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.
865
datasets available to search
ShareScore release 0.7.1
Dataset results
865 results for “mitochondrial genome”
Figure 2 in The complete mitochondrial genome of Lemyra melli (Daniel) (Lepidoptera: Erebidae) and a comparative analysis within the Noctuoidea
Figure 2. Relative Synonyous Codon Usage (RSCU) in L. melli, H. cunea, and A. formosae mitogenomes. Codons are provided on the x-axis.
Figure 6 in The complete mitochondrial genome of Lemyra melli (Daniel) (Lepidoptera: Erebidae) and a comparative analysis within the Noctuoidea
Figure 6. Phylogenetic analysis inferred from the concatenated nucleotide sequences of 13 PCGs in the mitogenome. D. melanogaster and E. regina were used as outgroups. The numbers above the branches specify bootstrap percentages (1 000 replicates) from software RAXMAL and the ML method. A, B, C, D, and E indicated the superfamily of Noctuoidea, Bombycoidea, Geometroidea, Pyraloidea and Tortricidea, respectively.
Figure 7 in The complete mitochondrial genome of Parnassius actius (Lepidoptera: Papilionidae: Parnassinae) with the related phylogenetic analysis
Figure 7. Bayesian Inference and maximum likelihood phylograms of the 45 Parnassius species in this study (Numbers on each node correspond to the posterior probability values of the BI analysis (left) and the ML bootstrap percentage values for 1000 replicates (right), posterior probability values below 0.5 or bootstrap percentage values below 50% was not shown on the diagram).
Figure 5 in General methods to obtain and analyze the complete mitochondrial genome of aphid species: Eriosoma lanigerum (Hemiptera: Aphididae) as an example
Figure 5. Bayesian inference (BI) and Maximum likelihood (ML) phylogenetic tree inferred from 11 aphids mt genome sequences. The support values on the nodes are the bootstrap (BS) values and the Bayesian posterior probabilities (BPP).
Figure 4 in General methods to obtain and analyze the complete mitochondrial genome of aphid species: Eriosoma lanigerum (Hemiptera: Aphididae) as an example
Figure 4. The secondary structure of the 22 transfer RNAs (tRNAs) in the Eriosoma lanigerum mt genome.
Figure 3 in General methods to obtain and analyze the complete mitochondrial genome of aphid species: Eriosoma lanigerum (Hemiptera: Aphididae) as an example
Figure 3. Circular map of the Eriosoma lanigerummt genome. Gene names not underlined indicate the direction of transcription in
Contrasting phylogeographic patterns of mitochondrial and genome-wide variation in the groundwater amphipod (Crangonyx islandicus) that survived the Ice age in Iceland
<p>In this zip "DataAvailability.zip" all the data and parameter files, as well as R scripts and bash codes used to perform the analyses of the mitochondrial and the RADseq data are provided. A ReadMe file is available at the root describing the content of the different folders and files.</p> <p>Below is the abstract of the associated manuscript:</p> <p>Analysis of phylogeographic patterns have often been based on mitochondrial DNA variation, but recent analyses dealing with nuclear DNA have in some instances revealed mito-nuclear discordances and complex evolutionary histories. These enigmatic scenarios which may involve stochastic lineage sorting, ancestral hybridization, past dispersal, and secondary contacts are increasingly scrutinized with a new generation of genomic tools such as RADseq, which pose also additional analytical challenges. Here, we revisited the previously inconclusive phylogeographic history, showing mito-nuclear discordance, of an endemic groundwater amphipod from Iceland, <em>Crangonyx islandicus,</em> which is the only metazoan known to have survived the Pleistocene beneath the glaciers. Previous studies based on three DNA markers documented a mitochondrial scenario with the main divergence occurring between populations in northern Iceland and an ITS scenario with the main divergence between the south and north. We used double digest restriction-site-associated DNA sequencing (ddRADseq) to clarify this mito-nuclear discordance by applying several statistical methods while estimating the sensitivity to different analytical approaches (data-type, differentiation indices and base call uncertainty). A majority of nuclear markers and methods support the ITS divergence. Nevertheless, a more complex scenario emerges, possibly involving introgression led by male-biased dispersal among northern locations or mitochondrial capture which may have been further strengthened by natural selection.</p>
Picea mariana isolate 40-10-1 mitochondrial genome assembly
<p><em>Picea mariana</em> isolate 40-10-1 mitochondrial genome assembly generated with Illumina HiSeq and 10x Genomics Chromium reads using ABySS v2.1.0, Tigmint v1.1.2, and ARCS v1.0.6.</p>
Picea glauca isolate WS77111 mitochondrial genome assembly
<p><em>Picea glauca</em> isolate WS77111 mitochondrial genome assembly generated with Illumina HiSeq reads using ABySS v2.1.4.</p>
Picea engelmannii isolate Se404-851 mitochondrial genome assembly
<p><em>Picea engelmannii</em> isolate Se404-851 mitochondrial genome assembly generated with Illumina HiSeq reads using ABySS v2.1.4.</p>
Genome-wide analysis resolves the radiation of New Zealand’s freshwater Galaxias vulgaris complex and reveals a candidate species obscured by mitochondrial capture
Open the record for dataset details and reuse information.
Mitochondrial reference genome for Teleopsis dalmanni
Open the record for dataset details and reuse information.
Data from: Repeated mitochondrial capture with limited genomic introgression in a lizard group
Open the record for dataset details and reuse information.
Potential causes and consequences of rapid mitochondrial genome evolution in thermoacidophilic Galdieria (Rhodophyta)
<p>The Cyanidiophyceae is an early-diverged red algal class that thrives in extreme conditions around acidic hot springs. Although this lineage has been highlighted as a model for understanding the biology of extremophilic eukaryotes, little is known about the molecular evolution of their mitochondrial genomes (mitogenomes).</p> <p>To fill this knowledge gap, we sequenced five mitogenomes from representative clades of Cyanidiophyceae and identified two major groups, here referred to as Galdieria-type (G-type) and Cyanidium-type (C-type). G-type mitogenomes exhibit the following three features: (i) reduction in genome size and gene inventory, (ii) evolution of unique protein properties including charge, hydropathy, stability, amino acid composition, and protein size, and (iii) distinctive GC-content and skewness of nucleotides. Based on GC-skew-associated characteristics, we postulate that unidirectional DNA replication may have resulted in the rapid evolution of G-type mitogenomes.</p> <p>The high divergence of G-type mitogenomes was likely driven by natural selection in the multiple extreme environments that Galdieria species inhabit combined with their highly flexible heterotrophic metabolism. We speculate that the interplay between mitogenome divergence and adaptation may help explain the dominance of Galdieria species in diverse extreme habitats.</p>
Data from: Structure, gene order, and nucleotide composition of mitochondrial genomes in parasitic lice from Amblycera
<p>Parasitic lice have unique mitochondrial (mt) genomes characterized by rearranged gene orders, variable genome structures, and less AT content compared to most other insects. However, relatively little is known about the mt genomes of Amblycera, the suborder sister to all other parasitic lice. Comparing among nine different genera (including representative of all seven families), we show that Amblycera have variable and highly rearranged mt genomes. Some genera have fragmented genomes that vary considerably in length, whereas others have a single mt chromosome. Notably, these genomes are more AT-biased than most other lice. We also recover genus-level phylogenetic relationships among Amblycera that are consistent with those reported from large nuclear datasets, indicating that mt sequences are reliable for reconstructing evolutionary relationships in Amblycera. However, gene order data cannot reliably recover these same relationships. Overall, our results suggest that the mt genomes of lice, already know to be distinctive, are even more variable than previously thought.</p>
Genome-scale target capture of mitochondrial and nuclear environmental DNA from water samples
<p>Environmental DNA (eDNA) provides a promising supplement to traditional sampling methods for population genetic inferences, but current studies have almost entirely focused on short mitochondrial markers. Here, we develop one mitochondrial and one nuclear set of target capture probes for the whale shark (<i>Rhincodon typus</i>) and test them on seawater samples collected in Qatar to investigate the potential of target capture for eDNA-based population studies. The mitochondrial target capture successfully retrieved ~235x (90x-352x per base position) coverage of the whale shark mitogenome. Using a minor allele frequency of 5%, we find 29 variable sites throughout the mitogenome, indicative of at least five contributing individuals. We also retrieved numerous mitochondrial reads from an abundant non-target species mackerel tuna<i> </i>(<i>Euthynnus affinis</i>), showing a clear relation between sequence similarity to the capture probes and the number of captured reads. The nuclear target capture probes retrieved only few reads and polymorphic variants from the whale shark, but we successfully obtained millions of reads and thousands of polymorphic variants with different allele frequencies from <i>E</i>. <i>affinis</i>. We demonstrate that target capture of complete mitochondrial genomes and thousands of nuclear loci is possible from aquatic eDNA samples. Our results highlight that careful probe design, taking into account the range of divergence between target and non-target sequences as well as presence of non-target species at the sampling site, is crucial to consider. Environmental DNA sampling coupled with target capture approaches provide an efficient means with which to retrieve population genomic data from aggregating and spawning aquatic species.</p>
The complete mitochondrial genome of dwarf form of Sthenoteuthis oualaniensis (Cephalopoda: Ommastrephidae) from the South China Sea
<p>The purpleback flying squid (<em>Sthenoteuthis oualaniensis</em>) is a pelagic squid with tremendous potential for commercial exploitation. <em>Sthenoteuthis oualaniensis</em> comprises two forms in the South China Sea, dwarf form and medium-sized form. In this study, we described the complete mitochondrial genome of dwarf form of <em>Sthenoteuthis oualaniensis.</em> The genome is 20320 bp in length, encoding the standard set of 13 protein-coding genes, 20 tRNA genes and 2 rRNA genes, with circular organization. The overall base composition of the whole mitochondrial genome was A (37.23%), T (32.78%), G (10.53%) and C (19.46%) with an AT bias of 70.01%. The longest protein-coding genes of these species was <em>ND5</em>, whereas the shortest <em>ATP8</em>.</p>
Data from: Strong selective effects of mitochondrial DNA on the nuclear genome
<p>Oxidative phosphorylation, the primary source of cellular energy in eukaryotes, requires gene products encoded in both the nuclear and mitochondrial genomes. As a result, functional integration between the genomes is essential for efficient adenosine triphosphate (ATP) generation. Although within populations this integration is presumably maintained by coevolution, the importance of mitonuclear coevolution in key biological processes such as speciation and mitochondrial disease has been questioned. In this study, we crossed populations of the intertidal copepod <i>Tigriopus californicus</i> to disrupt putatively coevolved mitonuclear genotypes in reciprocal F<sub>2</sub> hybrids. We utilized inter-individual variation in developmental rate among these hybrids as a proxy for fitness to assess the strength of selection imposed on the nuclear genome by alternate mitochondrial genotypes. Developmental rate varied among hybrid individuals, and <i>in vitro </i>ATP synthesis rates of mitochondria isolated from high fitness hybrids were approximately two-fold greater than those of mitochondria isolated from low fitness individuals. We then used Pool-seq to compare nuclear allele frequencies for high or low fitness hybrids. Significant biases for maternal alleles were detected on five (of 12) chromosomes in high fitness individuals of both reciprocal crosses, whereas maternal biases were largely absent in low fitness individuals. Therefore, the most fit hybrids were those with nuclear alleles that matched their mitochondrial genotype on these chromosomes, suggesting that mitonuclear effects underlie individual-level variation in developmental rate and that inter-genomic compatibility is critical for high fitness. We conclude that mitonuclear interactions can have profound impacts on both physiological performance and the evolutionary trajectory of the nuclear genome.</p>
Data from: Hare pseudo-reference genome from: the genomic impact of historical hybridization with massive mitochondrial DNA introgression
<p><b>Background:</b> The extent to which selection determines interspecific patterns of genetic exchanges enlightens the role of adaptation in evolution and speciation. Often reported extensive interspecific introgression could be selection-driven, but also result from demographic processes, especially in cases of invasive species replacements, which can promote introgression at their front. Because invasion and selective sweeps similarly mold variation, population genetics evidence for selection can only be gathered in an explicit demographic framework. The Iberian hare, <i>Lepus granatensis</i>, displays in its northern range extensive mitochondrial DNA introgression from <i>L. timidus</i>, an arctic/boreal species that it replaced locally after the last glacial maximum. We use whole-genome sequencing to infer geographic and genomic patterns of nuclear introgression and fit a neutral model of species replacement with hybridization, allowing us to evaluate how selection influenced introgression genome-wide, including for mtDNA.</p> <p><b>Results:</b> Although the average nuclear and mtDNA introgression patterns are strongly contrasted, they fit a single neutral model of post-glacial invasive replacement of <i>timidus</i> by <i>granatensis</i>. Outliers of elevated introgression include several genes related to immunity, spermatogenesis, and mitochondrial metabolism. Introgression is reduced on the X-chromosome and in low recombining regions.</p> <p><b>Conclusion:</b> General nuclear and mtDNA patterns of introgression can be explained by purely demographic processes. Hybrid incompatibilities and interplay between selection and recombination locally modulate levels of nuclear introgression. Selection promoted introgression of some genes involved in conflicts, either interspecific (parasites) or possibly cytonuclear. In the latter case, nuclear introgression could mitigate the potential negative effects of alien mtDNA on mitochondrial metabolism and male-specific traits.</p>
Supplementary data 'Mitochondrial genome sequence of the protist Ancyromonas sigmoides Kent, 1881 (Ancyromonadida) from the Sugluk Inlet, Hudson Strait, Nunavik, Québec'
<p>Fasta file with the transcripts obtained from RNAseq sequencing of Ancryomonas sigmoides (kmer 35) and file with datamining results.</p><p>Fasta file of the transcript matching the cox1 gene.</p><p>Scaffolds of the kmer 85 assembly of the genomic data of Ancryomonas sigmoides.</p><p>Databse used for datamining (fasta file)</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.