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410 results for “Mitochondrial gene”
Fig. 4. Maximum Parsimony consensus tree for the mitochondrial gene Cytochrome Oxidase I in New species of Moenkhausia Eigenmann, 1903 (Characiformes: Characidae) with comments on the Moenkhausia oligolepis species complex
Fig. 4. Maximum Parsimony consensus tree for the mitochondrial gene Cytochrome Oxidase I. Numbers represent values of 1000 bootstrap replicates.
Figure 4 in Systematics of Oreobates and the Eleutherodactylus discoidalis species group (Amphibia, Anura), based on two mitochondrial DNA genes and external morphology
Figure 4. Type localities of members of Oreobates: (1) O. quixensis, San José de Moti, Prov. Napo, Ecuador; (2) O. simmonsi, Río Piuntza, 1830 m a.s.l., Cordillera del Cóndor, Prov. Morona-Santiago, Ecuador; (3) O. saxatilis, Ponga de Shilcayo, 470 m a.s.l., Department San Martín, Peru; (4) O. lehri, Apurimac River Valley, 2445 m a.s.l., Department Cusco, Peru; (5) O. granulosus, Santo Domingo, Carabaya, Department Puno, Peru, 1800 m a.s.l.; (6) O. madidi, Arroyo Huacataya, Serranía Eslabón, 1500 m a.s.l., Department La Paz, Bolivia; (7) O. sanderi, Arroyo Bilunto, Chunirumi Valley, 1800 m a.s.l., near Santa Cruz de Valle Ameno, Department La Paz, Bolivia; (8) O. zongoensis, Valle de Zongo, 1250 m a.s.l., Department La Paz, Bolivia; (9) O. choristolemma, Serranía de Bellavista c. 1000 m a.s.l., Department La Paz, Bolivia; (10) O. cruralis, Department La Paz, Bolivia, 4000 m a.s.l. (in error); (11) O. heterodactylus, gruta Facendinha, State Mato-Grosso, Brazil; (12) O. ibischi, km 68.5 on Santa Cruz de la Sierra-Samaipata road c. 750 m a.s.l., Department Santa Cruz, Bolivia; (13) O. sanctaecrucis, El Chapé, Department Santa Cruz, Bolivia, 2060 m a.s.l.; (14) O. discoidalis, Tucumán, Prov. Tucumán, Argentina.
Figure 6 in Systematics of Oreobates and the Eleutherodactylus discoidalis species group (Amphibia, Anura), based on two mitochondrial DNA genes and external morphology
Figure 6. Type specimens of some members of Oreobates. A–B, holotype of O. cruralis (BM 1947.2.15.70); C–D, holotype of O. simmonsi (KU 147068); E–F, paralectotype of O. discoidalis (BM 1947.2.15.63); G–H, holotype of O. granulosus (BM 1947.2.15.72); I–J, lectotype of O. quixensis (MNCN 1708).
Figure 1 in Systematics of Oreobates and the Eleutherodactylus discoidalis species group (Amphibia, Anura), based on two mitochondrial DNA genes and external morphology
Figure 1. Majority rule consensus tree based on maximum parsimony (MP) and Bayesian phylogenetic analyses of combined data from the partial cytochrome b (c. 350 bp) and 16S (c. 590 bp) mitochondrial DNA. The numbers above branches indicate boostrap support (± 50%) for the MP topology, followed by Bayesian posterior probabilities for the Bayesian topology (± 95).
Figure 2 in Systematics of Oreobates and the Eleutherodactylus discoidalis species group (Amphibia, Anura), based on two mitochondrial DNA genes and external morphology
Figure 2. Majority rule consensus tree based on Bayesian phylogenetic analyses of partial 16S (c. 590 bp) mitochondrial DNA of some members of the genera Oreobates, Eleutherodactylus, and Craugastor. The numbers above branches are Bayesian posterior probabilities, followed by boostrap support for maximum parsimony topology. Values lower than 0.90 Bayesian posterior probability, or lower than 60 for boostrap, are not depicted.
Figure 2 in Phylogenetic structure of the Sphaeriinae, a global clade of freshwater bivalve molluscs, inferred from nuclear (ITS-1) and mitochondrial (16S) ribosomal gene sequences
Figure 2. Strict consensus of the 1040 equally most parsimonious trees (L = 445; CI = 0.724; RI = 0.886) obtained from the phylogenetic analysis of sphaeriid nuclear ITS1 rDNA sequences. The inferred evolutionary gain and loss of a ~160 nt fragment are indicated. Two Eupera species, E. cubensis and E. platensis, were designated as outgroups and inferred sequence gaps were considered as missing data. Numbers above the branches represent bootstrap values and numbers below indicate decay index values.
Figure 3 in Phylogenetic structure of the Sphaeriinae, a global clade of freshwater bivalve molluscs, inferred from nuclear (ITS-1) and mitochondrial (16S) ribosomal gene sequences
Figure 3. The single most-parsimonious tree (L = 951; CI = 0.568; RI = 0.793) obtained from the maximum parsimony analysis of combined (16S + ITS1) sequence dataset. Maximum likelihood analysis produced a largely congruent topology (HKY model; Ln likelihood = - 7034.61154) with the only difference being Pisidium dubium sister to Sphaerium/Musculium clade. Taxonomic names are arranged according to suggested sphaeriinid taxonomy in the present study and five major monophyletic lineages are indicated. Two Eupera species, E. cubensis and E. platensis, were designated as outgroups. MP bootstrap values are shown to the left of the slash and decay index values to the right above the branches. Numbers below the branches indicate ML bootstrap values.
Figure 1 in Phylogenetic structure of the Sphaeriinae, a global clade of freshwater bivalve molluscs, inferred from nuclear (ITS-1) and mitochondrial (16S) ribosomal gene sequences
Figure 1. Strict consensus of the four equally most parsimonious trees (L = 526; CI = 0.447; RI = 0.743) obtained from the phylogenetic analysis of sphaeriid mitochondrial 16S rDNA sequences. Two Eupera species, E. cubensis and E. platensis, were designated as outgroups and inferred sequence gaps were considered as missing data. Numbers above the branches represent bootstrap values and numbers below indicate decay index values.
Data from: Phylogenomics of a genus of ‘Great Speciators’ reveals rampant incomplete lineage sorting, gene flow, and mitochondrial capture in island systems
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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>
Data from: Sperm competitive advantage of a rare mitochondrial haplogroup linked to differential expression of mitochondrial oxidative phosphorylation genes
Maternal inheritance of mitochondria creates a sex-specific selective sieve through which mitochondrial mutations harmful to males but not females accumulate and contribute to sexual differences in longevity and disease susceptibility. Because eggs and sperm are under disruptive selection, sperm are predicted to be particularly vulnerable to the genetic load generated by maternal inheritance, yet evidence for mitochondrial involvement in male fertility is limited and controversial. Here, we exploit the coexistence of two divergent mitochondrial haplogroups (A and B2) in a Neotropical arachnid to investigate the role of mitochondria in sperm competition. DNA profiling demonstrated that B2-carrying males sired more than three times as many offspring in sperm competition experiments than A males, and this B2 competitive advantage cannot be explained by female mitochondrial haplogroup or male nuclear genetic background. RNA-Seq of testicular tissues implicates differential expression of mitochondrial oxidative phosphorylation (OXPHOS) genes in the B2 competitive advantage, including a 22-fold upregulation of <i>atp8</i> in B2 males. Previous comparative genomic analyses have revealed functionally significant amino acid substitutions in differentially expressed genes, indicating that the mitochondrial haplogroups differ not only in expression but also in DNA sequence and protein functioning. However, mitochondrial haplogroup had no effect on sperm number or sperm viability, and, when females were mated to a single male, neither male haplogroup, female haplogroup nor the interaction between male/female haplogroup significantly affected female reproductive success. Our findings therefore suggest that mitochondrial effects on male reproduction may often go undetected in noncompetitive contexts and may prove more important in nature than is currently appreciated.
Figure 1. - Bayesian phylogeny of Euptychia based on one mitochondrial (COI) and one nuclear (EF1-a) gene. Posterior probabilities are listed above and bootstrap values below branches. A dash denotes bootstrap support lower than 50%. (Euptychiaattenboroughi is not included in the analysis – see text for details.)
Figure 1. - Bayesian phylogeny of Euptychia based on one mitochondrial (COI) and one nuclear (EF1-a) gene. Posterior probabilities are listed above and bootstrap values below branches. A dash denotes bootstrap support lower than 50%. (Euptychiaattenboroughi is not included in the analysis – see text for details.)
Mass spectrometry data for: A small protein coded within the mitochondrial canonical gene nd4 regulates mitochondrial bioenergetics
<p><span><strong>Background</strong>:</span> <span>Mitochondria have a central role in cellular functions, aging and in certain diseases. They possess their own genome, a vestige of their bacterial ancestor. Over the course of evolution, most of the genes of the ancestor have been lost or transferred to the nucleus. In humans, the mtDNA is a very small circular molecule with a functional repertoire limited to only 37 genes. Its extremely compact nature with genes arranged one after the other and separated by short non-coding regions suggests that there is little room for evolutionary novelties. This is radically different from bacterial genomes, which are also circular but much larger, and in which we can find genes inside other genes. These sequences, different from the reference coding sequences, are called alternative open reading frames or altORFs, and they are involved in key biological functions. </span><span>However, whether altORFs exist in mitochondrial protein-coding genes or elsewhere in the human mitogenome has not been fully addressed.</span></p> <p><span><strong>Results</strong>:</span> <span>We found a downstream alternative ATG initiation codon in the +3 reading frame of the human mitochondrial <em>nd4</em> gene. This newly characterized altORF encodes a 99-amino acids long polypeptide, MTALTND4, which is conserved in primates. Our custom antibody, but not the pre-immune serum, was able to immunoprecipitate MTALTND4 from HeLa cell lysates, confirming the existence of an endogenous MTALTND4 peptide. The protein is localized in mitochondria and cytoplasm and is also found in the plasma, </span><span>and it impacts cell and mitochondrial physiology. </span></p> <p><span><strong>Conclusions</strong>:</span> <span>Many human-mitochondrial-translated ORFs might have so far gone unnoticed. By ignoring mtaltORFs, we have underestimated the coding potential of the mitogenome.</span> <span>Alternative mitochondrial peptides such as MTALTND4 may offer </span><span>a new framework for the investigation of mitochondrial functions and diseases.</span></p>
Alignments used for the phylogenies in "Caryophylliids (Anthozoa, Scleractinia) have a mitochondrial gene rearrangement: lesson learned from mitochondrial and nuclear phylogenomics"
<p>"mitochondrial_caryotree.phy": concatenated alignment of mitochondrial data in phylip format; "mitochondrial_caryotree.partitions.txt": indication of start/stop positions of each partition in the mitochondrial data alignment; "nuclear_caryotree_55taxa-50p.phylip": alignment of nuclear exons and ultraconserved elements in phylip format.</p>
A unique mitochondrial gene bock inversion in Antarctic Trematomin fishes: A cautionary tale
<p class="MsoNormal"><span>Many Antarctic notothenioid fishes have major rearrangements in their mitochondrial (mt) genomes. Here we report the complete mt genomes of three trematomin notothenioids: the bald notothen (<em>Trematomus</em> (<em>Pagothenia</em>) <em>borchgrevinki</em>); the spotted notothen (<em>T. nicolai</em>); and the emerald notothen (<em>T. bernacchii</em>). The three mt genomes were sequenced using next-generation Illumina technology, and the assemblies verified by Sanger sequencing. When compared with the canonical mt gene order of the Antarctic silverfish (<em>Pleuragramma antarctica</em>), we found a large gene inversion in the three trematomin mt genomes that included tRNA<sup>Ile</sup>, ND1, tRNA<sup>Leu2</sup>, 16S, tRNA<sup>Val</sup>, 12S, tRNA<sup>Phe</sup> and the control region. The trematomin mt genomes contained three intergenic spacers, which are thought to be the remnants of previous gene and control region duplications. All control regions included the characteristic conserved regulatory sequence motifs. Although next-generation DNA sequencing technology has allowed the rapid and cost-effective sequencing of a large number of complete mt genomes, it is essential in all cases to verify the assembly in order to prevent the publication and use of erroneous data.</span></p>
Fig. 1 in Mitochondrial DNA diversity in the acanthocephalan Prosthenorchis elegans in Colombia based on cytochrome c oxidase I (COI) gene sequence
Fig. 1. Photo showing the characteristic external morphology of Prosthenorchis elegans.
Figure S1 in A comprehensive phylogenetic analysis of Grapsoidea crabs (Decapoda: Brachyura) based on mitochondrial cytochrome oxidase subunit 1 (CO1) genes
Figure S1. Nucleotide sequences alignment information of the CO1 genes of eight Grapsoidea species.
Study on the role of AIMP1 gene activating PINK1/Parkin pathway in mediating mitochondrial autophagy in the pathogenesis of ARHL
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Fig. 1 in Phylogenetic analysis of the Common Krait (Bungarus caeruleus) in Pakistan based on mitochondrial and nuclear protein coding genes
Fig. 1. Sample collection sites in Pakistan for Common Krait (Bungarus caeruleus).
Fig. 4 in The complete mitochondrial genome of Platygaster robiniae (Hymenoptera: Platygastridae): A novel tRNA secondary structure, gene rearrangements and phylogenetic implications
Fig. 4. (continued).
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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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.