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Figures 24–25 in DNA sequencing reveals three new species of Chamberlainium (Corallinales, Rhodophyta) from South Africa, all formerly passing under Spongites yendoi
Figures 24–25: Vertical section through the outer thallus showing spermatangial conceptacle primordium with peripheral roof development (black arrows) and simple spermatangial systems (black arrowheads) confined to the conceptacle floor. Note the protective layer of epithallial cells (white arrow). Scale bar = 50 μm. Vertical section through the outer thallus showing a mature, raised spermatangial conceptacle with the mucilage plug (white arrow) that occludes the pore opening and simple, spermatangial systems (white arrowheads) confined to the conceptacle floor. Note that the pore canal is lined with terminal, elongate initials (black arrowheads) that project into the pore canal as papillae. Scale bar = 50 μm.
Figure 1 in DNA sequencing reveals three new species of Chamberlainium (Corallinales, Rhodophyta) from South Africa, all formerly passing under Spongites yendoi
Figure 1: Map of South Africa (gray shade), with an inset of False Bay, showing the coastal provinces, the biogeographic marine provinces and the approximate locations of collecting sites (● = Chamberlainium capense, ■ = C. glebosum,: = C. occidentale).
Figures 7–11 in DNA sequencing reveals three new species of Chamberlainium (Corallinales, Rhodophyta) from South Africa, all formerly passing under Spongites yendoi
Figures 7–11: Chamberlainium capense habit and vegetative anatomy. (7) Rock fragment showing holotype specimen (white arrow) (L 3986119, tetrasporangial). Scale bar = 20 mm. (8) Encrusting to variably lumpy and slightly protuberant, epilithic thalli showing crusts abutting and easily discernible. Scale bar = 10 mm. (9) Vertical section through the margin (black arrow) showing the monomerous thallus construction with plumose medulla (M) giving rise to cortical filaments (C) that terminate in a single layer of epithallial cells (black arrowhead) (UWC 16/17). Scale bar = 50 μm. (10) Vertical section of the inner thallus showing cell fusions (f) between adjacent medullary filaments (UWC 16/17). Scale bar = 20 μm. (11) Vertical section of the outer thallus showing a single layer of epithallial cells (e) subtended by a layer of subepithallial initials (i). Note the paired, bottle-shaped trichocytes (t) (UWC 16/24). Scale bar = 20 μm.
Figures 4–6 in DNA sequencing reveals three new species of Chamberlainium (Corallinales, Rhodophyta) from South Africa, all formerly passing under Spongites yendoi
Figures 4–6: Habit photographs of Chamberlainium capense, C. glebosum and C. occidentale. (4) Chamberlainium capense is moderately thick to mostly lumpy and only slightly protuberant. Scale bar = 20 mm. (5) Chamberlainium glebosum is thick, very lumpy and highly protuberant. Scale bar = 20 mm. (6) Chamberlainium occidentale is morphologically highly variable, occurring as thin encrusting (smooth) to thick warty (mostly) to lumpy plants, and are only slightly protuberant. Scale bar = 30 mm.
Figures 15–18 in DNA sequencing reveals three new species of Chamberlainium (Corallinales, Rhodophyta) from South Africa, all formerly passing under Spongites yendoi
Figures 15–18: Chamberlainium capense tetrasporangial anatomy. (15) Vertical section through the outer thallus showing a later stage tetrasporangial conceptacle primordium with peripheral roof development (black arrowheads) and tetrasporangial initials (t) arranged peripherally around a central columella (c). Note the persisting layer of protective epithallial cells (black arrow) (L 3986119). Scale bar = 50 μm. (16) Vertical section through a mature, raised tetrasporangial conceptacle showing tetrasporangia (t) with a stalk cell (black arrowhead), peripherally arranged around a well-defined central columella (C). Note the remains of a corona (white arrow) that surrounds the pore opening (L 3986119). Scale bar = 50 μm. (17) Vertical section through a mature raised tetrasporangial conceptacle showing tetrasporangia (t) with stalk cells (black arrowheads), appearing to be arranged across the chamber floor as the columella (c) has disintegrated. Note the absence of the corona (white arrow) (UWC 16/09). Scale bar = 50 μm. (18) Magnified view of the pore canal of a mature tetrasporangial conceptacle showing the base of the pore canal sunken (black arrowheads) into the chamber with terminal, elongate initials near the base pointing downward (black arrows) and the remains of a corona (white arrow) that surrounds and occludes the pore opening. (L 3986119). Scale bar = 20 μm.
Figures 12–14 in DNA sequencing reveals three new species of Chamberlainium (Corallinales, Rhodophyta) from South Africa, all formerly passing under Spongites yendoi
Figures 12–14: Chamberlainium capense spermatangial anatomy (UWC 16/21). (12) Vertical section through the outer thallus showing a spermatangial conceptacle primordium with peripheral roof development (black arrows) and simple, spermatangial systems (black arrowheads) confined to the conceptacle floor. Note the protective layer of epithallial cells (white arrow). Scale bar = 50 μm. (13) Vertical section through a mature, raised spermatangial conceptacle showing the mucilage plug (white arrowhead) that occludes the pore opening and simple, spermatangial systems (black arrowheads) confined to the conceptacle floor. Scale bar = 50 μm. (14) Magnified view through a mature spermatangial conceptacle showing the mucilage plug (white arrowhead) that occludes the pore opening and simple, spermatangial systems (black arrowheads) confined to the conceptacle floor. Note that the pore canal is lined with terminal, elongate initials (black arrows) that project into the pore canal as papillae. Scale bar = 20 μm.
Figure 3 in DNA sequencing reveals three new species of Chamberlainium (Corallinales, Rhodophyta) from South Africa, all formerly passing under Spongites yendoi
Figure 3: Bayesian inference tree based on rbcL sequences. Species with sequenced type/'topotype' material are highlighted in bold. Generitype species within Corallinales are identified by a star (+). Species names are followed by their GenBank accession number and their geographic location, including ocean basin where needed. Numbers in brackets, following the GenBank accession numbers, are the total number of identical sequences. Bootstrap support (BS) and Bayesian posterior probability (BPP) values are provided at branch nodes. BS and BPP values = 100 % and = 1 respectively, are denoted by an asterisk (*); BS and BPP values <75 % and <0.75 respectively. Atl = Atlantic Ocean, Ind = Indian Ocean, Med = Mediterranean, Pac = Pacific Ocean.
Figure 2 in DNA sequencing reveals three new species of Chamberlainium (Corallinales, Rhodophyta) from South Africa, all formerly passing under Spongites yendoi
Figure 2: Maximum likelihood tree based on psbA sequences. Species with sequenced type/'topotype' material are highlighted in bold. Generitype species and molecular references for generitype species within the Corallinales are identified by a star (+). Species names are followed by their GenBank accession number and their geographic location, including ocean basin where needed. Numbers in brackets, following the GenBank accession numbers, are the total number of identical sequences. Bootstrap support (BS) and Bayesian posterior probability (BPP) values are provided at branch nodes. BS and BPP values = 100% and = 1 respectively, are denoted by an asterisk (*); BS and BPP values <75 % and <0.75 respectively, are not shown. Atl = Atlantic Ocean, Ind = Indian Ocean, Med = Mediterranean, Nam = Namibia, NZ = New Zealand, Pac = Pacific Ocean.
Figure 2 in Examining metrics and magnitudes of molecular genetic differentiation used to delimit cetacean subspecies based on mitochondrial DNA control region sequences
Figure 2. Relationship between ΦST and Nei's estimate of net divergence (dA) among cetacean population, subspecies, and species pairs estimated using mitochondrial DNA control region sequence data. Specific values mentioned in the text are numbered: 1 = Neophocaena species; 2 = killer whale populations. The three green squares in the left-hand side of the figure (ΦST <0.07) represent, from bottom to top, the subspecies comparisons for S. attenuata, S. longirostris, and L. obscurus, respectively.
Figure 1 in Examining metrics and magnitudes of molecular genetic differentiation used to delimit cetacean subspecies based on mitochondrial DNA control region sequences
Figure 1. Box and whisker plots showing median and 1st and 3rd quartiles, and minimum and maximum values for six metrics of genetic divergence among cetacean population, subspecies, and species pairs estimated using mitochondrial DNA control region sequence data.
RNAseq sequences of the study "Transactive response DNA-binding Protein (TARDBP/TDP-43) regulates early HIV-1 entry and infection" (1/2)
<p>Each pair of FASTQ files corresponds to a specific sample condition:</p> <table> <thead> <tr> <th scope="col">Condition</th> <th scope="col">Sample</th> <th scope="col">FASTQ name R1</th> <th scope="col">FASTQ name R2</th> </tr> </thead> <tbody> <tr> <td>Cneg</td> <td>RNASEQ-AVF1</td> <td>RNASEQ-AVF1_S1_R1_001.fastq.gz</td> <td>RNASEQ-AVF1_S1_R2_001.fastq.gz</td> </tr> <tr> <td>Flag-wt-TDP-43</td> <td>RNASEQ-AVF2</td> <td>RNASEQ-AVF2_S2_R1_001.fastq.gz</td> <td>RNASEQ-AVF2_S2_R2_001.fastq.gz</td> </tr> <tr> <td>Flag-NLS-mut-TDP-43</td> <td>RNASEQ-AVF3</td> <td>RNASEQ-AVF3_S3_R1_001.fastq.gz</td> <td>RNASEQ-AVF3_S3_R2_001.fastq.gz</td> </tr> <tr> <td>Cneg</td> <td>RNASEQ-AVF4</td> <td>RNASEQ-AVF4_S4_R1_001.fastq.gz</td> <td>RNASEQ-AVF4_S4_R2_001.fastq.gz</td> </tr> <tr> <td>Scramble</td> <td>RNASEQ-AVF5</td> <td>RNASEQ-AVF5_S5_R1_001.fastq.gz</td> <td>RNASEQ-AVF5_S5_R2_001.fastq.gz</td> </tr> <tr> <td>TDP-43 siRNA A</td> <td>RNASEQ-AVF6</td> <td>RNASEQ-AVF6_S6_R1_001.fastq.gz</td> <td>RNASEQ-AVF6_S6_R2_001.fastq.gz</td> </tr> <tr> <td>TDP-43 siRNA B</td> <td>RNASEQ-AVF7</td> <td>RNASEQ-AVF7_S7_R1_001.fastq.gz</td> <td>RNASEQ-AVF7_S7_R2_001.fastq.gz</td> </tr> <tr> <td>TDP-43 siRNA C</td> <td>RNASEQ-AVF8</td> <td>RNASEQ-AVF8_S8_R1_001.fastq.gz</td> <td>RNASEQ-AVF8_S8_R2_001.fastq.gz</td> </tr> </tbody> </table> <p> </p>
RNAseq sequences of the study "Transactive response DNA-binding Protein (TARDBP/TDP-43) regulates early HIV-1 entry and infection" (2/2)
<p>Each pair of FASTQ files corresponds to a specific sample condition:</p> <table> <thead> <tr> <th scope="col">Condition</th> <th scope="col">Sample</th> <th scope="col">FASTQ name R1</th> <th scope="col">FASTQ name R2</th> </tr> </thead> <tbody> <tr> <td>TDP-43 siRNA D</td> <td>RNASEQ-AVF9</td> <td>RNASEQ-AVF9_S1_R1_001.fastq.gz</td> <td>RNASEQ-AVF9_S1_R2_001.fastq.gz</td> </tr> <tr> <td>Cneg</td> <td>RNASEQ-AVF10</td> <td>RNASEQ-AVF10_S2_R1_001.fastq.gz</td> <td>RNASEQ-AVF10_S2_R2_001.fastq.gz</td> </tr> <tr> <td>Flag-wt-TDP-43</td> <td>RNASEQ-AVF11</td> <td>RNASEQ-AVF11_S3_R1_001.fastq.gz</td> <td>RNASEQ-AVF11_S3_R2_001.fastq.gz</td> </tr> <tr> <td>Flag-NLS-mut-TDP-43</td> <td>RNASEQ-AVF12</td> <td>RNASEQ-AVF12_S4_R1_001.fastq.gz</td> <td>RNASEQ-AVF12_S4_R2_001.fastq.gz</td> </tr> <tr> <td>Cneg</td> <td>RNASEQ-AVF13</td> <td>RNASEQ-AVF13_S5_R1_001.fastq.gz</td> <td>RNASEQ-AVF13_S5_R2_001.fastq.gz</td> </tr> <tr> <td>Scramble</td> <td>RNASEQ-AVF14</td> <td>RNASEQ-AVF14_S6_R1_001.fastq.gz</td> <td>RNASEQ-AVF14_S6_R2_001.fastq.gz</td> </tr> <tr> <td>Oligos B+C</td> <td>RNASEQ-AVF15</td> <td>RNASEQ-AVF15_S7_R1_001.fastq.gz</td> <td>RNASEQ-AVF15_S7_R2_001.fastq.gz</td> </tr> <tr> <td>Oligos A+B+C</td> <td>RNASEQ-AVF16</td> <td>RNASEQ-AVF16_S8_R1_001.fastq.gz</td> <td>RNASEQ-AVF16_S8_R2_001.fastq.gz</td> </tr> </tbody> </table> <p> </p>
MetaCOXI: An integrated collection of metazoan cytochrome oxidase subunit-I DNA sequences
<p><strong>MetaCOXI Sequences Taxonomy and Metadata</strong></p> <p>This collection is based on the integration of the European Nucleotide Archive (ENA, release 142) and the Barcode of Life Data Systems (BOLD: <a href="http://www.boldsystems.org/">http://www.boldsystems.org/</a>) data.</p> <p><strong>CONTENT: </strong>Currently it contains 5,608,848 entries of metazoan COXI sequences and their corresponding taxonomic classification and metadata. <em>MetaCOXI_Seqs.tar.gz</em> contains the full sequence collection in 'fasta' format. <em>MetaCOXI_Taxonomy_Metadata.tar.gz</em> contains the entries-associated taxonomy path and additional metadata</p> <p>Taxonomic path are provided for the following seven levels with their NCBI-TaxIDs: Kingdom, Phylum, Class, Order, Family, Genus, Species.</p> <p>For additional information visit: https://github.com/bachob5/MetaCOXI</p>
Data from: Restriction site-associated DNA sequencing reveals local adaptation despite high levels of gene flow in Sardinella lemuru (Bleeker, 1853) along the northern coast of Mindanao, Philippines
<p>Stock identification and delineation are important in the management and conservation of marine resources. These were highlighted as priority research areas for Bali sardinella (<em>Sardinella lemuru</em>) which is among the most commercially important fishery resources in the Philippines. Previous studies have already assessed the stocks of <em>S. lemuru</em> between Northern Mindanao Region (NMR) and Northern Zamboanga Peninsula (NZP), yielding conflicting results. Phenotypic variation suggests distinct stocks between the two regions, while mitochondrial DNA did not detect evidence of genetic differentiation for this high gene flow species. This paper tested the hypothesis of regional structuring using genome-wide single nucleotide polymorphisms (SNPs) acquired through restriction-site associated DNA sequencing (RADseq). We examined patterns of population genomic structure using a full panel of 3,573 loci, which was then partitioned into a neutral panel of 3,348 loci and an outlier panel of 31 loci. Similar inferences were obtained from the full and neutral panels, which were contrary to the inferences from the outlier panel. While the full and neutral panels suggested a panmictic population (global F<sub>ST</sub> ~ 0, p > 0.05), the outlier panel revealed genetic differentiation between the two regions (global F<sub>ST</sub> = 0.161, p = 0.001; F<sub>CT</sub> = 0.263, p < 0.05). This indicated that while gene flow is apparent, selective forces due to environmental heterogeneity between the two regions play a role in maintaining adaptive variation. Annotation of the outlier loci returned five genes that were mostly involved in organismal development. Meanwhile, three unannotated loci had allele frequencies that correlated with sea surface temperature. Overall, our results provided support for local adaptation despite high levels of gene flow in <em>S. lemuru</em>. Management therefore should not only focus on demographic parameters (e.g., stock size, catch volume), but also consider the preservation of adaptive variation.</p>
MetaCOXI: An integrated collection of metazoan cytochrome oxidase subunit-I DNA sequences
<p><strong>MetaCOXI Sequences in fasta format</strong></p> <p>This collection is based on the integration of the European Nucleotide Archive (ENA, release 142) and the Barcode of Life Data Systems (BOLD: http://www.boldsystems.org/) data.</p> <p><strong>CONTENT: </strong>Currently it contains 5,608,848 entries of metazoan COXI sequences and their corresponding taxonomic classification and metadata. MetaCOXI_Seqs_1.tar.gz contains the full sequence collection in 'fasta' format. MetaCOXI_Taxonomy_Metadata.tar.gz contains the entries-associated taxonomy path and additional metadata</p> <p>Taxonomic path are provided for the following seven levels with their NCBI-TaxIDs: Kingdom, Phylum, Class, Order, Family, Genus, Species.</p> <p>For additional information visit: https://github.com/bachob5/MetaCOXI</p>
Fig. 3 in Application Of Dna Barcoding In Taxonomy And Phylogeny: An Individual Case Of Coi Partial Gene Sequencing From Seven Animal Species
Fig. 3. Phylogenetic position of Macrobiotus sp., Bayesian inference phylogenetic tree. Sequences obtained by us are written in bold.
Fig. 1 in Application Of Dna Barcoding In Taxonomy And Phylogeny: An Individual Case Of Coi Partial Gene Sequencing From Seven Animal Species
Fig. 1. Phylogenetic position of D. lindholmi and L. a. exigua, Bayesian inference phylogenetic tree. Sequences obtained by us are written in bold.
Morphological and DNA sequence data generated by Sanger sequencing and target capture methods for moss plants in the genus Fissidens from herbarium specimens
<p><span>Morphological evolution in mosses has long been hypothesized to accompany shifts in microhabitats and can be tested using comparative phylogenetics. These lines of inquiry have developed substantially, in part, by target capture sequencing allowing for phylogenomic scale data generated from herbarium specimens. In the present study, we test the relationship between taxonomically important morphological characters in the moss genus <em>Fissidens</em>, using both a 400-locus dataset generated using a target-capture approach as well as a three-locus phylogeny generated using sanger sequencing. Phylogenetic trees were generated using ASTRAL and Bayesian Inference and used to test the monophyly of subgenera/sections and provided the basis for ancestral character reconstruction and phylogenetic correlation analyses among five morphological characters as well as habitat moisture scored from literature. The characters <em>axillary hyaline nodules</em>, <em>limbidium</em>, <em>costa</em>, and <em>peristome morphology</em> as well as <em>sexual system</em>, <em>minimum habitat moisture</em>, <em>average habitat moisture</em>, <em>maximum habitat moisture</em>, and <em>habitat moisture niche breadth</em> each exhibit statistically significant phylogenetic signal. Significant correlations were found between the limbidium (phyllid/leaf border) and habitat moisture niche breadth, which could be interpreted as a more extensive <em>limbidium</em> enabling species to survive across a wider variety of habitats. Correlations were also found between <em>costa anatomy</em> and the <em>limbidum</em> of the gametophyte and sporophyte <em>peristome</em> <em>morphology</em>, as well as <em>average habitat moisture</em> and <em>sexual system</em>. Continued exploration of the relationships between morphological evolution, life history, and habitat will enable us to expand our understanding of functional morphology in mosses.</span></p>
Mitochondrial DNA sequencing results control and MELAS fibroblasts. Povea-Cabello, S. et al 2022.
<p>Mitochondrial DNA sequencing results from control and MELAS patients-derived dermal fibroblasts. Povea-Cabello, S. et al 2022. </p>
Parent-of-origin detection and chromosome-scale haplotyping using long-read DNA methylation sequencing and Strand-seq
<p>Hundreds of loci in human genomes have alleles that are methylated differentially according to their parent of origin. These imprinted loci generally show little variation across tissues, individuals, and populations. We show that such loci can be used to distinguish the maternal and paternal homologs for all autosomes, without the need for the parental DNA. We integrate methylation-detecting nanopore sequencing with the long-range phase information in Strand-seq data to determine the parent of origin of chromosome-length haplotypes for both DNA sequence and DNA methylation in five trios with diverse genetic backgrounds.</p>
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)
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.