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505 results for “Complete genomes”
Characterization of the complete chloroplast genome of the medicinal herb Veronica polita Fr. (Lamiales: Plantaginaceae)
<p><em>Veronica polita</em> Fr. (synonym: <em>Veronica didyma</em> Ten.), an annual herbaceous species with high medicinal values, is originally from Southwest Asia but has been naturalized widely in many regions of the world. In this study, the complete chloroplast genome of <em>V. polita</em> was determined to be 150,191 bp long with a typical quadripartite structure. It encodes a panel of 114 genes with 18 of them being completely or partially duplicated and 19 of them possessing one or two introns. The phylogenetic analysis appeared to support the tribal-level taxonomy of the family Plantaginaceae, and revealed that <em>V. polita</em> was most closely related to the congener <em>V. persica</em>.</p>
The complete chloroplast genome of Pedicularis rudis Maxim. (Lamiales: Orobanchaceae), a perennial herb endemic to China
<p><em>Pedicularis rudis</em> Maxim. is a species of perennial herb endemic to China. In this study, the complete chloroplast genome of <em>P. rudis</em> was determined to be 151,443 bp long with a typical quadripartite structure, comprising two inverted repeat regions (IRa and IRb, 25,719 bp each), a large single-copy (LSC) region (83,119 bp) and a small single-copy (SSC) region (16,886 bp). It encodes a panel of 110 genes with 19 of them being completely or partially duplicated and 18 of them possessing one or two introns. Phylogenetic analysis revealed that <em>P. rudis</em> was most closely related to the congener <em>P. shansiensis</em>.</p>
Figure 4 from: Li W, Qiu N, Du H (2022) Complete mitochondrial genome of Rhodeus cyanorostris (Teleostei, Cyprinidae): characterization and phylogenetic analysis. ZooKeys 1081: 111-125. https://doi.org/10.3897/zookeys.1081.77043
Figure 4 Phylogenetic trees derived from the maximum-likelihood (ML) and neighbor joining (NJ) approaches based on whole mitochondrial genomes. The numbers on the nodes are the bootstrap values of ML and NJ. The number after the species name is the GenBank accession number.
Figure 2 from: Li W, Qiu N, Du H (2022) Complete mitochondrial genome of Rhodeus cyanorostris (Teleostei, Cyprinidae): characterization and phylogenetic analysis. ZooKeys 1081: 111-125. https://doi.org/10.3897/zookeys.1081.77043
Figure 2 Codon distribution a and relative synonymous codon usage (RSCU) b in the mitogenome of Rhodeus cyanorostris.
Figure 1 from: Li W, Qiu N, Du H (2022) Complete mitochondrial genome of Rhodeus cyanorostris (Teleostei, Cyprinidae): characterization and phylogenetic analysis. ZooKeys 1081: 111-125. https://doi.org/10.3897/zookeys.1081.77043
Figure 1 Gene map of the mitochondrial genome of Rhodeus cyanorostris. The genome contained two rRNA genes (in yellow), 13 coding genes (in black), 22 tRNA genes (in red), and a control region (D-loop) (in brown).
Figure 6 from: Mar-Silva AF, Arroyave J, Díaz-Jaimes P (2022) The complete mitochondrial genome of the Mexican-endemic cavefish Ophisternon infernale (Synbranchiformes, Synbranchidae): insights on patterns of selection and implications for synbranchiform phylogenetics. ZooKeys 1089: 1-23. https://doi.org/10.3897/zookeys.1089.78182
Figure 6 Phylogenetic relationships of major synbranchiform lineages. Molecular phylogeny based on comparative mitochondrial PCGs from relevant available mitogenomes and the newly generated herein for O. infernale. Troglobitic cave-dwelling species are marked with an asterisk to distinguish them from surface-dwelling ones. Outgroup taxa not shown. Colored circles on nodes indicate degree of clade support as determined by bootstrap values.
Figure 3 from: Mar-Silva AF, Arroyave J, Díaz-Jaimes P (2022) The complete mitochondrial genome of the Mexican-endemic cavefish Ophisternon infernale (Synbranchiformes, Synbranchidae): insights on patterns of selection and implications for synbranchiform phylogenetics. ZooKeys 1089: 1-23. https://doi.org/10.3897/zookeys.1089.78182
Figure 3 Secondary structure of the 22 tRNA genes of the mitochondrial genome of O. infernale predicted by tRNAScan-SE 2.0.
Figure 4 from: Mar-Silva AF, Arroyave J, Díaz-Jaimes P (2022) The complete mitochondrial genome of the Mexican-endemic cavefish Ophisternon infernale (Synbranchiformes, Synbranchidae): insights on patterns of selection and implications for synbranchiform phylogenetics. ZooKeys 1089: 1-23. https://doi.org/10.3897/zookeys.1089.78182
Figure 4 Comparison (multiple sequence alignment) of the mtDNA control region of O. infernale with those of fellow teleosts Siniperca chuatsi and Cyprinion semiplotum. The alignment displays the three canonical domains distinguished by Termination Associated Sequences (TAS) of the upstream hypervariable region (in red), central conserved domain blocks (CSB-F, CSB-E, CSB-D) (in blue), and conserved sequence blocks of the downstream hypervariable region (CSB-1, CSB-2 and CSB-3) (in green).
Figure 5 from: Mar-Silva AF, Arroyave J, Díaz-Jaimes P (2022) The complete mitochondrial genome of the Mexican-endemic cavefish Ophisternon infernale (Synbranchiformes, Synbranchidae): insights on patterns of selection and implications for synbranchiform phylogenetics. ZooKeys 1089: 1-23. https://doi.org/10.3897/zookeys.1089.78182
Figure 5 Patterns of selection in mtDNA PCGs of synbranchiform fishes. Results from KA/KS ratio analysis on mitochondrial PCGs (x-axis) in synbranchiform fishes of the families Synbranchidae (a) and Mastacembelidae (b).
Figure 2 from: Mar-Silva AF, Arroyave J, Díaz-Jaimes P (2022) The complete mitochondrial genome of the Mexican-endemic cavefish Ophisternon infernale (Synbranchiformes, Synbranchidae): insights on patterns of selection and implications for synbranchiform phylogenetics. ZooKeys 1089: 1-23. https://doi.org/10.3897/zookeys.1089.78182
Figure 2 Results from analysis of Relative Synonymous Codon Usage (RSCU) of the mitochondrial genome of O. infernale. Codon families are plotted on the x-axis. The label for the 2, 4, or 6 codons that compose each family is shown in the boxes below the x-axis, and the colors correspond to those in the stacked columns. RSCU values are shown on the y-axis.
Figure 1 from: Mar-Silva AF, Arroyave J, Díaz-Jaimes P (2022) The complete mitochondrial genome of the Mexican-endemic cavefish Ophisternon infernale (Synbranchiformes, Synbranchidae): insights on patterns of selection and implications for synbranchiform phylogenetics. ZooKeys 1089: 1-23. https://doi.org/10.3897/zookeys.1089.78182
Figure 1 Annotated map of the mitochondrial circular genome of O. infernale. The outer ring corresponds to the H- (outermost) and L-strands, and depicts the location of PCGs (in black, except for ND6 which is encoded in the L-strand and is portrayed in red), the non-coding control region (in dark brown), tRNAs (in red), and rRNAs (in light brown). The inner ring (black sliding window) denotes GC content along the genome. Live specimen photograph taken in the Cenote Kancabchen (Homún, Yucatán), courtesy of cave diver Erick Sosa.
Figure 4 from: Lee Y, Park J-K (2022) Complete mitochondrial genome of Conus lischkeanus Weinkauff, 1875 (Neogastropoda, Conidae) and phylogenetic implications of the evolutionary diversification of dietary types of Conus species. ZooKeys 1088: 173-185. https://doi.org/10.3897/zookeys.1088.78990
Figure 4 Phylogenetic relationships of the genus Conus based on concatenated nucleotide sequences (13 protein coding genes plus two rRNA genes). Numbers above branches are statistical support values for ML (bootstrap values, > 70)/BI (posterior probability values, > 0.7). *: determined in this study.
Figure 2 from: Lee Y, Park J-K (2022) Complete mitochondrial genome of Conus lischkeanus Weinkauff, 1875 (Neogastropoda, Conidae) and phylogenetic implications of the evolutionary diversification of dietary types of Conus species. ZooKeys 1088: 173-185. https://doi.org/10.3897/zookeys.1088.78990
Figure 2 The relative synonymous codon usage (RSCU) frequency of the mitochondrial genome of Conus lischkeanus.
FIGURE 7 in Indocalamus chongzhouensis (Poaceae: Bambusoideae), a new synonym of I. emeiensis: evidence from morphology and complete chloroplast genome data
FIGURE 7. Geographical distribution of Indocalamus emeiensis (red pentacles).
Supplementary material 1 from: Wei Z (2022) The complete mitochondrial genomes of five Agrilinae (Coleoptera, Buprestidae) species and phylogenetic implications. ZooKeys 1092: 195-212. https://doi.org/10.3897/zookeys.1092.80993
Figures S1–S7
FIGURE 3 in The complete mitochondrial genome of Thereuopoda clunifera (Chilopoda: Scutigeridae) and phylogenetic implications within Chilopoda
FIGURE 3. Relative synonymous codon usage (RSCU) in the mitochondrial genomes of T. clunifera
FIGURE 6 in The complete mitochondrial genome of Thereuopoda clunifera (Chilopoda: Scutigeridae) and phylogenetic implications within Chilopoda
FIGURE 6. Linear maps of the mitochondrial genome of Chilopoda
FIGURE 2 in The complete mitochondrial genome of Thereuopoda clunifera (Chilopoda: Scutigeridae) and phylogenetic implications within Chilopoda
FIGURE 2. AT-skew and GC-skew of 25 species of Myriapoda
FIGURE 5 in The complete mitochondrial genome of Thereuopoda clunifera (Chilopoda: Scutigeridae) and phylogenetic implications within Chilopoda
FIGURE 5. The potential secondary structure of the 22 tRNAs in the mitogenome of T. Clunifera
FIGURE 1 in The complete mitochondrial genome of Thereuopoda clunifera (Chilopoda: Scutigeridae) and phylogenetic implications within Chilopoda
FIGURE 1. Circular map of the mitochondrial genome of T. clunifera
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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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.