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865 results for “Mitochondrial genomes”
Ancient mitochondrial genomes unveil the origins and evolutionary history of New Zealand's enigmatic takahe and moho
<p>Many avian species endemic to Aotearoa New Zealand were driven to extinction or reduced to relict populations following successive waves of human arrival, due to hunting, habitat destruction, and the introduction of mammalian predators. Among the affected species were the large flightless South Island takahe (<em>Porphyrio hochstetteri</em>) and the moho (North Island takahe; <em>P. mantelli</em>), with the latter rendered extinct and the former reduced to a single relictual population. Little is known about the evolutionary history of these species prior to their decline and/or extinction. Here we sequenced mitochondrial genomes from takahe and moho subfossils (12 takahe and four moho) and retrieved comparable sequence data from takahemuseum skins (n = 5) and contemporary individuals (n = 17) to examine the phylogeny and recent evolutionary history of these species. Our analyses suggest that prehistoric takahepopulations lacked deep phylogeographic structure, in contrast to moho, which exhibited significant spatial genetic structure, albeit based on limited sample sizes (n = 4). Temporal genetic comparisons show that takahe have lost much of their mitochondrial genetic diversity, likely due to a sudden demographic decline soon after human arrival (~750 years ago). Time-calibrated phylogenetic analyses strongly support a sister-species relationship between takahe and moho, suggesting these flightless taxa diverged around 1.5 million years ago, following a single colonisation of New Zealand by a flighted <em>Porphyrio </em>ancestor approximately four million year ago. This study highlights the utility of palaeogenetic approaches for informing the conservation and systematic understanding of endangered species whose ranges have been severely restricted by anthropogenic impacts.</p>
Novel mitochondrial genome rearrangements including duplications and extensive heteroplasmy could underlie temperature adaptations in Antarctic notothenioid fishes
<p>Mitochondrial genomes are known for their compact size and conserved gene order, however, recent studies employing long-read sequencing technologies have revealed the presence of atypical mitogenomes in some species. In this study, we assembled and annotated the mitogenomes of five Antarctic notothenioids, including four icefishes (Champsocephalus gunnari, C. esox, Chaenocephalus aceratus, and Pseudochaenichthys georgianus) and the cold-specialized Trematomus borchgrevinki. Antarctic notothenioids are known to harbor some rearrangements in their mt genomes, however the extensive duplications in icefishes observed in our study have never been reported before. In the icefishes, we observed duplications of the protein coding gene ND6, two transfer RNAs, and the control region with different copy number variants present within the same individuals and with some ND6 duplications appearing to follow the canonical Duplication-Degeneration-Complementation (DDC) model in C. esox and C. gunnari. In addition, using long-read sequencing and k-mer analysis, we were able to detect extensive heteroplasmy in C. aceratus and C. esox. We also observed a large inversion in the mitogenome of T. borchgrevinki, along with the presence of tandem repeats in its control region. This study is the first in using long-read sequencing to assemble and identify structural variants and heteroplasmy in notothenioid mitogenomes and signifies the importance of long-reads in resolving complex mitochondrial architectures. Identification of such wide-ranging structural variants in the mitogenomes of these fishes could provide insight into the genetic basis of the atypical icefish mitochondrial physiology and more generally may provide insights about their potential role in cold adaptation.</p>
The HIFI reads and assembled contigs used to construct the mitochondrial genome assembly of Glyphodes pyloalis
<p><span>Glyphodes pyloalis (Lepidoptera; Crambidae; Spilomelinae), known as the mulberry pyralid, is a notorious insect pest belonging to the Lepidopteran that threatens mulberry cultivation across China. <span>The mitochondrial genome is an invaluable genetic resource owing to its maternal inheritance, rapid evolution, and lack of recombination. A previous study documented the G. pyloalis mitochondrial genome (mtDNA) as NC_025933 using short-read next-generation sequences that, while pioneering, leaves room for improvement with modern long-read sequencing. PacBio’s high-fidelity circular consensus sequencing (HIFI CCS) generates extra-long sequences sufficient to produce complete mtDNA assemblies with base pair accuracy.</span></span></p>
Ion Torrent data for the genome assembly and phylogenomic placement of mitochondrial genomes with a focus on houndsharks (Chondrichthyes: Triakidae)
<p>Here, we present the Ion Torrent® next-generation sequencing (NGS) data for five houndsharks (Chondrichthyes: Triakidae), which include <em>Galeorhinus galeus</em> (17,487 bp; GenBank accession number ON652874), <em>Mustelus asterias</em> (16,708; ON652873), <em>Mustelus mosis</em> (16,755; ON075077), <em>Mustelus palumbes</em> (16,708; ON075076), and <em>Triakis megalopterus</em> (16,746 bp; ON075075). All assembled mitogenomes encode 13 protein-coding genes (PCGs), two ribosomal (r)RNA genes, and 22 transfer (t)RNA genes (<em>tRNA<sup>Leu</sup></em><sup> </sup>and <em>tRNA<sup>Ser</sup> </em>are duplicated), except for <em>G</em>. <em>galeus</em> which contains 23 tRNA genes where <em>tRNA<sup>Thr</sup> </em>is duplicated. The data presented in this paper can assist other researchers in further elucidating the diversification of triakid species and the phylogenetic relationships within Carcharhiniformes (groundsharks) as mitogenomes accumulate in public repositories.</p>
Figure 5 in Mitochondrial genomes of four pierid butterfly species (Lepidoptera: Pieridae) with assessments about Pieridae phylogeny upon multiple mitogenomic datasets
Figure 5. Predicted secondary structures of Pontia callidice and Pontia daplidice 22 tRNA genes.
Figure 10 in Mitochondrial genomes of four pierid butterfly species (Lepidoptera: Pieridae) with assessments about Pieridae phylogeny upon multiple mitogenomic datasets
Figure 10. Predicted secondary structure of Pontia callidice srRNA gene.
Figure 8 in Mitochondrial genomes of four pierid butterfly species (Lepidoptera: Pieridae) with assessments about Pieridae phylogeny upon multiple mitogenomic datasets
Figure 8. Predicted secondary structure of Talbotia naganum srRNA gene.
Figure 6 in Mitochondrial genomes of four pierid butterfly species (Lepidoptera: Pieridae) with assessments about Pieridae phylogeny upon multiple mitogenomic datasets
Figure 6. Predicted secondary structure of Baltia butleri srRNA gene.
Figure 4 in Mitochondrial genomes of four pierid butterfly species (Lepidoptera: Pieridae) with assessments about Pieridae phylogeny upon multiple mitogenomic datasets
Figure 4. Predicted secondary structures of Baltia butleri and Talbotia naganum 22 tRNA genes.
Figure 12 in Mitochondrial genomes of four pierid butterfly species (Lepidoptera: Pieridae) with assessments about Pieridae phylogeny upon multiple mitogenomic datasets
Figure 12. Predicted secondary structure of Pontia daplidice srRNA gene.
Supplementary files and data Files for "Discordance between mitochondrial, nuclear, and symbiont genomes in aphid phylogenetics: who is telling the truth?" Zoological journal of the Linnean society, 2024, vol 1, issue 4. https://doi.org/10.1093/zoolinnean/zlae098
<p>This repository comprises</p> <ul> <li>a file with all supplementary Tables (<strong>Supplementary_Tables</strong>). Table S1: Collection details and voucher ID for aphid samples from the CBGP-Inrae collection, data origin is given for other specimens. Table S2: Amplification success of long range DNA fragments from mitochondrial genomes . Table S3: Primers used for fluidigm aplification of nuclear genes and sequencing success. Table S4. Genomic features of newly sequenced Buchnera aphidicola with aphid taxonomic affiliation. Table S5: Summary of models used for each ML analysis and corresponding log-likelihood score of the best tree.Table S6: Output of RERConverge analyses.</li> <li>two Supplementary figures: Figure S1: Workflow of phylogenetic analyses as implemented on each dataset. Figure S2: Plot depicting the genome-wide pattern of molecular evolution (dN/dS) between disymbiotic (n = 15) and monosymbiotic aphid (n = 45) branches across the ML phylogeny (horizontal bars indicate 95% CI of the means). <em>P</em> value was calculated by using Wilcoxon Rank test.</li> <li>a word file (Text S1) with : Details of protocol for obtaining mitochondrial genomes through long-range DNA amplifications and Illumina sequencing, and two-step PCR protocole.</li> <li>an archive (archive1) with the mitochondrial AA and DNA matrices and alternative phylogenetic trees under ML and Bayesian analyses ; </li> </ul> <ul> <li>an archive (archive2) with the nuclear AA and DNA matrices and alternative phylogenetic trees under ML and Bayesian analyses</li> <li>an archive (archive 3) with the twelve new <em>Buchnera</em> genome drafts.</li> <li> an archive (archive4) with the <em>Buchnera</em> AA matrices and alternative topologies </li> </ul> <p> </p>
Data and code for: A naturally occurring mitochondrial genome variant confers broad protection from infection in Drosophila (doi: https://doi.org/10.1101/2024.03.28.587162)
<p><strong> </strong>Raw data and R code for:</p> <p>Tiina S. Salminen, Laura Vesala, Yuliya Basikhina, Megan Kutzer, Tea Tuomela, Ryan Lucas, Katy Monteith, Arun Prakash, Tilman Tietz<sup> </sup>and Pedro F. Vale. A naturally occurring mitochondrial genome variant confers broad protection from infection in <em>Drosophila </em>(<strong>doi:</strong> https://doi.org/10.1101/2024.03.28.587162)</p> <p><em> </em></p> <p><strong>Data files:</strong></p> <p>CFU_stats.R: statistics for CFU data</p> <p>Prettgeri_CFU.csv: colony forming units (CFUs) in <em>P. rettgeri</em>-infected flies</p> <p>Saureus_CFU.csv: colony forming units (CFUs) in <em>S. aureus</em>-infected flies</p> <p> </p> <p>gene exp_mitotypes-stats.R: statistics for the qPCR data</p> <p>gene exp_mitotypes.csv: data on the relative gene expression of <em>FucTC</em>, <em>AANATL3</em>, <em>Acp1</em> and <em>CG3397</em> among mitotypes</p> <p> </p> <p>copynumber_stats.R: statistics for the copynumber data</p> <p>copynumber.csv: Mitochondrial copy number as copies of the mtDNA target gene <em>16S</em> relative to nuclear target gene <em>RpL32 </em></p> <p> </p> <p>respirometry_stats.R: statistics for the respirometry data</p> <p>respirometry.csv: Mitochondrial respiration measured in uninfected male flies by measuring oxygen consumption of the OXPHOS complexes I, III and IV</p> <p> </p> <p>ROS_stats.R: statistics for ROS</p> <p>ROS.csv: hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) quantification (whole flies)</p> <p> </p> <p>wasp_stats.R: Statistics on the proportion of melanised and unmelanised wasp larvae</p> <p>Wasps_data.csv: Data on proportion of melanised (killed) and unmelanised (living) <em>L. boulardi</em> parasitoid wasp larvae found in <em>Drosophila</em> larvae</p> <p> </p> <p>CC_stats.R: statistics on crystal cell counts</p> <p>CC.csv: amount of hemocytes called crystal cell in the larvae</p> <p> </p> <p>HC_stats.R: statistics on hemocyte counts</p> <p>hc_uninf.csv: total and activated hemocyte (blood cell) counts in uninfected larvae</p> <p>hc_inf.csv: total and activated hemocyte (blood cell) counts in infected larvae (48 h after infection by <em>L. boulardi</em> parasitoid wasps)</p> <p> </p> <p>PPO3.R: statistics on PPO3 expression levels</p> <p>PPO3.csv: data on gene expression level of prophenoloxidase (PPO3)</p> <p> </p> <p>MMP.R: statistics on MMP</p> <p>cybridMMP.csv: mitochondrial membrane potential (MMP) measured from larval hemocytes using the TMRM dye</p> <p> </p> <p>CellROX.R: statistics on CellROX<sup>TM </sup>signal</p> <p>CellROX.csv: Reactive oxygen species (ROS) measured from larval hemocytes using CellROX<sup>TM</sup> green reagent</p> <p> </p> <p>Hazard.Rmd: hazard ratios</p> <p>Combined.xlsx: data on hazard ratios Hazard ratios of survival post <em>P. rettgeri, S. aureus, </em>Kallithea and DCVinfections</p> <p> </p> <p>Mito_priming.R: Statistics on the effect of priming</p> <p>mito_priming.csv: data on the effect of immune priming with heat-killed bacteria prior to infection</p> <p> </p> <p>hc_stats_supplementary.R: statistics for sex-specific differences in hemocyte counts (data: hc_uninf.csv & hc_inf.csv )</p> <p>PI_hc_stats.R: statistics on dead (Propidium iodide, PI-positive) vs. living (PI-negative) larval hemocytes (data: hc_uninf.csv & hc_inf.csv )</p> <p> </p> <p>melanisation_stats.R: statistics on melanisation response</p> <p>melanisation_males.csv: melanisation response in hemolymph</p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p>
The first mitochondrial genome of Creophilus Leach and Platydracus Thomson (Coleoptera: Staphylinidae: Staphylinini) and phylogenetic implications
<p><strong>Datasets</strong>: The trimmed data matrices and partition files as shown in Table 2.</p> <ol> <li>P1P2R_Phylip.phy: 1<sup>st</sup> and 2<sup>nd</sup> positions of PCG nucleotides and rRNAs.</li> <li>P1P2R_partition.txt: Partition scheme for P1P2R_Phylip.phy.</li> <li>P12R_Phylip.phy: the united first two positions of PCG nucleotides plus rRNAs.</li> <li>P12R_partition.txt: Partition scheme for P12R_Phylip.phy.</li> <li>P2R_Phylip.phy: 2<sup>nd</sup> position of PCG nucleotides and rRNAs.</li> <li>P2R_partition.txt: Partition scheme for P2R_Phylip.phy.</li> <li>AA_Phylip.phy: PCG amino acids.</li> <li>AA_partition.txt: Partition scheme for AA_Phylip.phy.</li> </ol> <p><strong>Trees: </strong>The expanded consensus trees constructed by all data compositions, partition schemes, and models shown in Table 2.</p> <ol> <li>P1P2R_FP.tree: edge-unlinked and full partitioned (FP) dataset of PCG positions 1 & 2 + rRNAs.</li> <li>P1P2R_MP.tree: edge-unlinked and merged partitioned (MP) dataset of PCG positions 1 & 2 + rRNAs.</li> <li>P1P2R_NP.tree: unpartitioned (NP) dataset of PCG positions 1 & 2 + rRNAs.</li> <li>P1P2R_NPH4.tree: NP dataset of PCG positions 1 & 2 + rRNAs under +H4 heterotachy model.</li> <li>P12R_FP.tree: FP dataset of united PCG positions 1 & 2 + rRNAs.</li> <li>P12R_MP.tree: MP dataset of united PCG positions 1 & 2 + rRNAs.</li> <li>P12R_NP.tree: NP dataset of united PCG positions 1 & 2 + rRNAs.</li> <li>P12R_NPH4.tree: NP dataset of united PCG positions 1 & 2 + rRNAs under +H4 heterotachy model.</li> <li>P2R_FP.tree: FP dataset of PCG position 2 + rRNAs.</li> <li>P2R_MP.tree: MP dataset of PCG position 2 + rRNAs.</li> <li>P2R_NP.tree: NP dataset of PCG position 2 + rRNAs.</li> <li>P2R_NPH4.tree: NP dataset of PCG position 2 + rRNAs under +H4 heterotachy model.</li> <li>AA_FP.tree: FP dataset of PCG amino acids.</li> <li>AA_MP.tree: MP dataset of PCG amino acids.</li> <li>AA_NP.tree: NP dataset of PCG amino acids.</li> <li>AA_NPC60.tree: NP dataset of PCG amino acids under +C60 mixture model.</li> </ol> <p><strong>Tables S1-2.xlsx:</strong></p> <ol> <li>Table S1: Pairwise similarity of nucleotide alignments between <em>Creophilus maxillosus</em> and the 92 sampled species in the Staphylinoidea.</li> <li>Table S2: Percentage of conserved sites in amino acid alignments between <em>Creophilus maxillosus</em> and the 92 sampled species in the Staphylinoidea.</li> </ol> <p>Data Use Statement. Data on genetic material contained in this paper are published for non-commercial use only. Utilization by third parties for purposes other than non-commercial scientific research may infringe the conditions under which the genetic resources were originally accessed, and should not be undertaken without obtaining consent from the corresponding author of the paper and/or obtaining permission from the original provider of the genetic material.</p> <p> </p>
Complete mitochondrial genome sequence of the Atlantic Mudskipper (Periophthalmus barbarus) (Linnaeus, 1766) (Perciformes: Gobiidae)
<p>The complete mitochondrial genome of the Atlantic mudskipper (<em>Periophthalmus barbarus</em>) was determined in this study. The specimen was collected from Abonnema, Nigeria (4.73075, 6.77565). The complete mitogenome sequence of <em>P. barbarus</em> would be useful for further studies on molecular phylogenetic relationship and population genetics of the subfamily Oxudercinae.</p>
Data and source code from: Contingency and selection in mitochondrial genome dynamics
<p>Eukaryotic cells contain numerous copies of mitochondrial DNA (mtDNA), allowing for the coexistence of mutant and wild-type mtDNA in individual cells. The fate of mutant mtDNA depends on their relative replicative fitness within cells and the resulting cellular fitness within populations of cells. Yet the dynamics of the generation of mutant mtDNA and features that inform their fitness remain unaddressed. Here we utilize long read single-molecule sequencing to track mtDNA mutational trajectories in Saccharomyces cerevisiae. We show a previously unseen pattern that constrains subsequent excision events in mtDNA fragmentation. We also provide evidence for the generation of rare and contentious non-periodic mtDNA structures that lead to persistent diversity within individual cells. Finally, we show that measurements of relative fitness of mtDNA fit a phenomenological model that highlights important biophysical parameters governing mtDNA fitness. Altogether, our study provides techniques and insights into the dynamics of large structural changes in genomes that may be applicable in more complex organisms.</p>
Data and scripts for the manuscript of svaRetro and svaNUMT: modular packages for annotating retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data
<p>This upload include data and scripts supporting the results described in the manuscript of <em>svaRetro and svaNUMT: modular packages for annotating retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data</em><em>. </em>Detailed description of the contents can be found in README.txt.</p>
Dissecting the sequential evolution of a selfish mitochondrial genome in Caenorhabditis elegans data
<p>Mitochondrial genomes exist in a nested hierarchy of populations where mitochondrial variants are subject to genetic drift and selection at each level of organization, sometimes engendering conflict between different levels of selection, and between the nuclear and mitochondrial genomes. Deletion mutants in the <em>Caenorhabditis elegans</em> mitochondrial genome can reach high intracellular frequencies despite strongly detrimental effects on fitness. During a mutation accumulation (MA) experiment in <em>C. elegans</em>, a 499 bp deletion in <em>ctb-1</em> rose to 90% frequency within cells while significantly reducing fitness. During the experiment, the deletion-bearing mtDNA acquired three additional mutations in <em>nd5</em>, namely two single insertion frameshift mutations in a homopolymeric run, and a base substitution. Despite an additional fitness cost of these secondary mutations, all deletion-bearing molecules contained the <em>nd5 </em>mutations at the termination of the MA experiment. The presence of mutant mtDNA was associated with increased mtDNA copy-number. Variation in mtDNA copy-number was greater in the MA lines than in a wildtype nuclear background, including a severe reduction in copy-number at one generational timepoint. Evolutionary replay experiments using different generations of the MA experiment as starting points suggests that two of the secondary mutations contribute to the proliferation of the original <em>ctb-1</em> deletion by unknown mechanisms. </p>
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).
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.
EGP Mitochondrial Genome Analysis on Human Genome Diversity Project Whole-Genome Sequencing Data
<p><strong>Summary: </strong>This dataset consists of running EGP version 1.3 on whole-genome sequencing data from the HGDP. The link to EGP is here https://github.com/tycheleturner/ElGenomaPequeno.</p> <p><strong>Author: </strong>Tychele N. Turner, Ph.D.</p> <p><strong>Short Writeup: EGP version 1.3 on Simons Genome Diversity Project</strong>: Short-read WGS CRAM files were downloaded from the EMBL-EBI Public Data Globus Endpoint from the <code>/1000g/ftp/data_collections</code> directory. Post-download, the data was run through EGP version 1.3. The results are shown below:</p> <div> <table> <tbody> <tr> <td>Public Dataset</td> <td>EGP Result File Type</td> <td>MD5</td> </tr> <tr> <td>Human Genome Diversity Project</td> <td>Mitochondrial Genome Fasta Files for MEGA</td> <td>2b388c1fa446ecec70e33ea0471e06f8</td> </tr> <tr> <td>Human Genome Diversity Project</td> <td>Mitochondrial Genome MitoMaster Result File</td> <td>50b80ed32b1ae542c8967cc31986dd19</td> </tr> <tr> <td>Human Genome Diversity Project</td> <td>Mitochondrial Genome Variant Tables</td> <td>995f30b74c4bb094a674b1a994853246</td> </tr> <tr> <td>Human Genome Diversity Project</td> <td>Mitochondrial Genome Copy Number</td> <td>e79e61efab4c491fa2825b7d1853df58</td> </tr> </tbody> </table> </div> <div>Please note: I have found that with Zenodo you must use "Download All" for the copy number table to properly open.</div>
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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