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865 results for “Mitochondrial genomes”
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).
Pycnogonid mitochondrial genomes data
<p>Pycnogonida, or sea spiders, is a speciose clade with ~1,300 described species that is especially diverse in the Southern Ocean. Evolutionary patterns within sea spiders remain unresolved between and within the ten putative, extant families due to due to shared morphological traits and highly reduced forms. Herein, we find that the order of mitochondrial protein coding genes is consistent between all sampled sea spiders, even though arrangement of tRNA genes, as well as placement and length of the control region, vary. The presence of large noncoding introns present in multiple families indicates that pycnogonid mtDNA have a fast evolutionary rate. A consensus phylogeny of recognized families is still debated, and previous work based on various methodologies has produced contrasting hypotheses of relationships. To better understand phylogenetic relationships between major clades of sea spiders, we constructed a dataset of whole mitochondrial genomes from representatives of all ten currently recognized families. Our results suggest a novel familial-level phylogeny within Pycnogonida, with a monophyletic clade containing Callipallenidae and Nymphonidae placed as the sister to all other recognized families.</p>
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.
A phased chromosome-level genome and full mitochondrial sequence for the dikaryotic myrtle rust pathogen, Austropuccinia psidii
<p>The fungal plant pathogen <em>Austropuccinia psidii</em> is spreading globally and causing myrtle rust disease symptoms on plants in the family Myrtaceae. <em>A. psidii </em>is dikaryotic, with two nuclei that do not exchange genetic material during the dominant phase of its life-cycle. Phased and scaffolded genome resources for rust fungi are important for understanding heterozygosity, mechanisms of pathogenicity, pathogen population structure and for determining the likelihood of disease spread. We have assembled a chromosome-level phased genome for the pandemic biotype of <em>A. psidii </em>and, for the first time, show that each nucleus contains 18 chromosomes, in line with other distantly related rust fungi. We show synteny between the two haplo-phased genomes and provide a new tool, ChromSyn, that enables efficient comparisons between chromosomes based on conserved genes. Our genome resource includes a fully assembled and circularised mitochondrial sequence for the pandemic biotype. Please cite the following manuscript: https://www.biorxiv.org/content/10.1101/2022.04.22.489119v1</p>
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 2 in Seven new mitochondrial genomes of phytophagous scarab beetles (Coleoptera Scarabaeidae) and phylogenetic implications
FIGURE 2. Relative synonymous codon usage (RSCU) of six mitogenomes.
FIGURE 1 in Seven new mitochondrial genomes of phytophagous scarab beetles (Coleoptera Scarabaeidae) and phylogenetic implications
FIGURE 1. Map of the Anomala russiventris mitogenome.
The mitochondrial genome datasets of phylogenetic analysis from the subfamily Coelidiinae
<p>58 leafhopper and 5 treehoppers species were selected to participate in the phylogenetic tree construction after the removal of unverified, lacks the accurate scientific name, and repeated species sequences. Phylogenetic analysis was performed using alignments of the 13 PCGs of leafhopper with the other complete or near complete genomes of the treehopper species. The two species of Cosmoscarta bispecularis (KP064511) and Tettigades auropilosa (KM000129) (Yan & Zu, 2019) were used as the outgroup.</p>
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
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
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)
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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.