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865 results for “mitochondrial genome”
Data from: Genomics overrules mitochondrial DNA, siding with morphology on a controversial case of species delimitation
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Origin of minicircular mitochondrial genomes in red algae
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Data and source code from: Contingency and selection in mitochondrial genome dynamics
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Genomics of new ciliate lineages provides insight into the evolution of obligate anaerobiosis - single gene datasets for phylogenomic analysis of anaerobic ciliates (SAL, Ciliophora), protein datasets for mitochondrial pathways prediction, and mitochondrial genomes
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Data from: Strong selective effects of mitochondrial DNA on the nuclear genome
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Data from: The genomic impact of historical hybridization with massive mitochondrial DNA introgression
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FIGURE 7 in The complete mitochondrial genome of Zicrona caerulea (Linnaeus) (Hemiptera: Pentatomidae: Asopinae) and its phylogenetic implications
FIGURE 7. Inferred phylogenetic relationships among Pentatomoidea based on the concatenated nucleotide sequences of 13 mitochondrial protein-coding genes using maximum likelihood (ML) (quadrangles: Phyllocephalinae; circles: Pentatominae; heart: Podopinae; pentagons: Asopinae). Numbers on branches are bootstrap percentages.
FIGURE 4 in Comparative mitochondrial genomics of Shoveliteratura triangula (Orthoptera Tettigoniidae, Meconematinae) and the first description of a female specimen
FIGURE 4. Phylogenetic reconstruction of the Meconematinae using mitochondrial PCGs and rRNA of the concatenated dataset. Applicable posterior probability values are shown. Numbers in the ML tree represent SH-aLRT support/ultrafast bootstrap support values.
FIGURE 2 in Comparative mitochondrial genomics of Shoveliteratura triangula (Orthoptera Tettigoniidae, Meconematinae) and the first description of a female specimen
FIGURE 2. Relative synonymous codon usage of Shoveliteratura triangula mitochondrial protein-coding genes. Codon families are shown on the x-axis.
The insertion of a mitochondrial selfish element into the nuclear genome and its consequences: supporting data sets and scripts
<p>Supplementary data sets and script for the article "The insertion of a mitochondrial selfish element into the nuclear genome and its consequences".</p> <p>The original source code with versioning is available at https://gitlab.gwdg.de/molsysevol/umag_11064 .</p>
Data from: The sugarcane mitochondrial genome: assembly, phylogenetics and transcriptomics
<p><strong>Background:</strong> Chloroplast genomes provide insufficient phylogenetic information to distinguish between closely related sugarcane cultivars, due to the recent origin of many cultivars and the conserved sequence of the chloroplast. In comparison, the mitochondrial genome of plants is much larger and more plastic and could contain increased phylogenetic signals. We assembled a consensus reference mitochondrion with Illumina TruSeq synthetic long reads and ONT MinION long reads. Based on this assembly we also analyzed the mitochondrial transcriptomes of sugarcane and sorghum and improved the annotation of the sugarcane mitochondrion as compared with other species.</p> <p><strong>Methods</strong>: Mitochondrial genomes were assembled from genomic read pools using a bait and assemble methodology. The mitogenome was exhaustively annotated using BLAST and transcript datasets were mapped with HISAT2 prior to analysis with the Integrated Genome Viewer.</p> <p><strong>Results</strong>: The sugarcane mitochondrion is comprised of two independent chromosomes, for which there is no evidence of recombination. Based on the reference assembly from the sugarcane cultivar SP80-3280 the mitogenomes of four additional cultivars (R570, LCP85-384, RB72343 and SP70-1143) were assembled (with the SP70-1143 assembly utilizing both genomic and transcriptomic data and the R570 data based on MinION assembly). We demonstrate that the sugarcane plastome is completely transcribed and we assembled the chloroplast genome of SP80-3280 using transcriptomic data only. Phylogenomic analysis using mitogenomes allow closely related sugarcane cultivars to be distinguished and supports the discrimination between <em>Saccharum officinarum</em> and <em>Saccharum cultum</em> as modern sugarcane's female parent. From whole chloroplast comparisons, we demonstrate that modern sugarcane arose from a limited number of S. cultum female founders. Transcriptomic and spliceosomal analyses reveal that the two chromosomes of the sugarcane mitochondrion are combined at the transcript level and that splice sites occur more frequently within gene coding regions than without. We reveal one confirmed and one potential cytoplasmic male sterility factor in the sugarcane mitochondrion, both of which are transcribed</p> <p><strong>Conclusion</strong>: Transcript processing in the sugarcane mitochondrion is highly complex with diverse splice events, the majority of which span the two chromosomes. PolyA baited transcripts are consistent with the use of polyadenylation for transcript degradation. For the first time we annotate two cytoplasmic male sterility factors within the sugarcane mitochondrion and demonstrate that sugarcane possesses all the molecular machinery required for cytoplasmic male sterility and rescue. A mechanism of cross-chromosomal splicing based on guide RNAs is proposed. We also demonstrate that mitogenomes can be used to perform phylogenomic studies on sugarcane cultivars.</p>
Supplementary material 2 from: Macher J-N, Drakou K, Papatheodoulou A, Hoorn B, Vasquez M (2020) The mitochondrial genomes of 11 aquatic macroinvertebrate species from Cyprus. Metabarcoding and Metagenomics 4: e58259. https://doi.org/10.3897/mbmg.4.58259
Supplementary tables showing reads numbers, coverage and length of mitochondrial genomes, and length and blast results of 18S and 28S rRNAs
House mouse Mus musculus dispersal in East Eurasia inferred from 98 newly determined complete mitochondrial genome sequences
<div> <p><span><span><span><span><span><span><span><span><span><span><span>The Eurasianhouse mouse <i>Mus musculus</i>is useful for tracing prehistorical human movement related to the spread of farming. We determined whole mitochondrial DNA (mtDNA) sequences (ca. 16,000 bp) of 98 wild-derived individuals of two subspecies, <i>M</i>. <i>m</i>. <i>musculus </i>(MUS) and <i>M</i>. <i>m</i>. <i>castaneus </i>(CAS). We revealed directional dispersals reaching as far asthe Japanese Archipelagofrom their homelands. Our phylogenetic analysis indicated that the eastward movement of MUS was characterised by five step-wise regional extension events: 1) broad spatial expansion into eastern Europe and the western part of western China, 2) dispersal to the eastern part of western China, 3) dispersal tonorthern China, 4) dispersal to the Korean Peninsula and 5) colonisation and expansion in the Japanese Archipelago. These events were estimated to have occurred during the last 2,000–18,000 years. The dispersal of CAS was characterised by three events: initial divergences(ca. 7,000–9,000 years ago) of haplogroups in northern most China and the eastern coast of India, followed by two population expansion events that likely originated from the Yangtze River basinto broad areas of South and Southeast Asia, including Sri Lanka, Bangladesh and Indonesia (ca. 4,000–6,000 years ago) and to Yunnan, southern China and the Japanese Archipelago (ca. 2,000–3,500). This study provides a solid framework for the spatiotemporal movementof the human-associated organisms in Holocene Eastern Eurasia using whole mtDNA sequences, reliable evolutionary rates and accurate branching patterns. The information obtained here contributes to the analysis of a variety of animals and plants associated with prehistoric human migration.</span></span></span></span></span></span></span></span></span></span></span></p> </div>
Data from: The first complete mitochondrial genome of the Indian Tent Turtle, Pangshura tentoria (Testudines: Geoemydidae): characterization and comparative analysis
Characterization of complete mitogenome is a widely used genomics study for species delineation and evolutionary research. However, the sequences and structural motifs contained within the mitogenome have been rarely examined to understand the phylogeny and evolutionary history among Testudines. Hence, the mitogenomic features of several Testudines taxa are still anonymous to the scientific communities. The present study decodes the first complete mitochondrial genome of the Indian Tent Turtle, Pangshura tentoria (16,657 bp) by using next-generation sequencing. This denovo assembly encodes 37 genes: 13 protein coding genes (PCGs), 22 transfer RNA (tRNAs), two ribosomal RNA (rRNAs), and one control region (CR). The mitogenome contained 19 intergenic spacer and six overlapping regions. Most of the genes were encoded on majority strand, except for one PCG (NADH dehydrogenase subunit 6) and eight tRNAs. Most of the PCGs were started with an ATG initiation codon, except for cytochrome oxidase subunit 1 with 'GTG' and NADH dehydrogenase subunit 5 with 'ATA'. The termination codons, 'TAA' and 'AGA' were observed in NADH dehydrogenase subunit 4l and NADH dehydrogenase subunit 6 respectively. The Relative Synonymous Codon Usage analysis revealed the maximum abundance of Alanine, Isoleucine, Leucine, and Threonine. The non-synonymous/synonymous ratios were <1 in all PCGs, which indicates strong negative selection among all Geoemydid species. The study also found the typical cloverleaf secondary structure in most of the tRNA genes, except for Serine (trnS1) with lack of the conventional DHU arm. The Wobble base pairing was observed in the different stems (DHU, acceptor, and anticodon) of 11 tRNAs. The comparative study of Geoemydid mitogenomes revealed the occurrence of tandem repeats was frequent in the 3´ end of CR. Further, two copies of a unique tandem repeat 'TTCTCTTT' were identified in P. tentoria. The Bayesian and Maximum Likelihood phylogenetic trees using concatenation of 13 PCGs revealed the close relationships of P. tentoria with Batagur trivittata in the studied dataset. All the Geoemydid species showed distinct clustering with high bootstrap support congruent with previous evolutionary hypotheses. We suggest that the generations of more mitogenomes of Geoemydid species, especially for Batagurinae subfamily, are required to improve our understanding their in-depth phylogenetic and evolutionary relationships.
Lasionycteris noctivagans mitochondrial genomes raw data
<p>The geographic distributions of eastern and western <i>Lasionycteris noctivagans</i> populations suggest they could be geneticially isolated from each other, but this has rarely been assessed using genetic data. Here, we evaluate this possibility by sequencing the complete mitochondrial genome of four silver-haired bats from eastern and western populations. The three usable mitogenomes were closely associated with other Vespertilionid bats and the phylogenetic tree revealed the two western individuals grouping together to form their own clade. Our results support the idea that small but significant genetic differences exist between eastern and western populations of these bats.</p>
FIG. 4 in The complete mitochondrial genome of the Eurasian wryneck Jynx torquilla (Aves Piciformes: Picidae) and its phylogenetic inference
FIG. 4. Phylogenetic trees of 17 piciform species based on the amino acid dataset. The numbers abutting branches refer to Bayesian posterior probabilities (left) and ML bootstraps (right), ‾ not recovered. Branch lengths and topology are from the BI analysis. Halcyon pileata (Coraciiformes) was used to root the trees as an outgroup.
FIG. 2 in The complete mitochondrial genome of the Eurasian wryneck Jynx torquilla (Aves Piciformes: Picidae) and its phylogenetic inference
FIG. 2. Genetic distance within subfamily, between subfamily and family. Each boxplot represents the P distance based on the nucleotide and the amino acid datasets from 13 mitochondrial PCGs. Lower horizontal bar represents smallest observation, lower edge of rectangle represents 25 percentile, central bar within rectangle represents median, upper edge of rectangle represents 75 percentile, upper horizontal bar represents largest observation.
FIG. 1 in The complete mitochondrial genome of the Eurasian wryneck Jynx torquilla (Aves Piciformes: Picidae) and its phylogenetic inference
FIG. 1. Circular map of the J. torquilla mitogenome. The inner circle shows the GC content, which is calculated based on a window-sliding method. The outer circle shows the gene features, orange for rRNA, red for tRNA, and blue for CDS. Genes inside the circle (on the J strand) are transcribed clockwise, while the outsides (on the N strand) are transcribed counterclockwise.
FIG. 3 in The complete mitochondrial genome of the Eurasian wryneck Jynx torquilla (Aves Piciformes: Picidae) and its phylogenetic inference
FIG. 3. Phylogenetic trees of 17 piciform species based on the nucleotide dataset inferred from Bayesian inference (a) and maximum likelihood (b). The numbers abutting branches refer to Bayesian posterior probabilities (BPP) and bootstrap support (BS). Halcyon pileata (Coraciiformes) was used to root the trees as an outgroup.
FIGURE 8 in The mitochondrial genome of Smerinthus planus (Lepidoptera: Sphingidae) and its comparative analysis with other Lepidoptera species
FIGURE 8. Tree showing the phylogenetic relationships among Lepidoptera species, constructed using Maximum Likelihood method. Bootstrap values (1000 repetitions) of the branches are indicated. Drosophila incompta (NC_025936) and Anopheles gambiae (NC_002084) were used as outgroups.
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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.