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FIGURE 4 in The complete mitochondrial genome of Thereuopoda clunifera (Chilopoda: Scutigeridae) and phylogenetic implications within Chilopoda
FIGURE 4. Evolutionary rates of PCGs among T. clunifera and other 8 species of Chilopoda. Ka: nonsynonymous substitution rate; Ks: synonymous substitution rate. Box and whisker plots represented the value of Ka/Ks for each PCGEvolutionary rates of PCGs among T. clunifera and other 8 species of Chilopoda. Ka: nonsynonymous substitution rate; Ks: synonymous substitution rate. Box and whisker plots represented the value of Ka/Ks for each PCG.
Complete mitochondrial genome of the forensically important carrion beetle, Necrodes nigricornis (Coleoptera: Silphidae)
<p>To enrich the genomic data pools of the family Silphidae for subsequent mitogenome-based large-scale phylogenetic study and development of a diverse type of molecular marker (e.g., species identification by restriction fragment length polymorphism and loop-mediated isothermal amplification), which have considerable forensic importance, we sequenced the complete mitogenome of the <em>N. nigricornis</em> for the first time. This sequence was analyzed for mitogenome characteristics, along with a brief comparison to other familial species, and used for phylogenetic analysis within the family Silphidae.</p>
FIGURE 4 in The complete mitochondrial genome of the Korean endemic millipede Anaulaciulus koreanus (Verhoeff, 1937), with notes on the gene arrangement of millipede orders
FIGURE 4. Comparison diagram of mitochondrial gene arrangement patterns of nine millipede species. One-letter codes corresponding to the amino acids of the tRNAs are used. Diagram is adapted and modified from Brewer et al. (2013).
FIGURE 2 in The complete mitochondrial genome of the Korean endemic millipede Anaulaciulus koreanus (Verhoeff, 1937), with notes on the gene arrangement of millipede orders
FIGURE 2. Potential stem and loop structures of the junctional sequences of (A) COI-COII, (B) ATP8-ATP6, (C) ND6- Cytb, (D) ND4L-ND4, and (E) ATP6-COIII, and (F) a non-coding region in the mitochondrial genome of Anaulaciulus koreanus (Verhoeff, 1937). The anticodon sequences are boxed, and termination codons or incomplete termination codons are drawn with an underline or side-line. The number of nucleotide sequences in each loop is shown.
FIGURE 1 in The complete mitochondrial genome of the Korean endemic millipede Anaulaciulus koreanus (Verhoeff, 1937), with notes on the gene arrangement of millipede orders
FIGURE 1. The mitochondrial genome structures of Anaulaciulus koreanus (Verhoeff, 1937). The direction of transcription for each gene is shown by an arrow. The hatch-marked area is a large non-coding region.
FIGURE 3 in The complete mitochondrial genome of the Korean endemic millipede Anaulaciulus koreanus (Verhoeff, 1937), with notes on the gene arrangement of millipede orders
FIGURE 3. Putative secondary structures of the 22 tRNAs observed from the mitochondrial genome of Anaulaciulus koreanus (Verhoeff, 1937)
Supplementary material 1 from: Yuhui X, Lijun Z, Yue H, Xiaoqi W, Chen Z, Huilun Z, Ruoran W, Da P, Hongying S (2017) Complete mitochondrial genomes from two species of Chinese freshwater crabs of the genus Sinopotamon recovered using next-generation sequencing reveal a novel gene order (Brachyura, Potamidae). ZooKeys 705: 41-60. https://doi.org/10.3897/zookeys.705.11852
Figure S1 : Explanation note: Comparisons of the consensus sequence and variable sites in the entire mNCR for Sinopotamon yaanense, S. yangtsekiense and S. xiushuiense. The conserved central domain is grey shaded, and the extended termination associated sequences (ETAS) is underlined.
Gene annotation of complete genome sequence of Achromobacter sp. strain E1
Open the record for dataset details and reuse information.
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 :
FGMP: assessing fungal genome completeness
<p>Datasets for FGMP tool (7,773 protein markers)</p> <p>7773_markers.fa.gz (A single representative sequence per orthologous group)</p> <p>7773_profiles_cutOff.tbl (FGMP significance thresholds)</p> <p>AllOneR.hmm.gz (FGMP hidden Markov models)</p> <p> </p> <p> </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.
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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.