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865 results for “Mitochondrial genomes”
Supporting data for: "mtGrasp: Streamlined mitochondrial genome reference-grade assembly and standardization to enhance mitogenome resources and improve the development of environmental DNA assays"
<p>Here, we provide supporting data for the manuscript "mtGrasp: Streamlined mitochondrial genome reference-grade assembly and standardization to enhance mitogenome resources and improve the development of environmental DNA assays".</p> <p>Phylogenetic_analysis.tar.gz contains the script and fasta files used for the phylogenetic analysis, and Mitogenomes.tar.gz contains the mitochondrial sequences utilized that are not publicly available in GenBank.</p>
Comparative mitochondrial genome and phylogenetic analysis of malaria mosquitoes Anopheles hyrcanus and Anopheles messeae supplementary files
<p><strong>T</strong><strong><span>able</span></strong><strong> S1.</strong> This study encompassed 105 species, along with their corresponding taxonomy and GenBank registration numbers.</p> <p><strong>Figure S1</strong> Inferred secondary structures of tRNAs in the mt genome of <em>An. </em><em><span>h</span></em><em>yrcanus</em><em> </em><span>(A)</span><em> </em><span>and </span><em>An. </em><em><span>m</span></em><em>esseae</em><em> </em><span>(B)</span>, with corresponding amino acids labeled next to the tRNAs.</p>
The complete mitochondrial genomes of five lichenized fungi in the genus Usnea (Ascomycota: Parmeliaceae)
<p>ABSTRACT: Known colloquially as ‘Old Man’s Beard’, <em>Usnea</em> is a genus of lichenized Ascomycete fungi characterized by having a fruticose growth form and cartilaginous central axis. The complete mitochondrial genomes of <em>Usnea halei</em>, <em>U. mutabilis</em>, <em>U. subfusca</em>, <em>U. subgracilis</em>, and <em>U. subscabrosa</em> were sequenced using Illumina data and then assembled <em>de novo</em>. These mitogenomes ranged in size from 52,486 bp (<em>U. subfusca</em>) to 94,464 bp (<em>U. subgracilis</em>). All were characterized by having high levels of intronic and intergenic variation, such as ORFs that encode proteins with homology to two homing endonuclease types, LAGLIDADG and GIY-YIG. Genes annotated within these mitogenomes include 14 protein-coding genes, the large and small ribosomal subunits (LSU and SSU), and 23–26 tRNAs. Notably, the <em>atp9</em> gene was absent from each genome. Genomic synteny was highly conserved across the five species. Five conserved mitochondrial genes (<em>nad2</em>, <em>nad4</em>, <em>cox1</em>, <em>cox2</em>, and <em>cox3</em>) were used to infer a best estimate maximum likelihood phylogeny among these five <em>Usnea</em> and other relatives, which yielded relationships consistent with prior published phylogenies.</p>
Supplementary material 6 from: Xi B-W, Zhang D, Li W-X, Yang B-J, Xie J (2018) Characterization of the complete mitochondrial genome of Parabreviscolex niepini Xi et al., 2018 (Cestoda, Caryophyllidea). ZooKeys 783: 97-112. https://doi.org/10.3897/zookeys.783.24674
Figure S3. Amino acid alignment for sites under positive selection for cytb : Explanation note: The positions of each site are denoted on the top. An asterisk * denotes sites with posterior probability value ≥ 0.95 in Bayes Empirical Bayes (BEB) analysis.
Supplementary material 3 from: Xi B-W, Zhang D, Li W-X, Yang B-J, Xie J (2018) Characterization of the complete mitochondrial genome of Parabreviscolex niepini Xi et al., 2018 (Cestoda, Caryophyllidea). ZooKeys 783: 97-112. https://doi.org/10.3897/zookeys.783.24674
Table S3. Nucleotide composition and skewness of different elements of the studied mitochondrial genome :
Supplementary material 5 from: Xi B-W, Zhang D, Li W-X, Yang B-J, Xie J (2018) Characterization of the complete mitochondrial genome of Parabreviscolex niepini Xi et al., 2018 (Cestoda, Caryophyllidea). ZooKeys 783: 97-112. https://doi.org/10.3897/zookeys.783.24674
Figure S2. Relative Synonymous Codon Usage (RSCU) of Parabreviscolexniepini : Explanation note: Codon families are labelled on the x-axis. Values on the top of the bars denote amino acid usage.
Supplementary material 4 from: Xi B-W, Zhang D, Li W-X, Yang B-J, Xie J (2018) Characterization of the complete mitochondrial genome of Parabreviscolex niepini Xi et al., 2018 (Cestoda, Caryophyllidea). ZooKeys 783: 97-112. https://doi.org/10.3897/zookeys.783.24674
Figure S1. Sequence alignment of trnS1 for Parabreviscolexniepini and other cestodes : Explanation note: The position of the anticodon sequences was indicated.
Supplementary material 2 from: Xi B-W, Zhang D, Li W-X, Yang B-J, Xie J (2018) Characterization of the complete mitochondrial genome of Parabreviscolex niepini Xi et al., 2018 (Cestoda, Caryophyllidea). ZooKeys 783: 97-112. https://doi.org/10.3897/zookeys.783.24674
Table S2. The list of cestodes species and outgroups used for comparative mitogenomic and phylogenetic analyses :
Supplementary material 1 from: Xi B-W, Zhang D, Li W-X, Yang B-J, Xie J (2018) Characterization of the complete mitochondrial genome of Parabreviscolex niepini Xi et al., 2018 (Cestoda, Caryophyllidea). ZooKeys 783: 97-112. https://doi.org/10.3897/zookeys.783.24674
Table S1. Primers used to amplify and sequence the mitochondrial genomes of Parabreviscolexniepini :
Population genetics of Paramecium mitochondrial genomes; genome assemblies and annotation files
<p>Because of issues arising during submission to GenBank of Paramecium mitochondrial genomes due to the highly unconventional nature of the genetic code used in these genomes, we are initially making the genomes publicly available here (while we are still working on a submission to official databases).</p>
FIGURE 3. Inferred phylogenetic relationship among 23 in The complete mitochondrial genome of the jumping grasshopper Sinopodisma pieli (Orthoptera: Acrididae) and the phylogenetic analysis of Melanoplinae
FIGURE 3. Inferred phylogenetic relationship among 23 taxa based on nucleotide sequences of mitochondrial 13 PCGs using Bayesian Inference (BI) (a) and maximum likelihood (ML) (b).
FIGURE 2. Predicted secondary structures for 22 in The complete mitochondrial genome of the jumping grasshopper Sinopodisma pieli (Orthoptera: Acrididae) and the phylogenetic analysis of Melanoplinae
FIGURE 2. Predicted secondary structures for 22 tRNA genes of the S. pieli mitogenome. The tRNAs are labeled with the abbreviations of their corresponding amino acids. The minus sign (-) indicates Watson-Crick base pairing and plus sign (.) indicates G-U base pairing.
FIGURE 4 in A new species of the genus Hilethera Uvarov, 1923 (Orthoptera: Acrididae: Oedipodinae) from China and its complete mitochondrial genome
FIGURE 4. Genetic distance of individual genes within Oedipodinae. Each boxplot represents P distance for 13 PCGs, rrnL and rrnS in sixteen Oedipodinae species. Lower horizontal bar, non-outlier smallest observation; lower edge of rectangle, 25 percentile; central bar within rectangle, median; upper edge of rectangle, 75 percentile; upper horizontal non-outlier largest observation; open circle, outlier.
FIGURE 1 in A new species of the genus Hilethera Uvarov, 1923 (Orthoptera: Acrididae: Oedipodinae) from China and its complete mitochondrial genome
FIGURE 1. Hilethera xinjiangensis sp. nov. male: A. body dorsal view; B. head frontal view; C. head and pronotum lateral view; D. body lateral view; E. head and pronotum dorsal view; F. end of abdomen dorsal view; G. epiphallus.
FIGURE 6 in A new species of the genus Hilethera Uvarov, 1923 (Orthoptera: Acrididae: Oedipodinae) from China and its complete mitochondrial genome
FIGURE 6. Phylogenetic reconstruction of Oedipodinae using mitochondrial PCGs and rRNAs concatenated dataset inferred from Bayesian inference (BI, on the left of figure) and Maximum likelihood (ML, on the right of figure). Values on nodes indicate branch support, BI posterior probabilities (PP) / Maximum likelihood Bootstrap support values (BV). Asterisks are used to indicate maximum support (1.0 for PP and 100% for BV). Accession number of each species recorded in GenBank was indicated in brackets.
Fig. 1 Mitochondrial genome structure and genes variability. a in Historical biogeography and mitogenomics of two endemic Mediterranean gorgonians (Holaxonia, Plexauridae)
Fig. 1 Mitochondrial genome structure and genes variability. a Mitogenomes of Paramuricea clavata and Paramuricea macrospina with genome size and gene annotation. GC-content and AT-content are shown in blue and green on the inner and outer surface of the ring, respectively. b Sliding window analysis of the complete mitochondrial genomes of P. clavata and P. macrospina. The black line indicates
Fig. 3 in Mitochondrial genomes of the genus Ephydatia Lamouroux, 1816: can palindromic elements be used in species-level studies?
Fig. 3 Secondary structures and corresponding alignments of palindromic repetitive elements in Ephydatia fluviatilis divided into four distinct families (H7, H8, H9s and H11). The numbers in the alignment
Fig. 2 a in Mitochondrial genomes of the genus Ephydatia Lamouroux, 1816: can palindromic elements be used in species-level studies?
Fig. 2 a Alignment of nad2 (NADH dehydrogenase subunit 2) gene from Ephydatia fluviatilis (EF), Eunapius subterraneus (ES), Ephydatia muelleri (EM), Lubomirskia baicalensis (LB), Baikalospongia intermedia profundalis (BIP), Rezinkovia echinata (RE) and Swartschewskia papyracea (SP), respectively; parts containing palindromic
Fig. 7 in Diversification of Hemidactylus geckos (Squamata: Gekkonidae) in coastal plains and islands of southwestern Arabia with descriptions and complete mitochondrial genomes of two endemic species to Saudi Arabia
Fig. 7 Digital elevation model of coastal southwestern Arabia showing the distributions of the Hemidactylus species included in this study. Note the sharp elevation gradient between the Tihama plain
Fig. 3 in Diversification of Hemidactylus geckos (Squamata: Gekkonidae) in coastal plains and islands of southwestern Arabia with descriptions and complete mitochondrial genomes of two endemic species to Saudi Arabia
Fig. 3 Species tree of the southwestern Arabian Hemidactylus clade. Posterior probability values are indicated only for branches with pp ≥ 0.9. For a tree with all posterior probability values, see Supplementary Fig. S3. Boxplots to the right of the tree show some key morphological and ecological characteristics for the species. Body size is SVL of adult specimens; the head-to-body ratio was calculated as HL/SVL (adults only); elevation indicates the range of elevations
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International Brain Laboratory public data
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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.