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”
FIGURE 3 in The complete mitochondrial genome of a tessaratomid bug, Eusthenes cupreus (Hemiptera: Heteroptera: Pentatomomorpha: Tessaratomidae)
FIGURE 3. Predicted secondary structure of the rrnL gene in E. cupreus. Roman numerals denote the conserved domain structure. The numbering system follows Gillespie et al. (2006) (established at the Comparative RNA Website). Dashed (–) indicate Watson-Crick base pairing and dot () indicate G-U base pairing.
FIGURE 1 in The complete mitochondrial genome of a tessaratomid bug, Eusthenes cupreus (Hemiptera: Heteroptera: Pentatomomorpha: Tessaratomidae)
FIGURE 1. Map of the mitogenome of E. cupreus. The tRNAs are denoted by the color blocks and are labeled according to the IUPAC-IUB single-letter amino acid codes. Gene name without underline indicates the direction of transcription from left to right, and with underline indicates right to left. Overlapping lines within the circle denote PCR fragments amplified used for cloning and sequencing.
FIGURE 6 in Complete nucleotide sequence and organization of the mitochondrial genome of Sirthenea flavipes (Hemiptera: Reduviidae: Peiratinae) and comparison with other assassin bugs
FIGURE 6. Phylogenetic tree of four sequenced assassin bugs. Bayesian inference and Maximum likelihood analysis inferred from all genes recovered the same topological structure. Bootstrap values and Bayesian posterior probabilities are indicated at each node.
FIGURE 3 in Complete nucleotide sequence and organization of the mitochondrial genome of Sirthenea flavipes (Hemiptera: Reduviidae: Peiratinae) and comparison with other assassin bugs
FIGURE 3. Predicted secondary structure of the rrnL in S. flavipes. Regions in red indicate the high variability in the four assassin bugs. Roman numerals denote the conserved domain structure. Dashed (-) indicate Watson-Crick base pairing and dot () indicate G-U base pairing.
FIGURE 2 in Complete nucleotide sequence and organization of the mitochondrial genome of Sirthenea flavipes (Hemiptera: Reduviidae: Peiratinae) and comparison with other assassin bugs
FIGURE 2. Inferred secondary structures of 22 tRNAs of S. flavipes. The tRNAs are labeled with the abbreviations of their corresponding amino acids. Dashed (-) indicate Watson-Crick base pairing and dot () indicate G-U base pairing.
FIGURE 4 in Complete nucleotide sequence and organization of the mitochondrial genome of Sirthenea flavipes (Hemiptera: Reduviidae: Peiratinae) and comparison with other assassin bugs
FIGURE 4. Predicted secondary structure of the rrnS in S. flavipes. Regions in red indicate the high variability in the four assassin bugs. Roman numerals denote the conserved domain structure. Dashed (-) indicate Watson-Crick base pairing and dot () indicate G-U base pairing.
FIGURE 5 in Complete nucleotide sequence and organization of the mitochondrial genome of Sirthenea flavipes (Hemiptera: Reduviidae: Peiratinae) and comparison with other assassin bugs
FIGURE 5. (A) The conserved region of the mitochondrial control region of S. flavipes, A. dohrni, T. dimidiata and V. hoffmanni. (B) The structural organization of the mitochondrial control region of S. flavipes. The control region flanking genes rrnS, trnI (I), trnQ (Q), and trnM (M) are represented in purple and green boxes. The light blue boxes with roman numerals indicate the tandem repeat region. "G+C" indicates high G+C content region. "A+T" indicates high A+T content region. The black box indicates G element.
FIGURE 1 in Complete nucleotide sequence and organization of the mitochondrial genome of Sirthenea flavipes (Hemiptera: Reduviidae: Peiratinae) and comparison with other assassin bugs
FIGURE 1. Map of the mtochondrial genome of S. flavipes. Direction of gene transcription is indicated by the arrows. PCGs are shown as blue arrows, rRNA genes as purple arrows, tRNA genes as red arrows and large non-coding regions (>100 bp) as cyan rectangles. tRNA genes are labeled according to single-letter IUPAC-IUB abbreviations (L1: UUR; L2:CUN; S1:AGN; S2:UCN). The GC content is plotted using a black sliding window, as the deviation from the average GC content of the entire sequence. GC Skew is plotted as the deviation from the average GC skew of the entire sequence. Ticks in the inner cycle indicate the sequence length.
Figure 5 in The complete mitochondrial genome of the mackerel icefish, Champsocephalus gunnari (Actinopterygii: Channichthyidae), with reference to the evolution of mitochondrial genomes in Antarctic notothenioids
Figure 5. Phylogenetic relationships of control regions inferred by the maximum likelihood (ML) method. Statistical support is shown on the branches: bootstrap values (above) and posterior probability (below). BI, Bayesian inference; CR, control region.
Figure 1 in The complete mitochondrial genome of the mackerel icefish, Champsocephalus gunnari (Actinopterygii: Channichthyidae), with reference to the evolution of mitochondrial genomes in Antarctic notothenioids
Figure 1. Evolution of mitochondrial genomes in Antarctic notothenioids modified from Zhuang & Cheng (2010). Abbreviations: 12S, 12S ribosomal RNA; CR, control region; Cyt b, cytochrome b; E, tRNAGlu; F, tRNAPhe; ND, nicotinamide adenine dinucleotide (reduced form) dehydrogenase; P, tRNAPro; T, tRNAThr.
Figure 4. A in The complete mitochondrial genome of the mackerel icefish, Champsocephalus gunnari (Actinopterygii: Channichthyidae), with reference to the evolution of mitochondrial genomes in Antarctic notothenioids
Figure 4. A, linear representation of three types of gene content from the partial cytochrome b (Cyt b) to 12S rRNA in the mitochondrial (mt) genome of the mackerel icefish. Black and dark grey arrows respectively represent the first and the second duplicates. The first duplicate of the type-1 genome contains full-length nicotinamide adenine dinucleotide (reduced form) dehydrogenase subunit 6 (ND6) and tRNAGlu. Type-2 contains a half-sized ND6 only. Type-3 does not contain ND6 or tRNAGlu. B, PCR amplifications for detecting ND6 and tRNAGlu in the three types of mt genome of the mackerel icefish. PCR fragments between Cyt b and control region (CR) 2 (Cyt b-CR2) and between CR2 and CR3 (CR2-CR3) contain the first and second copies of ND6, respectively. The PCR fragment between ND5 and Cyt b (ND5-Cyt b) did not contain ND6 or tRNAGlu. M, size marker. Lanes 1, 2, 7, and 10 are type-1 individuals. Lanes 3, 4, 8 and 11 are type-2 individuals. Lanes 5, 6, 9, and 12 are type-3 individuals. Abbreviations: E, tRNAGlu; F, tRNAPhe; P, tRNAPro; T, tRNAThr.
Figure 3 in The complete mitochondrial genome of the mackerel icefish, Champsocephalus gunnari (Actinopterygii: Channichthyidae), with reference to the evolution of mitochondrial genomes in Antarctic notothenioids
Figure 3. Map of the mackerel icefish mitochondrial (mt) genome as a circular diagram. The map represents the mt genome of a type-1 individual in which ND6 and tRNAGlu were transposed to a position between tRNAThr and tRNAPro flanked by intergenic spacers (UN3 and UN4), and the ND6- to -CR segment was duplicated once. Fourteen protein-coding genes, two rRNA genes, and noncoding regions are labelled with abbreviations. Twenty-four tRNA genes are shown by a one-letter amino acid code. Different codons used by each of tRNALeu and tRNASer are shown in parentheses. Genes transcribed from the heavy strand and light strand are respectively presented outside and inside the circle. Heavy- and light-strand replication origins are represented by OH and OL, respectively. Abbreviations: 12S, 12S ribosomal RNA; 16S, 16S ribosomal RNA; A, tRNAAla; ATP, ATP synthase; C, tRNACys; CO, cytochrome oxidase; Cyt b, cytochrome b; D, tRNAAsp; E, tRNAGlu; F, tRNAPhe; G, tRNAGly; H, tRNAHis; I, tRNAIle; K, tRNALys; L, tRNALeu; M, tRNAMet; N, tRNAAsn; ND, nicotiamide adenine dinucleotide (reduced form) dehydrogenase; P, tRNAPro; Q, tRNAGln; R, tRNAArg; S, tRNASer; T, tRNAThr; V, tRNAVal; W, tRNATrp; Y, tRNATyr.
Rhizophora complete chloroplast genome sequences
<p>Historical processes of long-distance migration and ocean-wide expansion feature the global biogeographic pattern of <i>Rhizophora</i> species. Throughout the Indian Ocean, <i>R. stylosa</i> and <i>R. mucronata</i> appear as a young phylogenetic group with expansion of <i>R. mucronata</i> towards the Western Indian Ocean (WIO) driven by the South Equatorial Current. Nuclear microsatellites revealed genetic patterns and breaks, however, estimating propagule dispersal routes requires maternally inherited cytoplasmic markers. Here, we examine the phylogeography of 21 <i>R. mucronata</i> provenances across a >4,200 km coastal stretch in the WIO using <i>R. stylosa</i> as outgroup. Full length chloroplast genome (164,474 bp) and nuclear ribosomal RNA cistron (8,033 bp) sequences were assembled. Boundaries, junction point, sequence orientation and stretch between LSC/IRb/SSC/IRa/LSC showed no differences with the <i>R. stylosa</i> chloroplast genome. A total of 58 mutations in <i>R. mucronata</i> encompassing transitions/transversions, insertion-deletions and mononucleotide repeats revealed three major haplogroups. Haplonetwork, Bayesian ML and Approximate Bayesian Computation (ABC) analyses supported discrete historical migration events. An ancient haplogroup A in the Seychelles and eastern Madagascar was as divergent from other <i>R. mucronata</i> haplogroups as it was from <i>R. stylosa</i>. A star-like haplonetwork referred to recent range expansion of haplogroup B from northern Madagascar towards the African mainland coastline, including a single variant spanning >1,800 km across the Mozambique Channel Area. Populations south of Delagoa Bight contained haplogroup C and originate from a unique bottleneck dispersal event. Divergence estimates of pre- and post-Last Glacial Maximum illustrated a recent emergence of WIO <i>Rhizophora </i>mangroves compared to other oceans. Connectivity patterns could be aligned with directionality of major ocean currents. Madagascar and the Seychelles each harbored haplogroups A and B, albeit among spatially separated populations, explained from a different migration era. Likewise, the Aldabra Atoll harbored spatially distinct haplotypes. Nuclear ribosomal cistron (8,033bp) variants corresponded to haplogroups and confirmed admixtures in the Seychelles and Aldabra. These findings shed new light on the origins and dispersal routes of <i>R. mucronata</i> lineages that have shaped their contemporary populations in large regions of the WIO, which may be important information for defining marine conservation units, both at ocean scale and at level of small islands.</p>
Comparative Analysis of Complete Chloroplast Genomes of 13 Species in Epilobium, Circaea, and Chamaenerion and Insights into Phylogenetic Relationships of Onagraceae
<p>This is all the alignments which used to constructed a phylogenetic tree in our study about Onagraceae. The evening primrose family, Onagraceae, is a well defined family of the order Myrtales, which comprises 22 genera widely distributed from boreal to tropical areas. In the present study, we report and characterize the complete chloroplast genome sequences of 13 species in <em>Circaea</em>,<em> Chamaenerion</em>, and <em>Epilobium</em> using a next-generation sequencing method. We also retrieved plastome sequences from two other Onagraceae genera to characterize the chloroplast genome of the family. The complete plastomes of Onagraceae showed a typical quadripartite structure and encoded an identical set of 112 genes (with exclusion of duplication), including 78 protein-coding genes, 30 transfer RNAs, and four ribosomal RNAs. The results show that chloroplast genomes are basically conserved in gene arrangement across the family. Whereas, a large segment of inversion was detected in the LSC region of all samples in the<em> Oenothera </em>subsect. <em>Oenothera</em>. An inverted repeat (IR) contraction was found in <em>Circaea</em> and<em> Ludwigia </em>samples. We also compared chloroplast genomes across the Onagraceae samples and revealed similarities in some features, including nucleotide content, codon usage, RNA editing sites, and simple sequence repeats (SSRs). Phylogeny was inferred by the chloroplast genome data using maximum-likelihood (ML) and Bayesian inference (BI) methods. The generic relationship of Onagraceae was well resolved by the complete plastome sequences, showing potential value in inferring phylogeny within the family. <em>Oenothera </em>phylogeny was better resolved than other densely sampled genera. Biparental transmission may be the main cause of higher variation in the genus<em> Oenothera</em>.</p>
Supplementary material 9 from: Zhang R, Tang Q, Deng L (2021) The complete mitochondrial genome of Microphysogobio elongatus (Teleostei, Cyprinidae) and its phylogenetic implications. ZooKeys 1061: 57-73. https://doi.org/10.3897/zookeys.1061.70176
Figure S5. Phylogenetic relationships of Gobioninae based on complete mitochondrial genomes using Bayesian analyses
Supplementary material 7 from: Zhang R, Tang Q, Deng L (2021) The complete mitochondrial genome of Microphysogobio elongatus (Teleostei, Cyprinidae) and its phylogenetic implications. ZooKeys 1061: 57-73. https://doi.org/10.3897/zookeys.1061.70176
Figure S3. Putative secondary structures of the 22 tRNA genes identified in the mitochondrial genome of M. elongatus
Complete mitochondrial genome of the hawthorn moth Scythropia crataegella (Linnaeus, 1767) (Lepidoptera: Scythropiidae)
<p>Currently, only a limited number of mitochondrial genomes (mitogenomes) are available in the superfamily Yponomeutoidea. In the present study, we report on the complete mitogenome of the hawthorn moth <em>Scythropia crataegella </em>(Linnaeus, 1767), the first species in the family Scythropiidae to enrich the catalog of Yponomeutoidea mitogenomes. The <em>S. crataegella </em>mitogenome was 15,350 bp in size and consisted of the set of genes and major non-coding A+T-rich region that are typical of insect mitogenomes. The <em>COI</em> gene had a CGA start codon; however, the other PCGs began with ATN codons. The A/T content was 80.3% in PCGs, 81.8% in tRNAs, 85.3% in <em>lrRNA</em>, 87.3% in <em>srRNA</em>, 81.8% in the whole genome, and 95.8% in the A+T-rich region. Phylogenetic analyses based on the concatenated sequences of 13 PCGs and two rRNA genes placed Scythropiidae, represented by <em>S. crataegella</em>, as a sister group to Yponomeutidae, represented by <em>Yponomeuta sedellus</em>; however, the nodal support for this group was very low (bootstrap support = 18%), indicating that extended taxon diversity is required for further robust phylogenetic inference in Yponomeutoidea.</p>
Dataset: Complete Genome Sequences of Sathuperi and Shamonda viruses isolated in Japan
<p>This file contains supplementary information corresponding to the manuscript: "Complete Genome Sequences of</p> <p>Sathuperi and Shamonda viruses isolated in Japan".</p>
Inversion polymorphism in a complete human genome assembly
<p>Supplementary data including code for an journal article titled 'Inversion polymorphism in a complete human genome assembly'.</p>
FIGURE 3. Correlation between the genetic p in Complete Mitochondrial genome of Eisenia nordenskioldi pallida Malevich, 1956 from Korea, with remarks on the phylogeny of the E. nordenskiodi complex (Megadrili; Lumbricidae)
FIGURE 3. Correlation between the genetic p-distances of the barcoding region (cox1) and the 13PCGs of the E. nordenskioldi s.l. taxa.
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.