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410 results for “Mitochondrial gene”
Fig. 3 in The complete mitochondrial genome of Platygaster robiniae (Hymenoptera: Platygastridae): A novel tRNA secondary structure, gene rearrangements and phylogenetic implications
Fig. 3. The secondary structure of 22 tRNA in Platygaster robiniae.
Figure 5 in Systematics of Oreobates and the Eleutherodactylus discoidalis species group (Amphibia, Anura), based on two mitochondrial DNA genes and external morphology
Figure 5. Altitudinal distribution across habitat types of members of the genus Oreobates.
Mitochondrial genome evolution in Annelida: A systematic study on conservative and variable gene orders and the factors influencing its evolution
<p><span>The mitochondrial genomes of Bilateria are relatively conserved in their protein-coding, rRNA and tRNA gene complement, but the order of these genes can range from very conserved to very variable depending on the taxon. The supposedly conserved gene order of Annelida has been used to support the placement of some taxa within Annelida. Recently, authors have cast doubts on the conserved nature of the annelid gene order. Various factors may influence gene-order variability including, among others, increased substitution rates, base composition differences, structure of non-coding regions, parasitism, living in extreme habitats, short generation times and biomineralization. However, these analyses were neither done systematically, nor based on well-established reference trees. Several focused on only a few of these factors and biological factors were usually explored ad-hoc without rigorous testing or correlation analyses. Herein, we investigated the variability and evolution of the annelid gene order and the factors that potentially influenced its evolution, using a comprehensive and systematic approach. The analyses were based on 170 genomes, including 33 previously unrepresented species. Our analyses included 706 different molecular properties, 20 life-history and ecological traits and a reference tree corresponding to recent improvements concerning the annelid tree. The results showed that the gene order with and without tRNAs is generally conserved. However, individual taxa exhibit higher degrees of variability. None of the analyzed life-history and ecological traits explained the observed variability across mitochondrial gene orders. In contrast, the combination and interaction of the best predicting factors for substitution rate and base composition explained up to 30% of the observed variability. Accordingly, correlation analyses of different molecular properties of the mitochondrial genomes showed an intricate network of direct and indirect correlations between the different molecular factors. Hence, gene order evolution seems to be driven by molecular evolutionary aspects rather than by life history or ecology. On the other hand, gene order variability does not predict difficulty in placing certain taxa within molecular phylogenetic studies. We also discuss the molecular properties of annelid mitochondrial genomes considering canonical views on gene evolution and potential reasons why they do not always fit to the observed patterns without nuisance.</span></p>
Phylomitogenomics reveals mito-nuclear concordance in social wasps: the performance of mitochondrial markers and gene order for hymenopteran systematics.
<p>Mitochondrial (mtDNA) genes have served as widely utilized genetic loci for animal phylogenetics and phylogeography studies. However, the phylogenetic performance of many mtDNA genes has not been empirically evaluated across lineages within hymenopteran wasps. To address this question, we assembled and analyzed mitogenomic data from social wasps, representing the four recognized tribes of Polistinae and also all Epiponini genera. Additionally, we evaluated whether mtDNA gene order in Polistinae is congruent with its tribal classification. Using concatenation phylogenetic methods, we show phylogenetic congruence between mitogenomic and nuclear data. Statistically comparing the phylogenetic performance of individual mtDNA genes, we demonstrate that for social wasps the molecular markers COI, 16S, NAD5, and NAD2 perform best, while ATP6, COII, and 12S show the worst results. Finally, we verified that the tRNA cluster close to the noncoding region is a hotspot of rearrangement in Vespidae and can be used as additional information for the systematics of this group. Together, these results indicate that mitogenomes contain robust phylogenetic signal to elucidate the evolutionary history of Vespidae. Moreover, our study identifies the best choice of mitochondrial markers for systematic investigations of social wasps.</p>
Dataset from: The origin and fate of fungal mitochondrial horizontal gene transferred sequences in orchids (Orchidaceae)
<p>The transfer of DNA among distantly related organisms is relatively common in bacteria but less prevalent in eukaryotes. Among fungi and plants, few of these events have been reported. Two segments of fungal mitochondrial DNA have been discovered in the mitogenome of orchids. Here, we build on their work to understand the timing of those transfer events, which orchids retain the fungal DNA, and the fate of the foreign DNA during orchid evolution. We update the content of the large DNA fragment and establish that it was transferred to the most recent common ancestor of a highly diverse clade of epidendroid orchids that lived ~28–43 Mya. Also, we present hypotheses of the origin of the small transferred fragment. Our findings deepen the knowledge of these interesting DNA transfers among organelles and we formulate a probable mechanism for these horizontal gene transfer events.</p>
Mitochondrial MICOS complex genes, implicated in hypoplastic left heart syndrome, maintain cardiac contractility and actomyosin integrity
<p>Hypoplastic left heart syndrome (HLHS) is a severe congenital heart disease (CHD) with a likely oligogenic etiology, but our understanding of the genetic complexities and pathogenic mechanisms leading to HLHS is limited. We therefore performed whole genome sequencing (WGS) on a large cohort of HLHS patients and their families to identify candidate genes that were then tested in <em>Drosophila</em> heart model for functional and structural requirements. Bioinformatic analysis of WGS data from an index family comprised of a HLHS proband born to consanguineous parents and postulated to have a homozygous recessive disease etiology, prioritized 9 candidate genes with rare, predicted damaging homozygous variants. Of the candidate HLHS gene homologs tested, cardiac-specific knockdown (KD) of mitochondrial MICOS complex subunit dCHCHD3/6 resulted in drastically compromised heart contractility, diminished levels of sarcomeric actin and myosin, reduced cardiac ATP levels, and mitochondrial fission-fusion defects. Interestingly, these heart defects were similar to those inflicted by cardiac KD of ATP synthase subunits of the electron transport chain (ETC), consistent with the MICOS complex's role in maintaining cristae morphology and ETC complex assembly. Analysis of 183 genomes of HLHS patient-parent trios revealed five additional HLHS probands with rare, predicted damaging variants in CHCHD3 or CHCHD6. Hypothesizing an oligogenic basis for HLHS, we tested 60 additional prioritized candidate genes in these cases for genetic interactions with CHCHD3/6 in sensitized fly hearts. Moderate KD of CHCHD3/6 in combination with Cdk12 (activator of RNA polymerase II), RNF149 (E3 ubiquitin ligase), or SPTBN1 (scaffolding protein) caused synergistic heart defects, suggesting the potential involvement of a diverse set of pathways in HLHS. Further elucidation of novel candidate genes and genetic interactions of potentially-disease-contributing pathways is expected to lead to a better understanding of HLHS and other CHDs.</p>
Data from: Structure, gene order, and nucleotide composition of mitochondrial genomes in parasitic lice from Amblycera
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Mitochondrial genome evolution in Annelida: A systematic study on conservative and variable gene orders and the factors influencing its evolution
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Data from: Sperm competitive advantage of a rare mitochondrial haplogroup linked to differential expression of mitochondrial oxidative phosphorylation genes
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A snakemake toolkit for the batch assembly, annotation, and phylogenetic analysis of mitochondrial genomes and ribosomal genes from genome skims of museum collections
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Dataset from: The origin and fate of fungal mitochondrial horizontal gene transferred sequences in orchids (Orchidaceae)
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A unique mitochondrial gene bock inversion in Antarctic Trematomin fishes: A cautionary tale
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Mass spectrometry data for: A small protein coded within the mitochondrial canonical gene nd4 regulates mitochondrial bioenergetics
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Data from: Spatial analysis of mitochondrial gene expression reveals dynamic translation hubs and remodeling in stress
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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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Mitochondrial MICOS complex genes, implicated in hypoplastic left heart syndrome, maintain cardiac contractility and actomyosin integrity
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FIGURE 1 in Uncovering a hidden diversity: a new species of freshwater shrimp Macrobrachium (Decapoda: Caridea: Palaemonidae) from Neotropical region (Brazil) revealed by morphological review and mitochondrial genes analyses
FIGURE 1. Characterization and location of the São Francisco river basin in Brazil. The red border indicates the location of Grande Sertão Veredas National Park and the distribution range of Macrobrachium veredensis sp. nov. Modified from MMA 2006 and ANA 2016.
Fig. 2. 95 in Taxonomic Evaluation of the Greater Horseshoe Bat Rhinolophus ferrumequinum (Chiroptera: Rhinolophidae) in Iran Inferred from the Mitochondrial D-loop Gene
Fig. 2. 95% minimum spanning haplotype network of D-loop haplotypes of the greater horseshoe bat, Rhinolophus ferrumequinum, in Iran. The size of the shape is proportional to the frequency of that haplotype. Gray and white circles correspond to the clade 1- sub- clade A and clade 1-subclade B in Fig. 4 respectively.
Fig. 4 in Taxonomic Evaluation of the Greater Horseshoe Bat Rhinolophus ferrumequinum (Chiroptera: Rhinolophidae) in Iran Inferred from the Mitochondrial D-loop Gene
Fig. 4. Maximum likelihood (ML) tree of D-loop sequences of the greater horseshoe bat, Rhinolophus ferrumequinum from Iran, Turkey, and Europe. Numbers above branches represent bootstrap support for NJ (3000 replicates)/ML (1000) inherence, and numbers below branches indicate Bayesian posterior probabilities. Values below 50% are not shown.
III Average nucleotide distances (%) based on the Kimura 2-parameter (K2P) model between Aselliscus spp., and associated outgroups based on complete mitochondrial Cytb (1,140 bp, below the diagonal) and COI (657 bp, above the diagonal) gene sequences in Description of a new species of the genus Aselliscus (Chiroptera, Hipposideridae) from Vietnam
III Average nucleotide distances (%) based on the Kimura 2-parameter (K2P) model between Aselliscus spp., and associated outgroups based on complete mitochondrial Cytb (1,140 bp, below the diagonal) and COI (657 bp, above the diagonal) gene sequences
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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.