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Figure 2 in Molecular systematics of the genus Pseudocerastes (Ophidia: Viperidae) based on the mitochondrial cytochrome b gene
Figure 2. Maximum parsimony strict consensus tree of the 2 most parsimonious trees recovered in the analysis. Eristicophis macmahonii was used as an outgroup taxon for rooting the tree. The phylogenetic tree produced by NJ has the same topology as the presented tree with regard to the major lineages. Numbers above branches on the right side of slashes are bootstrap percentages (8000 replicates) for MP and on the left side are bootstrap percentages (6000 replicates) for NJ.
Figure 1 in Molecular systematics of the genus Pseudocerastes (Ophidia: Viperidae) based on the mitochondrial cytochrome b gene
Figure 1. Map showing the localities of collected Iranian specimens used in the study. Solid circle for the western specimens of P. urarachnoides (KF314714–16) and P. persicus (KF314707–10); solid square for the only specimen from the northern populations of P. persicus (KF314705); solid octagon for the only specimen of the central populations of P. persicus (KF314706); and solid triangle for specimens of the southern populations (KF314711–13).
Figure 3 in A comprehensive phylogenetic analysis of Grapsoidea crabs (Decapoda: Brachyura) based on mitochondrial cytochrome oxidase subunit 1 (CO1) genes
Figure 3. Inferred phylogenetic relationships based on nucleotide sequence of mitochondrial CO1 genes using BI (A) and ML (B) analyses. A. distinguendus was used as the outgroup.
Data from "Mitochondrial genomes of the European sardine (Sardina pilchardus) reveal Pliocene diversification, extensive gene flow and pervasive purifying selection"
<p>INFORMATION ON THE FILES PROVIDED</p> <p>File:<br>European_sardine_whole_mitogenome_139.fasta</p> <p>Content:<br>Alignment of 139 European sardine whole mitogenome sequences</p> <p>:::::::::::::::::::::::::::::::::::::::::::::::::::::::::</p> <p>File:<br>European_sardine_13_genes_139_IQTree.nex</p> <p>Content:<br>Alignment of 13 mitochondrial genes from 139 European sardine samples </p> <p>:::::::::::::::::::::::::::::::::::::::::::::::::::::::::</p> <p>File:<br>European_sardine_13_genes_139_Partitions.nex</p> <p>Content:<br>Partition file for IQtree analysis of Sardina_13_genes_139_IQTree.nex</p> <p>:::::::::::::::::::::::::::::::::::::::::::::::::::::::::</p> <p>File:<br>European_sardine_12_genes_63.fasta</p> <p>Content:<br>Alignment of 12 mitochondrial genes from 60 European sardine and 3 Sardinops samples</p> <p>:::::::::::::::::::::::::::::::::::::::::::::::::::::::::</p> <p>File:<br>BEAST_infile_calibration.xml </p> <p>Content:<br>Input file for the BEAST analysis of European_sardine_12_genes_63.fasta</p>
Table 1 in Complete mitochondrial genome of the terrestrial isopod Cubaris murina Brandt, 1833: new family gene order and novel tRNA secondary structures
<p><b>Table 1.</b> Arrangement and annotation of the mitochondrial genome of Cubaris murina.</p><table><tbody><tr><th></th><th></th><th></th><th></th><th></th><th>Length</th><th></th><th></th><th></th><th></th></tr></tbody><tbody><tr><th>Name</th><td>Type</td><td>Start</td><td>Stop</td><td>Strand</td><td>(bp)</td><td>Start</td><td>Stop</td><td>Inter-genic space</td><td>Overlap</td></tr><tr><th>Cox1</th><td>Coding</td><td>1</td><td>1536</td><td>+</td><td>1536</td><td>ATG</td><td>TAA</td><td>1</td><td></td></tr><tr><th>trnL2(tta)</th><td>tRNA</td><td>1538</td><td>1598</td><td>+</td><td>61</td><td></td><td></td><td>48</td><td></td></tr><tr><th>Cox2</th><td>Coding</td><td>1647</td><td>2282</td><td>+</td><td>636</td><td>ATA</td><td>TAG</td><td></td><td>2</td></tr><tr><th>trnK(aaa)</th><td>tRNA</td><td>2281</td><td>2336</td><td>+</td><td>56</td><td></td><td></td><td></td><td>8</td></tr><tr><th>trnD(gac)</th><td>tRNA</td><td>2329</td><td>2403</td><td>+</td><td>75</td><td></td><td></td><td></td><td>17</td></tr><tr><th>atp8</th><td>Coding</td><td>2387</td><td>2533</td><td>+</td><td>147</td><td>ATA</td><td>TAA</td><td></td><td>4</td></tr><tr><th>atp6</th><td>Coding</td><td>2530</td><td>3192</td><td>+</td><td>663</td><td>ATA</td><td>TAA</td><td>2</td><td></td></tr><tr><th>Cox3</th><td>Coding</td><td>3195</td><td>3989</td><td>+</td><td>795</td><td>ATG</td><td>TAG</td><td></td><td>2</td></tr><tr><th>trnR(cga)</th><td>tRNA</td><td>3988</td><td>4055</td><td>+</td><td>68</td><td></td><td></td><td>55</td><td></td></tr><tr><th>nad3</th><td>Coding</td><td>4111</td><td>4407</td><td>+</td><td>297</td><td>ATA</td><td>TAA</td><td></td><td>9</td></tr><tr><th>trnA(gca)</th><td>tRNA</td><td>4399</td><td>4446</td><td>+</td><td>48</td><td></td><td></td><td></td><td>8</td></tr><tr><th>nad1 CR putative</th><td>Coding</td><td>4439 5219</td><td>5218 5360</td><td>−</td><td>780 142</td><td>ATG</td><td>TAG</td><td></td><td>14</td></tr><tr><th>NCR1</th><td>tRNA</td><td>5361</td><td>5429</td><td>+</td><td>69</td><td></td><td></td><td></td><td>17</td></tr><tr><th>rrnS</th><td>rRNA</td><td>5413</td><td>6139</td><td>+</td><td>727</td><td></td><td></td><td>48</td><td></td></tr><tr><th>trnW(tga)</th><td>tRNA</td><td>6188</td><td>6244</td><td>+</td><td>57</td><td></td><td></td><td></td><td>7</td></tr><tr><th>trnS1(aga)</th><td>tRNA</td><td>6238</td><td>6296</td><td>−</td><td>59</td><td></td><td></td><td></td><td></td></tr><tr><th>NCR2</th><td></td><td>6297</td><td>6666</td><td></td><td>370</td><td></td><td></td><td></td><td></td></tr><tr><th>trnL1(cta)</th><td>tRNA</td><td>6667</td><td>6731</td><td>−</td><td>65</td><td></td><td></td><td>29</td><td></td></tr><tr><th>cob</th><td>Coding</td><td>6759</td><td>7907</td><td>−</td><td>1,149</td><td>ATA</td><td>TAG</td><td>38</td><td></td></tr><tr><th>trnT(aca)</th><td>tRNA</td><td>7946</td><td>8017</td><td>−</td><td>72</td><td></td><td></td><td>29</td><td></td></tr><tr><th>nad5</th><td>Coding</td><td>8047</td><td>9648</td><td>+</td><td>1,602</td><td>ATG</td><td>TAG</td><td></td><td>3</td></tr><tr><th>trnF(ttc)</th><td>tRNA</td><td>9646</td><td>9707</td><td>+</td><td>62</td><td></td><td></td><td></td><td>15</td></tr><tr><th>trnH(cac)</th><td>tRNA</td><td>9693</td><td>9758</td><td>−</td><td>66</td><td></td><td></td><td></td><td>23</td></tr><tr><th>nad4</th><td>Coding</td><td>9736</td><td>11,082</td><td>−</td><td>1,312</td><td>ATA</td><td>TAA</td><td>13</td><td></td></tr><tr><th>nad4L</th><td>Coding</td><td>11,096</td><td>11,374</td><td>−</td><td>279</td><td>ATA</td><td>TAA</td><td></td><td>13</td></tr><tr><th>trnP(cca)</th><td>tRNA</td><td>11,362</td><td>11,422</td><td>−</td><td>61</td><td></td><td></td><td>25</td><td></td></tr><tr><th>nad6</th><td>Coding</td><td>11,448</td><td>11,903</td><td>+</td><td>456</td><td>ATA</td><td>TAG</td><td></td><td>2</td></tr><tr><th>trnS2(tca)</th><td>tRNA</td><td>11,902</td><td>11,962</td><td>+</td><td>61</td><td></td><td></td><td>17</td><td></td></tr><tr><th>rrnL</th><td>rRNA</td><td>11,980</td><td>12,549</td><td>−</td><td>570</td><td></td><td></td><td></td><td></td></tr><tr><th>NCR3</th><td></td><td>12,550</td><td>12,753</td><td></td><td>204</td><td></td><td></td><td></td><td></td></tr><tr><th>trnE(gaa)</th><td>tRNA</td><td>12,754</td><td>12,812</td><td>−</td><td>59</td><td></td><td></td><td></td><td></td></tr><tr><th>NCR4</th><td></td><td>12,813</td><td>12,950</td><td></td><td>138</td><td></td><td></td><td></td><td></td></tr><tr><th>trnV(gta)</th><td>tRNA</td><td>12,951</td><td>13,019</td><td>−</td><td>69</td><td></td><td></td><td></td><td>5</td></tr><tr><th>trnQ(caa)</th><td>tRNA</td><td>13,015</td><td>13,077</td><td>−</td><td>63</td><td></td><td></td><td></td><td>6</td></tr><tr><th>trnM(atg)</th><td>tRNA</td><td>13,072</td><td>13,141</td><td>+</td><td>70</td><td></td><td></td><td>25</td><td></td></tr><tr><th>nad2</th><td>Coding</td><td>13,167</td><td>14,123</td><td>+</td><td>978</td><td>ATA</td><td>TAG</td><td></td><td>15</td></tr><tr><th>trnC(tgc)</th><td>tRNA</td><td>14,109</td><td>14,158</td><td>−</td><td>50</td><td></td><td></td><td></td><td></td></tr><tr><th>trnY(tac)</th><td>tRNA</td><td>14,159</td><td>14,205</td><td>−</td><td>47</td><td></td><td></td><td>7</td><td></td></tr></tbody></table>
Table 2 in Complete mitochondrial genome of the terrestrial isopod Cubaris murina Brandt, 1833: new family gene order and novel tRNA secondary structures
<p><b>Table 2.</b> Base composition (%) of nucleotide, AT content, and AT- and GC-skew of the mitochondrial genome of <i>Cubaris murina.</i> Values in bold indicate positive AT-skew.</p><table><tbody><tr><th></th><th></th><th></th><th>Base composition (%)</th><th></th><th></th><th></th><th></th></tr></tbody><tbody><tr><th>Total</th><td></td><td>A</td><td>C</td><td>G</td><td>T</td><td>%AT</td><td>AT skew</td><td>GC skew</td></tr><tr><th>14,212 bp</th><td>28.90%</td><td>15.80%</td><td>23.40%</td><td>31.90%</td><td>60.80%</td><td>−0.049</td><td>0.194</td></tr><tr><th></th><td></td><td></td><td>Base composition (%)</td><td></td><td></td><td></td><td></td></tr><tr><th>Gene Strand</th><td>A</td><td>C</td><td>G</td><td>T</td><td>%AT</td><td>AT skew</td><td>GC skew</td></tr><tr><th><i>cox1</i></th><td>(+)</td><td>22.4%</td><td>18.6%</td><td>24.2%</td><td>34.8%</td><td>57.2%</td><td>−0.217</td><td>0.131</td></tr><tr><th><i>cox2</i></th><td>(+)</td><td>20.6%</td><td>21.7%</td><td>27.7%</td><td>30.0%</td><td>50.6%</td><td>−0.186</td><td>0.121</td></tr><tr><th><i>atp8</i></th><td>(+)</td><td>21.1%</td><td>15.0%</td><td>34.7%</td><td>29.3%</td><td>50.4%</td><td>−0.163</td><td>0.396</td></tr><tr><th><i>atp6</i></th><td>(+)</td><td>20.4%</td><td>19.8%</td><td>29.1%</td><td>30.8%</td><td>51.2%</td><td>−0.203</td><td>0.190</td></tr><tr><th><i>cox3</i></th><td>(+)</td><td>17.2%</td><td>23.6%</td><td>28.6%</td><td>30.6%</td><td>47.8%</td><td>−0.280</td><td>0.096</td></tr><tr><th><i>nad3</i></th><td>(+)</td><td>20.2%</td><td>16.2%</td><td>32.3%</td><td>31.3%</td><td>51.5%</td><td>−0.216</td><td>0.332</td></tr><tr><th><i>nad1</i></th><td>(−)</td><td>31.7%</td><td>22.2%</td><td>27.6%</td><td>18.6%</td><td>50.3%</td><td><b>0.260</b></td><td>0.108</td></tr><tr><th><i>NCR1</i></th><td></td><td>28.9%</td><td>27.5%</td><td>19.7%</td><td>23.9%</td><td>52.8%</td><td>0.095</td><td>−0.165</td></tr><tr><th><i>NCR2</i></th><td></td><td>27.0%</td><td>22.2%</td><td>18.1%</td><td>32.7%</td><td>59.7%</td><td>−0.095</td><td>−0.102</td></tr><tr><th><i>cob</i></th><td>(−)</td><td>36.0%</td><td>12.0%</td><td>23.5%</td><td>28.5%</td><td>64.5%</td><td><b>0.116</b></td><td>0.324</td></tr><tr><th><i>nad5</i></th><td>(+)</td><td>28.5%</td><td>10.5%</td><td>21.7%</td><td>39.3%</td><td>67.8%</td><td>−0.159</td><td>0.348</td></tr><tr><th><i>nad4</i></th><td>(−)</td><td>38.4%</td><td>11.9%</td><td>22.8%</td><td>26.9%</td><td>65.3%</td><td><b>0.176</b></td><td>0.314</td></tr><tr><th><i>nad4L</i></th><td>(−)</td><td>41.9%</td><td>12.2%</td><td>17.6%</td><td>28.3%</td><td>70.2%</td><td><b>0.194</b></td><td>0.181</td></tr><tr><th><i>nad6</i></th><td>(+)</td><td>25.7%</td><td>10.5%</td><td>17.8%</td><td>46.1%</td><td>71.8%</td><td>−0.284</td><td>0.258</td></tr><tr><th><i>NCR3</i></th><td></td><td>36.8%</td><td>9.8%</td><td>19.1%</td><td>34.3%</td><td>71.1%</td><td>0.035</td><td>0.322</td></tr><tr><th><i>NCR4</i></th><td></td><td>35.5%</td><td>13.0%</td><td>15.2%</td><td>36.2%</td><td>71.7%</td><td>−0.010</td><td>0.078</td></tr><tr><th><i>nad2</i></th><td>(+)</td><td>28.9%</td><td>12.4%</td><td>22.6%</td><td>36.1%</td><td>65.0%</td><td>−0.111</td><td>0.291</td></tr></tbody></table>
Alignment of mitochondrial genes of Potamometra species
<p>Alignment of mitochondrial genes of Potamometra species. Sequences of rRNAs and tRNAs are aligned using MAFFT 7.402 under the G-INS-i strategy and alignments of 13 PCGs are performed based on amino acid sequences using Muscle implemented in Mega 7.0. </p>
Data from: Mitochondrial genotype and phenotypic plasticity of gene expression in response to cold acclimation in killifish
Adjustments of aerobic metabolic processes are critical components of organismal responses to environmental change that require tight co-ordination between the nuclear and mitochondrial genomes. Intraspecific differences in mitochondrial genotype can affect gene transcription in both genomes. Thus, variation in mitochondrial genotype may be associated with differences in the plasticity of gene expression when organisms are faced with changes in environmental conditions. Cold acclimation is known to result in metabolic responses involving increases in mitochondrial amount and capacity, suggesting that low temperatures may pose a particular challenge when co-ordinating the functions of the nuclear and mitochondrial genomes. In this study, we utilized RNA-seq to assess transcriptome-wide gene expression in the muscle of Atlantic killifish (Fundulus heteroclitus) from a population that contains segregating variation in mitochondrial genotype. We examined gene expression plasticity in response to 5°C acclimation and the effects of mitochondrial genotype on this plasticity. Cold acclimation resulted in changes in gene expression consistent with up-regulation of genes involved in many cellular functions, including spliceosomal and proteasomal processes, and with down-regulation of genes involved in extracellular matrix, muscle contraction and oxidative phosphorylation functions. There were few differences in gene expression between killifish with different mitochondrial genotypes: 14 genes demonstrated significant interactions between mitochondrial genotype and acclimation temperature and 3 genes demonstrated effects of mitochondrial genotype alone. These results indicate that variation in mitochondrial genotype has modest effects on gene expression; the majority of which are revealed as differences in plasticity as a result of environmental change.
Figure 1 from: Minton RL, Martinez Cruz MA, Farman ML, Perez KE (2016) Two complete mitochondrial genomes from Praticolella mexicana Perez, 2011 (Polygyridae) and gene order evolution in Helicoidea (Mollusca, Gastropoda). ZooKeys 626: 137-154. https://doi.org/10.3897/zookeys.626.9633
Figure 1 - Mitochondrial genome of Praticolella mexicana UTRGV and McAllen illustrated with an image of the species holotype (ANSP 426031). Gene order and sizes are shown relative to one another, not including non-coding regions. Genes are color coded by H (black) or L (red) strand. IUPAC single letter codes are used to identify tRNA genes.
Figure 3 from: Minton RL, Martinez Cruz MA, Farman ML, Perez KE (2016) Two complete mitochondrial genomes from Praticolella mexicana Perez, 2011 (Polygyridae) and gene order evolution in Helicoidea (Mollusca, Gastropoda). ZooKeys 626: 137-154. https://doi.org/10.3897/zookeys.626.9633
Figure 3 - Maximum likelihood phylogeny of gene order. Analysis in MLGO yielded a single tree. Branch support >50% is shown based on 100 bootstrap replicates. Bradybaenidae and Helicidae were recovered as monophyletic, but Helicoidea was not.
Figure 4 from: Minton RL, Martinez Cruz MA, Farman ML, Perez KE (2016) Two complete mitochondrial genomes from Praticolella mexicana Perez, 2011 (Polygyridae) and gene order evolution in Helicoidea (Mollusca, Gastropoda). ZooKeys 626: 137-154. https://doi.org/10.3897/zookeys.626.9633
Figure 4 - Ancestral gene order reconstructions for Helicoidea. Columns (A–E) correspond to labeled nodes in Figure 2. IUPAC single letter codes are used to identify tRNA genes. Rearrangements in red and blue are unique to Helicidae. The convergent rearrangement seen in Bradybaenidae, Camaena, and Praticolella is shown in yellow. The green rearrangement is unique to Aegista.
Figure 2 from: Minton RL, Martinez Cruz MA, Farman ML, Perez KE (2016) Two complete mitochondrial genomes from Praticolella mexicana Perez, 2011 (Polygyridae) and gene order evolution in Helicoidea (Mollusca, Gastropoda). ZooKeys 626: 137-154. https://doi.org/10.3897/zookeys.626.9633
Figure 2 - Maximum likelihood phylogeny of Stylommatophora protein coding genes. Analysis in IQTREE yielded a single tree (log likelihood = -89104.188) under the mtZOA+F+I+G4 model. Branch support >50% is shown based on 10,000 ultra-fast bootstrap replicates. Helicoidea, Bradybaenidae, and Helicidae were recovered as monophyletic. Nodes A-E refer to rearrangements shown in Figure 4.
FIGURE 1 in Mitochondrial genome of Poecilimon cretensis (Orthoptera: Tettigoniidae: Phaneropterinae): Strong phylogenetic signals in gene overlapping regions
FIGURE 1. The map of mitochondrial genome and habitus of Poecilimon cretensis
Data from: Elevated genetic diversity of mitochondrial genes in asexual populations of bark lice ("Psocoptera": Echmepteryx hageni)
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Data from: Phylogeny of Anophelinae using mitochondrial protein coding genes
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Data from: Metazoan mitochondrial gene sequence reference datasets for taxonomic assignment of environmental samples
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Data from: Additional Support for Afrotheria and Paenungulata, the Performance of Mitochondrial versus Nuclear Genes, and the Impact of Data Partitions with Heterogeneous Base Composition
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Data from: Demography or selection on linked cultural traits or genes? Investigating the driver of low mtDNA diversity in the sperm whale using complementary mitochondrial and nuclear genome analyses
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Data from: Two complete mitochondrial genomes from Praticolella mexicana Perez, 2011 (Polygyridae) and gene order evolution in Helicoidea (Mollusca, Gastropoda)
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Data from: Incongruence of mitochondrial and nuclear gene trees in the carabid beetles Ohomopterus
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