. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 6 in Characterization of the complete mitochondrial genomes of Diplodiscus japonicus and Diplodiscus mehari (Trematoda: Diplodiscidae): Comparison with the members of the superfamily Paramphistomoidea and phylogenetic implication
Fig. 6. Phylogenetic relationships of Diplodiscus japonicus and Diplodiscus mehari with other 30 representative Digenea trematodes based on concatenated amino acid sequences of 12 protein coding genes analyzed by maximum likelihood (ML) and Bayesian inference (BI) using Gyrodactylus salaris as the outgroup. Statistical support values (Bootstrap/posterior probability) of ML/BI analysis are shown above the nodes. Circles indicate ML/BI = 100/1.0, other values are given above the nodes. Suborders and families are highlighted by individual colors. Accession numbers are given for each species at the end of each sequence. The scale bar corresponds to the estimated number of substitutions per site. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 3 in The complete mitochondrial genome of Corydoras nattereri (Callichthyidae: Corydoradinae)
Fig. 3. Maximum likelihood tree (log likelihood = -2410.0522) of Corydoras samples with at least 90% similarity to the mitochondrial cytochrome oxidase I sequences of C. nattereri from the rio Suruí. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. Bootstrap robustness is indicated next to selected branches. Samples of C. nattereri have the locality name appended to the sample ID (those for which mitogenomes were produced are from de rio "Surui"), outgroups have the genus name and other samples of Corydoras have the species epithet name appended to the ID code (Table 1).
Fig. 2 in The complete mitochondrial genome of Corydoras nattereri (Callichthyidae: Corydoradinae)
Fig. 2. Sequencing depth over the complete mitogenomes of the three individuals of Corydoras nattereri: KT239008 (A), KT239009 (B), and KT239010 (C). Read counts (y-axis) are shown in logarithmic scale and sharp decreases correspond to the punctuation model of mitochondrial transcription (positions correspond to those shown in Fig. 1 and Table 3). Black vertical bars indicate position of gaps that were filled with Sanger sequencing (Table 2). Reads were mapped to the mitogenomes using Bowtie and visualized at the Integrative Genome Viewer (IGV, Bernt et al., 2013; Thorvaldsdóttir et al., 2013).
Fig. 1 in The complete mitochondrial genome of Corydoras nattereri (Callichthyidae: Corydoradinae)
Fig. 1. Circular representation of the mitochondrial genome of Corydoras nattereri. Genes encoded in the heavy strand are shown in the outer circle and genes encoded in the light strand are offset inwards. The inner circle represents the CG-content. Figure was generated by the online server MitoFish, http://mitofish.aori.u-tokyo.ac.jp (Iwasaki et al., 2012).
Figure 3 in The complete mitochondrial genome of Lemyra melli (Daniel) (Lepidoptera: Erebidae) and a comparative analysis within the Noctuoidea
Figure 3. Putative secondary cloverleaf structures of the tRNA genes in the Lemyra melli mitogenome with mismatched bases. The blue dots, and red dots indicate Watson- Crick base pairing A-U and G-C, respectively, and the blanks indicate mismatched bases. Seven mismatches (five U-U, one A-A and one U-G) lie in five tRNA genes (three in the amino acid acceptor stems, three in the anticodon stems and one in pseudouridine (TΨC)).
Figure 1 in The complete mitochondrial genome of Lemyra melli (Daniel) (Lepidoptera: Erebidae) and a comparative analysis within the Noctuoidea
Figure 1. Map of the mitogenome of Lemyra melli. Genes lying outside and inside of the outer circle are transcribed in the counterclockwise and clockwise directions, respectively. The transfer RNA genes trnL1, trnL2, trnS1 and trnS2 are denoted trnL(UUR), trnL(CUN), trnS(AGN) and trnS(UCN), respectively. Area dashed darker gray in the inner circle denotes the GC content while the lighter gray denotes the AT content of the genome.
Figure 4 in The complete mitochondrial genome of Lemyra melli (Daniel) (Lepidoptera: Erebidae) and a comparative analysis within the Noctuoidea
Figure 4. The structure in the A+T-rich region of the Leymra melli mitogenome. The ATAGA + polyT, the duplicated 14-bp repeat element, the ATTTA + (AT)10 element, and the polyA structure are shown in the sequence.
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.