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865 results for “Mitochondrial genomes”
Supplementary Materials associated with paper 'Complete linear mitochondrial genomes for Cephea cephea and Mastigias albipunctata (Scyphozoa: Rhizostomeae), with an analysis of phylogenetic relationships'
<p>This is a repository for coverage depth graphs and ML-phylogenetic trees that are associated with the paper 'Complete linear mitochondrial genomes for Cephea cephea and Mastigias albipunctata (Scyphozoa: Rhizostomeae), with an analysis of phylogenetic relationships' by Tan KC, Collins AG and Ames CL.</p>
Mitochondrial genome sequencing and analysis of the invasive Microstegium vimineum: a resource for systematics, invasion history, and management
<p>Table S1: Accession data for Microstegium samples included in this study.</p> <p>File S1: Alignment of Mitochondrial CDS for Poales mitochondrial sequences.</p> <p>File S2: SNP data for Microstegium vimineum mitochondrial variants.</p> <p>Figure S1: Transposable element content in the Microstegium vimineum mitogenome.</p> <p>Figure S2: Summary of Kraken2 output.</p> <p> </p>
Figure 3. The phylogenetic relationship between G in The Complete Mitochondrial Genome of Glischropus bucephalus (Vespertilionidae; Chiroptera) Provides New Evidence for Pipistrellus Paraphyly
Figure 3. The phylogenetic relationship between G. bucephalus and the other Pipistrellini species is inferred by maximum likelihood analysis based on cytb sequences. The numbers in the branches show the bootstrap values. Vespertilio species are used as outgroups.
Figure 1 in The Complete Mitochondrial Genome of Glischropus bucephalus (Vespertilionidae; Chiroptera) Provides New Evidence for Pipistrellus Paraphyly
Figure 1. Map of the G. bucephalus mitogenome. Gray color indicates the PCG regions; red color— tRNAs; yellow color—rRNAs. The heavy strand in the outer circle encodes 28 genes, whereas 9 genes are encoded in the light strand in the inner circle.
Figure 2. The phylogenetic relationship between G in The Complete Mitochondrial Genome of Glischropus bucephalus (Vespertilionidae; Chiroptera) Provides New Evidence for Pipistrellus Paraphyly
Figure 2. The phylogenetic relationship between G. bucephalus and the other Vespertilioninae species is inferred by the maximum likelihood analysis based on the concatenated protein-coding gene sequences. The bootstrap values (indicated by the slashes on the branches) correspond to the trees constructed on full sequences (three codon positions), the first two codon positions (third positions omitted), and two positions with the exclusion of the Nd6 gene. The asterisks mark branches that in the second or third case have a different topology than shown. Myotis species are used as outgroups.
PacBio HiFi de-novo assembled genome and mitochondrial genome for Orbicella faveolata
<p>Final assembly using Funannotate of <i>Orbicella faveolata</i> from PacBio HiFi reads. For full methods please see the publication. </p>
Figure 1 in Mitochondrial genomes of four pierid butterfly species (Lepidoptera: Pieridae) with assessments about Pieridae phylogeny upon multiple mitogenomic datasets
Figure 1. Circular map of Baltia butleri, Talbotia naganum, Pontia callidice, Pontia daplidice mitochondrial genome. COI, COII, and COIII refer to the cytochrome oxidase subunits; CytB refers to cytochrome B; ATP6 and ATP8 refer to subunits 6 and 8 of F0 ATPase; ND1-6 refers to the components of NADH dehydrogenase. The tRNAs locations are marked by the color blocks and labeled by the IUPAC-IUB single letter amino acid code. L1, L2, S1, and S2 denote tRNALeu (CUN), tRNALeu (UUR), tRNASer (AGN), and tRNASer (UCN), respectively. The non-underlined genes are transcribed on the majority strand whereas the underlined genes are transcribed on the minority strand.
Figure 16 in Mitochondrial genomes of four pierid butterfly species (Lepidoptera: Pieridae) with assessments about Pieridae phylogeny upon multiple mitogenomic datasets
Figure 16. Bayesian inference (BI) and Maximum likehood (ML) phylogenetic trees inferred from mitochondrial genomes of pierid family based on 22tRNA genes.
Figure 3 in Mitochondrial genomes of four pierid butterfly species (Lepidoptera: Pieridae) with assessments about Pieridae phylogeny upon multiple mitogenomic datasets
Figure 3. Relative Synonymous Codon Usage (RSCU) of the four pierid butterfly mitogenomes newly determined in this study.
Figure 15 in Mitochondrial genomes of four pierid butterfly species (Lepidoptera: Pieridae) with assessments about Pieridae phylogeny upon multiple mitogenomic datasets
Figure 15. Bayesian inference (BI) and Maximum likehood (ML) phylogenetic trees inferred from mitochondrial genomes of pierid family based on four datasets (13PCGs, 13PCGs+2rRNAs, 2rRNAs, 2rRNAs+22tRNAs).
Figure 5 in Characterization of the first mitochondrial genome of Aclerdidae (Hemiptera: Coccoidea) with a novel gene arrangement
Figure 5. Sternorrhyncha phylogenetic tree inferred from mitochondrial genome matrix. The phylogenetic tree were reconstruct using Bayesian inference method. Numbers at the nodes indicate Bayesian posterior probabilities.
Figure 4 in Characterization of the first mitochondrial genome of Aclerdidae (Hemiptera: Coccoidea) with a novel gene arrangement
Figure 4. Comparison of the mitochondrial gene arrangement among Nipponaclerda biwakoensis, ancestral insect, other representative species of Psyllidae, Aphididae and Aleyrodidae and four public Coccocidea species.
Figure 2 in Characterization of the first mitochondrial genome of Aclerdidae (Hemiptera: Coccoidea) with a novel gene arrangement
Figure 2. The codon number and relative synonymous codon usage (RSCU) in the Nipponaclerda biwakoensis mitochondrial genome.
Figure 1 in Characterization of the first mitochondrial genome of Aclerdidae (Hemiptera: Coccoidea) with a novel gene arrangement
Figure 1. Gene map of the Nipponaclerda biwakoensis mitochondrial genome. Arrows indicate the orientation of gene transcription. The inner circles show G+C content.
Figure 3 in Characterization of the first mitochondrial genome of Aclerdidae (Hemiptera: Coccoidea) with a novel gene arrangement
Figure 3. Predicted secondary structures of the 17 detected tRNA genes of Nipponaclerda biwakoensis mitochondrial genome. Watson–Crick pairs is indicated by lines, wobble GU pairs is indicated by dots and other noncanonical pairs is indicated by circles.
Figure 13. A in Erratum: JING LIU, HAIYU LUO, XIANGYI LU & XUN BIAN (2021) New additions to the Chinese Agraeciini Redtenbacher, 1891 (Orthoptera, Tettigoniidae: Conocephalinae) with report the complete mitochondrial genome of Palaeoagraecia brunnea Ingrisch, 1998. Zootaxa, 5072: 238–254.
Figure 13. A phylogenetic tree obtained from bayesian inference analysis based on 13 protein-coding genes.
Genome-wide analysis resolves the radiation of New Zealand's freshwater Galaxias vulgaris complex and reveals a candidate species obscured by mitochondrial capture
<p>Aim: Freshwater fish radiations are often characterized by multiple closely-related species in close proximity, which can lead to introgression and associated discordance of mitochondrial and nuclear characterizations of species diversity. As a case in point, single locus nuclear versus mitochondrial analyses of New Zealand's stream-resident <em>Galaxias vulgaris</em> complex have yielded conflicting phylogenies. Our goal is to use genome-wide divergence patterns among these fishes to evaluate the potential role of mitochondrial capture in obscuring species diversity and to understand how ancient and anthropogenic drainage modification explains this diversity.</p> <p>Location: Freshwater ecosystems of New Zealand. Methods: We generate and analyze a genome-wide data set comprising 52,352 SNPs across 187 <em>Galaxias</em> specimens to resolve the phylogeny of this recent fish radiation. We conduct phylogenetic, PCA, STRUCTURE, and ABBA-BABA analyses to evaluate the evolutionary relationships of lineages in the context of natural and anthropogenic river drainage alterations.</p> <p>Results: In addition to the 11 previously recognized stream-resident lineages, genome-wide data reveal a twelfth candidate species (<em>G</em>. 'Pomahaka'), apparently obscured by introgressive mitochondrial capture. We identify additional examples of mito-nuclear discordance and putative mitochondrial capture, likely mediated by geological and anthropogenic modification of drainage boundaries.</p> <p>Main conclusions: Our study highlights the need for genome-wide approaches for delimiting freshwater biodiversity. Genetic data also reveal the influence of drainage history on freshwater biodiversity, including the rapid divergence of recently fragmented fish populations, and the conservation genetic risks of anthropogenic translocations events.</p>
Fig. 3 in Sequencing and analysis of the complete mitochondrial genome of the giant dobsonfly Acanthacorydalis orientalis (McLachlan) (Insecta: Megaloptera: Corydalidae)
Fig. 3. Predicted secondary structure of the rrnl in the Acanthacorydalis orientalis mt genome. Roman numerals denote the conserved Watson-Crick base pairing and dot (•) indicates G-U base pairing.
Fig. 4 in Sequencing and analysis of the complete mitochondrial genome of the giant dobsonfly Acanthacorydalis orientalis (McLachlan) (Insecta: Megaloptera: Corydalidae)
Fig. 4. Predicted secondary structure of the rrns in the A. orientalis mt genome. Roman numerals denote the conserved domain structure. Dash (-) indicates Watson-Crick base pairing and dot (•) indicates G-U base pairing.
Fig. 1 in Sequencing and analysis of the complete mitochondrial genome of the giant dobsonfly Acanthacorydalis orientalis (McLachlan) (Insecta: Megaloptera: Corydalidae)
Fig. 1. Mitochondrial genome map of Acanthacorydalis orientalis. 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
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.