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Figure 5 in Characterisation of the complete mitochondrial genome of the imperiled Pearl darter Percina aurora (Perciformes: Percidae)

Figure 5. Features present in the Control Region (CR) (987 bp) of the Percina aurora mitogenome. The CR is separated into an extended termination-associated sequence domain (ETAS), a core domain, and a conserved sequence block (CSB) domain. The underlined portion denotes the long tandem repeat sequence within the ETAS domain. The blue-green highlighted sequence represents the ETAS 1 region while the blue highlighted sequence represents the ETAS 2 region. Nucleotides in green, yellow and pink correspond to the F-box, E-box and D-box regions within the central domain, respectively. Nucleotides in cyan, red and dark green correspond to the CSB-1, CSB-2 and CSB-3 regions, respectively.

Figure 5 in The complete mitochondrial genome of the leopard shark Triakis semifasciata (Triakidae)

Figure 5. Phylomitogenomic analysis of the leopard shark Triakis semifasciata and related species in the family Triakidae. Total-evidence phylogenetic tree obtained from a maximum likelihood analysis based on a concatenated alignment of the 13 protein-coding genes (translated) encoded in the mitochondrial genome. Numbers above or below branches are bootstrap support values for the different internal nodes. Photograph of Triakis semifasciata from Matthew Field (used with permisssion).

Figure 3 in The complete mitochondrial genome of the leopard shark Triakis semifasciata (Triakidae)

Figure 3. Selective pressure analysis in the mitochondrial protein-coding genes of the leopard shark Triakis semifasciata. The estimated Ka/Ks ratio for each protein-coding gene is shown.

Figure 4 in Characterisation of the complete mitochondrial genome of the imperiled Pearl darter Percina aurora (Perciformes: Percidae)

Figure 4. Visualisation of the tRNA secondary structure in the mitochondrial genome of Percina aurora.

Figure 2 in Characterisation of the complete mitochondrial genome of the imperiled Pearl darter Percina aurora (Perciformes: Percidae)

Figure 2. Codon usage in 13 protein coding genes of Percina aurora. Columns indicate the relative frequency of synonymous codons separated by amino acid.

Figure 1 in Complete mitochondrial genome of the terrestrial isopod Cubaris murina Brandt, 1833: new family gene order and novel tRNA secondary structures

Figure 1. Mitochondrial genome synteny in Cubaris murina and closely related species. A dash (-) before the gene name means that the gene is encoded on the light strand. NCR means a non-coding region that is longer than 100 bp. Cubaris murina is marked in bold black and shades of grey.

Figure 2 in Complete mitochondrial genome of the terrestrial isopod Cubaris murina Brandt, 1833: new family gene order and novel tRNA secondary structures

Figure 2. Secondary structure of each transfer RNA (tRNA) visualised in Forna (http://rna.tbi.univie.ac. at/forna).

Table 3 in Complete mitochondrial genome of the terrestrial isopod Cubaris murina Brandt, 1833: new family gene order and novel tRNA secondary structures

Table 3. Characteristic (AT content, repeat, number of predicted secondary structure, range of ΔG value (kcal/mol)) of control region of Cubaris murina by RNAstructure.<table><tbody><tr><th></th><th></th><th></th><th></th><th>Length</th><th></th><th></th><th></th><th>Number of predicted</th><th></th></tr></tbody><tbody><tr><th>Species [reference]</th><td>Name</td><td>Start</td><td>Stop</td><td>(bp)</td><td>Location</td><td>%AT</td><td>Repeat</td><td>secondary structures</td><td>ΔG value (kcal/mol)</td></tr><tr><th>Cubaris murina</th><td>NCR1</td><td>5219</td><td>5360</td><td>142</td><td>Between nad1 and trnN</td><td>52.80%</td><td></td><td>7</td><td>−16.9 to −15.4</td></tr><tr><th>[present study]</th><td>NCR2</td><td>6297</td><td>6666</td><td>370</td><td>Between trnS1 and trnL1</td><td>59.70%</td><td>CT-rich & AT-loop</td><td>20</td><td>−103.7 to −101.0</td></tr><tr><th></th><td>NCR3</td><td>12,550</td><td>12,753</td><td>204</td><td>Between rrnL and trnE</td><td>71.10%</td><td>poly-A</td><td>7</td><td>−17.5 to −17.1</td></tr><tr><th></th><td>NCR4</td><td>12,813</td><td>12,950</td><td>138</td><td>Between trnE and trnV</td><td>71.70%</td><td>AG-rich</td><td>5</td><td>−13.4 to −12.3</td></tr><tr><th>Panulirus argus [Baeza, 2018]</th><td>NCR</td><td>13,525</td><td>14,326</td><td>801</td><td>Between rrnS and trnI</td><td>69.60%</td><td>AT-rich</td><td>7</td><td>−99.20 to −94.52</td></tr><tr><th>Synalpheus microneptunus [Chak et al., 2020]</th><td>NCR</td><td>13,365</td><td>14,198</td><td>834</td><td>Between rrnS and trnI</td><td>79.50%</td><td>AT-rich</td><td>20</td><td>− 104 (lowest)</td></tr></tbody></table>

opencc-by-4.0Jul 2021View details →

Comparative Analysis of Complete Chloroplast Genomes and Multiple DNA Sequences Reveals Interspecific Relationships of C. bretschneideri and Related Species in China

ITS, and LEAFY intron 1 sequencing of 36 Crataegus accessions.

opennotspecifiedJul 2012View details →

Figure 1 in The complete mitochondrial genome of the Chinese Sika deer (Cervus nippon Temminck, 1838), and phylogenetic analysis among Cervidae, Moschidae and Bovidae

Figure 1. Molecular phylogenetic tree derived from complete DNA sequence of 12 mitochondrial protein-coding genes using Bayesian inference and maximum parsimony analysis. The numbers beside the nodes are Bayesian posterior probabilities and bootstrap proportions. Equus asinus and Equus caballus were set as out-groups.

Figure 1 in Molecular phylogeny of major lineages of the avian family Phasianidae inferred from complete mitochondrial genome sequences

Figure 1. Molecular phylogenetic tree derived from complete DNA sequences of the 12 mitochondrial protein-coding genes using Bayesian inference, maximum parsimony and maximum likelihood analysis. The numbers beside the nodes are Bayesian posterior probabilities (≥ 0.95 retained) and bootstrap proportions (≥ 50% retained). Anas platyrhynchos was set as outgroup. ∗demonstrates that MP analysis does not support this branch.

opennotspecifiedNov 2010View details →

Figure 2 in Complete mitochondrial genome of Tetraophasis szechenyii Madarász, 1885 (Aves: Galliformes: Phasianidae), and its genetic variation as inferred from the mitochondrial DNA Control Region

Figure 2. Median-joining network of all the control region haplotypes found in Tetraophasis szechenyii. Notes: Missing haplotypes in the network are represented by black dots; circle sizes are proportional to the number of individuals sharing the same haplotypes (n); each mutation step is shown as a short line connecting neighbouring haplotypes; numbers of mutations between haplotypes are indicated near branches if greater than 1.

opennotspecifiedNov 2010View details →

Figure 1 in Complete mitochondrial genome of Tetraophasis szechenyii Madarász, 1885 (Aves: Galliformes: Phasianidae), and its genetic variation as inferred from the mitochondrial DNA Control Region

Figure 1. Molecular phylogenetic tree derived from the complete DNA sequences of 12 mitochondrial protein-coding genes using Bayesian inference and maximum likelihood analyses. Notes:The numbers beside the nodes are Bayesian posterior probabilities (≥ 0.9 retained) and bootstrap proportions of maximum likelihood analyses calculated with 100 replicates (≥ 50% retained); Anas platyrhynchos and Alectura lathami were set as outgroups; *clades not supported by Bayesian inference.

opennotspecifiedMay 2009View details →

Figure 1 in The complete mitochondrial genome and phylogenetic analysis of forest musk deer (Moschus berezovskii)

Figure 1. Phylogenetic relationships by partitioned Bayesian and maximum parsimony (MP) methods of selected Cetartiodactyla taxa as inferred from 12 heavy-strand protein-coding genes (A), RNA genes (B), and their combination (C). Values above branches represent the posterior probabilities of Bayesian analysis and bootstrap values with 1000 replicates for the MP method. No numbers above a branch indicate that Bayesian posterior probability,0.95 and MP bootstrap values are,50.

FIGURE 4 in The complete mitochondrial genome of the flat bug Aradacanthia heissi (Hemiptera: Aradidae)

FIGURE 4. Predicted secondary structure of the srRNA in A. heissi. The annotation is the same as in Fig. 3.

FIGURE 6 in The complete mitochondrial genome of the flat bug Aradacanthia heissi (Hemiptera: Aradidae)

FIGURE 6. Phylogenetic tree of 15 Pentatomomorpha insects. Bayesian analyses and ML show the same topology. Bayesian posterior probabilities and bootstrap values of ML were indicated at each node.

FIGURE 2 in The complete mitochondrial genome of the flat bug Aradacanthia heissi (Hemiptera: Aradidae)

FIGURE 2. Inferred secondary structure of 22 tRNAs of A. heissi. The tRNAs are labeled with the abbreviations of their corresponding amino acids. Dashed (–) indicate Watson-Crick base pairing and (+) indicate G-U base pairing.

FIGURE 1 in The complete mitochondrial genome of the flat bug Aradacanthia heissi (Hemiptera: Aradidae)

FIGURE 1. Map of the mitochondrial genome of A. heissi. The tRNAs are denoted by the color blocks and are labeled according to the IUPACIUB single-letter amino acid codes. Gene name without underline indicates the direction of transcription from left to right, and with underline indicates right to left. Overlapping lines within the circle denote PCR fragments amplified used for cloning and sequencing.

opennotspecifiedMar 2013View details →

FIGURE 5 in The complete mitochondrial genome of a tessaratomid bug, Eusthenes cupreus (Hemiptera: Heteroptera: Pentatomomorpha: Tessaratomidae)

FIGURE 5. Control region of the E. cupreus mitogenome. (A) Structure elements found in the control region of E. cupreus. The red, yellow and green box represent three different repetitive sequences found in the control region and tRNAIle -tRNAGln - tRNAMet -ND2 gene cluste. (B) The putative stem-loops structure was found in the control region. The light green and pink indicates highly conserved flanking sequence. (C) Predicted secondary clover-leaf structure of one extra tRNAGln-like sequences in the control region (gray indicates the sequences are identical to the typical tRNAGln; the light green indicates the different sequences). Alignments with the corresponding regular tRNAGln sequences also provided. The boxed nucleotides indicate the anticodon, which designates the corresponding tRNA.