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FIGURE 8 in The complete mitochondrial genome of the styloperlid stonefly species Styloperla spinicercia Wu (Insecta: Plecoptera) with family-level phylogenetic analyses of the Pteronarcyoidea
FIGURE 8. Genetic distance between Styloperla sp. and Styloperla. spinicercia based on 13 PCGs, srRNA and lrRNA.
FIGURE 2 in The complete mitochondrial genome of the styloperlid stonefly species Styloperla spinicercia Wu (Insecta: Plecoptera) with family-level phylogenetic analyses of the Pteronarcyoidea
FIGURE 2. Relative synonymous codon usage (RSCU) in the Styloperla. spinicercia mitogenome. Codon families are provided on the x-axis.
FIGURE 7 in The complete mitochondrial genome of the styloperlid stonefly species Styloperla spinicercia Wu (Insecta: Plecoptera) with family-level phylogenetic analyses of the Pteronarcyoidea
FIGURE 7. Phylogenetic tree of five sequenced Pteronarcyoidea and two Capniidae stoneflies. Bayesian inference and Maximum likelihood analysis inferred from PCG+rRNAs supported the same topological structure. ML bootstrap values (up) and Bayesian posterior probabilities (down) are indicated at each node.
FIGURE 6. a in The complete mitochondrial genome of the styloperlid stonefly species Styloperla spinicercia Wu (Insecta: Plecoptera) with family-level phylogenetic analyses of the Pteronarcyoidea
FIGURE 6. a. Control region of Styloperla spinicercia mitogenome. TR1 and TR2 are the abbreviation of tandem repeat units. The colored panes indicate the structural elements in control region, leading sequences are shown as a blue pane, strings of TR1 as orange panes, A+T-rich sequences as red panes, strings of TR2 as purple panes and the end of control regions as a green pane. b. Lateral view of terminalia of S. spinicercia, arrow showing the diagnostic apex of the spur.
FIGURE 5 in The complete mitochondrial genome of the styloperlid stonefly species Styloperla spinicercia Wu (Insecta: Plecoptera) with family-level phylogenetic analyses of the Pteronarcyoidea
FIGURE 5. Predicted secondary structure of the srRNA gene in Styloperla spinicercia. Roman numerals denote the conserved domain structure. Dashed (-) indicate Watson-Crick base pairing and dot () indicate G-U base pairing.
FIGURE 1 in The complete mitochondrial genome of the styloperlid stonefly species Styloperla spinicercia Wu (Insecta: Plecoptera) with family-level phylogenetic analyses of the Pteronarcyoidea
FIGURE 1. Map of the mitochondrial genome of Styloperla spinicercia. Direction of gene transcription is indicated by the arrows. PCGs are shown as blue arrows, rRNA genes as purple arrows, tRNA genes as red arrows and large non-coding regions (>100 bp) as cyan rectangles. tRNA genes are labeled according to single-letter IUPAC-IUB abbreviations (L1: UUR; L2: CUN; S1: AGN; S2: UCN). The GC content is plotted using a black sliding window, as the deviation from the average GC content of the entire sequence. GC Skew is plotted as the deviation from the average GC skew of the entire sequence.
FIGURE 9 in Complete mitochondrial genome and taxonomic revision of Cardiodactylus muiri Otte, 2007 (Gryllidae: Eneopterinae: Lebinthini)
FIGURE 9. Evolutionary rate of each protein-coding (PCG) in the mitogenomes of Eneopterinae and Gryllinae.
FIGURE 6. A in Complete mitochondrial genome and taxonomic revision of Cardiodactylus muiri Otte, 2007 (Gryllidae: Eneopterinae: Lebinthini)
FIGURE 6. A, Maximum likelihood phylogeny of the family Gryllidae inferred from rrnS partial sequences available in GenBank. B, Maximum likelihood phylogeny of the family Gryllidae inferred from cytb partial sequences available in GenBank. The red star indicates the species under study.
FIGURE 4 in Complete mitochondrial genome and taxonomic revision of Cardiodactylus muiri Otte, 2007 (Gryllidae: Eneopterinae: Lebinthini)
FIGURE 4. Calling song of Cardiodactylus muiri Otte, 2007. A, oscillogram of 19 syllables (= echemes); B–C, detailled oscillogram (B) and sonogram (C) of five syllables; D, detailed oscillogram of one syllable; E, frequency spectrum of one syllable.
FIGURE 2 in Complete mitochondrial genome and taxonomic revision of Cardiodactylus muiri Otte, 2007 (Gryllidae: Eneopterinae: Lebinthini)
FIGURE 2. Tree trunk with males of Cardiodactylus muiri Otte, 2007 engaged in singing activity during late afternoon in Kumawa forest (Papua, Indonesia). Red circles mark males' positions; height ca. 4 m.
FIGURE 1 in Complete mitochondrial genome and taxonomic revision of Cardiodactylus muiri Otte, 2007 (Gryllidae: Eneopterinae: Lebinthini)
FIGURE 1. Habitat of Cardiodactylus muiri Otte, 2007. A, dead tree trunk in Kumawa (Papua, Indonesia); B, C, male sitting on dead tree (A) during the day.
FIGURE 3 in Complete mitochondrial genome and taxonomic revision of Cardiodactylus muiri Otte, 2007 (Gryllidae: Eneopterinae: Lebinthini)
FIGURE 3. Females of Cardiodactylus muiri Otte, 2007. A, walking on leaf litter during early night; B, ovipositing in a mossy tree root at night; in Kumawa (Papua, Indonesia).
FIGURE 8 in Complete mitochondrial genome and taxonomic revision of Cardiodactylus muiri Otte, 2007 (Gryllidae: Eneopterinae: Lebinthini)
FIGURE 8. Percentage of pairwise identical bases (% identity) of mitogenome and each gene between the two subfamilies and within Gryllinae.
FIGURE 2 in An additional record of Fejervarya manoharani Garg and Biju from the Western Ghats with a description of its complete mitochondrial genome
FIGURE 2. Newly collected specimens of Fejervarya manoharani from a new locality in the Western Ghats. (a-c) Lateral, lateral view with vocal sac and dorsal, (d) Ventral view of snout, ventral view of (e) foot (f) hand of a male in life (ZSI A 14170), and (g–h) lateral and dorsal view of another male (ZSI A 14171).
FIGURE 4 in An additional record of Fejervarya manoharani Garg and Biju from the Western Ghats with a description of its complete mitochondrial genome
FIGURE 4. Map showing the organization of genes in the mitochondrial genome of Fejervarya manoharani. Arrow represents the direction of gene transcription.
FIGURE 1. A in An additional record of Fejervarya manoharani Garg and Biju from the Western Ghats with a description of its complete mitochondrial genome
FIGURE 1. A map showing the distribution of our specimens, F. manoharani and F. rufescens in Western Ghats of India.
High genomic plasticity and unique features of Xanthomonas translucens pv. graminis revealed through comparative analysis of complete genome sequences
<p><strong>Background:</strong> <i>Xanthomonas</i> <i>translucens</i> pv. <i>graminis</i> (<i>Xtg</i>) is a major bacterial pathogen of economically important forage grasses, causing severe yield losses. So far, genomic resources for this pathovar consisted mostly of draft genome sequences, and only one complete genome sequence was available, preventing comprehensive comparative genomic analyses. Such comparative analyses are essential in understanding the mechanisms involved in the virulence of pathogens and to identify virulence factors involved in pathogenicity.</p><p><strong>Results:</strong> In this study, we produced high-quality, complete genome sequences of four strains of <i>Xtg</i>, complementing the recently obtained complete genome sequence of the <i>Xtg </i>pathotype strain. These genomic resources allowed for a comprehensive comparative analysis, which revealed a high genomic plasticity with many chromosomal rearrangements, although the strains were highly related, with 99.9 to 100% average nucleotide identity. A high number of transposases were exclusively found in <i>Xtg </i>and corresponded to 413 to 457 insertion/excision transposable elements per strain. These mobile genetic elements are likely to be involved in the observed genomic plasticity and may play an important role in the adaptation of <i>Xtg</i>. The pathovar was found to lack a type IV secretion system, and it possessed the smallest set of type III effectors in the species. However, three XopE and XopX family effectors were found, while in the other pathovars of the species two or less were present. Additional genes that were specific to the pathovar were identified, including a unique set of minor pilins of the type IV pilus, 17 TonB-dependent receptors (TBDRs), and 11 degradative enzymes. </p><p><strong>Conclusion:</strong> These results suggest a high adaptability of <i>Xtg</i>, conferred by the abundance of mobile genetic elements, which may have led to the loss of many features. Conserved features that were specific to <i>Xtg </i>were identified, and further investigation will help to determine genes that are essential to pathogenicity and host adaptation of <i>Xtg</i>.</p>
Figure 1 in Two new decapod (Crustacea: Malacostraca) complete mitochondrial genomes: bearings on the phylogenetic relationships within the Decapoda
Figure 1. Mitochondrial genome maps of Alpheus distinguendus and Panulirus ornatus. Protein-coding genes in the majority strand (J strand) are transcribed in a clockwise direction, except for those in the minority strand (N strand) indicated by underlining. The two ribosomal RNA genes are encoded by the N strand. All the darkly coloured transfer RNA (tRNA) genes encoded by the J and N strand are presented outside and inside the circular gene map, respectively. The tRNA genes are given as single-letter amino acid codes, except those encoding leucine and serine, which are labelled L1 (trnL(CUN)) and L2 (trnL (UUR)), and as S1 (trnS(AGN)) and S2 (trnS(UCN)), respectively. Numbers inside the circles represent the size of the fragments separating two adjacent genes (positive values) or the amount of shared nucleotides between two overlapping genes (negative values).
Figure 3 in Two new decapod (Crustacea: Malacostraca) complete mitochondrial genomes: bearings on the phylogenetic relationships within the Decapoda
Figure 3. The secondary structures of the noncoding regions in the mt genome of Panulirus ornatus and Panulirus japonicus are labelled by A and B, respectively. The duplicate 89 bp sequences in the noncoding region of P. ornatus are compared in their secondary structures by arrows pointing to four numbers i.e. 1, 89, 428, and 516 sites in A, which correspond to Repeat sequence 1 and 2 (RS1 & RS2), in C.
Figure 2 in Two new decapod (Crustacea: Malacostraca) complete mitochondrial genomes: bearings on the phylogenetic relationships within the Decapoda
Figure 2. Comparisons amongst the putative secondary structures for functional trnR (CGA) (A) and pseudogene-like trnS (AGN) (B) from the mitochondrial (mt) genome of Alpheus distinguendus, and the functional trnS (AGN) (C) from the mt genome of Panulirus ornatus. AU/GC pairs are indicated by dashes and GU bonds are indicated by dots. The nucleotide base located in the third codon positions of pseudogene-like trnS (AGN) is G instead of the usual base U, which is indicated by an arrow.
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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)
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.