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1,696 results for “DNA sequence”
Data from: Sequence capture versus restriction site associated DNA sequencing for shallow systematics
Sequence capture and restriction site associated DNA sequencing (RAD-Seq) are two genomic enrichment strategies for applying next-generation sequencing technologies to systematics studies. At shallow timescales, such as within species, RAD-Seq has been widely adopted among researchers, although there has been little discussion of the potential limitations and benefits of RAD-Seq and sequence capture. We discuss a series of issues that may impact the utility of sequence capture and RAD-Seq data for shallow systematics in non-model species. We review prior studies that used both methods, and investigate differences between the methods by re-analyzing existing RAD-Seq and sequence capture datasets from a Neotropical bird (Xenops minutus). We suggest that the strengths of RAD-Seq datasets for shallow systematics are the wide dispersion of markers across the genome, the relative ease and cost of laboratory work, the deep coverage and read overlap at recovered loci, and the high overall information that results. Sequence capture's benefits include flexibility and repeatability in the genomic regions targeted, success using low-quality samples, more straightforward read orthology assessment, and higher per-locus information content. The utility of a method in systematics, however, rests not only on its performance within a study, but on the comparability of datasets and inferences with those of prior work. In RAD-Seq datasets, comparability is compromised by low overlap of orthologous markers across species and the sensitivity of genetic diversity in a dataset to an interaction between the level of natural heterozygosity in the samples examined and the parameters used for orthology assessment. In contrast, sequence capture of conserved genomic regions permits interrogation of the same loci across divergent species, which is preferable for maintaining comparability among datasets and studies for the purpose of drawing general conclusions about the impact of historical processes across biotas. We argue that sequence capture should be given greater attention as a method of obtaining data for studies in shallow systematics and comparative phylogeography.
FIGURE 2 in Mitochondrial DNA sequence analysis of the spectacled salamander, Salamandrina terdigitata (Urodela: Salamandridae), supports the existence of two distinct species
FIGURE 2. Map of Italy showing the sampling sites of Salamandrina terdigitata.
Data from: Advanced characterization of DNA molecules in rAAV vector preparations by single-stranded virus next-generation sequencing
Recent successful clinical trials with recombinant adeno-associated viral vectors (rAAVs) have led to a renewed interest in gene therapy. However, despite extensive developments to improve vector-manufacturing processes, undesirable DNA contaminants in rAAV preparations remain a major safety concern. Indeed, the presence of DNA fragments containing antibiotic resistance genes, wild-type AAV, and packaging cell genomes has been found in previous studies using quantitative polymerase chain reaction (qPCR) analyses. However, because qPCR only provides a partial view of the DNA molecules in rAAV preparations, we developed a method based on next-generation sequencing (NGS) to extensively characterize single-stranded DNA virus preparations (SSV-Seq). In order to validate SSV-Seq, we analyzed three rAAV vector preparations produced by transient transfection of mammalian cells. Our data were consistent with qPCR results and showed a quasi-random distribution of contaminants originating from the packaging cells genome. Finally, we found single-nucleotide variants (SNVs) along the vector genome but no evidence of large deletions. Altogether, SSV-Seq could provide a characterization of DNA contaminants and a map of the rAAV genome with unprecedented resolution and exhaustiveness. We expect SSV-Seq to pave the way for a new generation of quality controls, guiding process development toward rAAV preparations of higher potency and with improved safety profiles.
Phylogeny of the supertribe Nebriitae (Coleoptera: Carabidae) based on analyses of DNA sequence data
<p>The phylogeny of the carabid beetle supertribe Nebriitae is inferred from analyses of DNA sequence data from eight gene fragments including one nuclear ribosomal gene (28S), four nuclear-protein coding genes (CAD, topoisomerase 1, PEPCK and <i>wingless</i>) and three mitochondrial gene fragments (16S + tRNA-Leu + ND1, COI ("barcode" region) and COI ("Pat/Jer" region)). Our taxon sample included 264 exemplars representing 241 species and subspecies (25% of the known nebriite fauna), 39 of 41 currently accepted genera and subgenera (all except <i>Notiokasis</i> and <i>Archileistobrius</i>), and eight outgroup taxa. Separate maximum likelihood (ML) analyses of individual genes, combined ML analyses of nuclear, nuclear protein-coding and mitochondrial genes, and combined ML and Bayesian analyses of the eight-gene-fragment matrix resulted in a well-resolved phylogeny of the supertribe, with most nodes in the tree strongly supported. Within Nebriitae, 167 internal nodes of the tree (out of the maximum possible 255) are supported by maximum-likelihood bootstrap values of 90% or more. Tribes Notiophilini, Opisthiini, Pelophilini, Nebriini are well supported as monophyletic but relationships among these are not well resolved. <i>Nippononebria</i> is a distinct genus more closely related to <i>Leistus</i> than <i>Nebria</i>. <i>Archastes, Oreonebria, Spelaeonebria, and Eurynebria</i>, previously treated as distinct genera by some authors,<i> </i>are all nested within a monophyletic genus <i>Nebria. </i>Within <i>Nebria</i>, four major clades are recognized: (1) the <i>Oreonebria</i> Series, including eight subgenera arrayed in two subgeneric complexes (the <i>Eonebria</i> and <i>Oreonebria</i> Complexes); (2) the <i>Nebriola</i> Series, including only subgenus <i>Nebriola</i>; (3) the <i>Nebria</i> Series, including ten subgenera arrayed in two subgeneric complexes, the <i>Boreonebria</i> and <i>Nebria </i>Complexes, with the latter further subdivided into three subgeneric subcomplexes (the <i>Nebria</i>, <i>Epinebriola</i> and <i>Eunebria</i> Subcomplexes)); and (4) the <i>Catonebria</i> Series, including seven subgenera arrayed in two subgeneric complexes (the <i>Reductonebria</i> and <i>Catonebria</i> Complexes). A strong concordance of biogeography with the inferred phylogeny is noted and some evident vicariance patterns are highlighted. A revised classification, mainly within the Nebriini, is proposed to reflect the inferred phylogeny. Three genus-group taxa (<i>Nippononebria</i>, <i>Vancouveria</i> and <i>Archastes</i>) are given revised status and seven are recognized as new synonymies (<i>Nebriorites</i> Jeannel, 1941 and <i>Marggia</i> Huber, 2014 = <i>Oreonebria</i> Daniel, 1903; <i>Pseudonebriola</i> Ledoux and Roux, 1989 = <i>Boreonebria</i> Jeannel, 1937; <i>Patrobonebria </i>Bänninger, 1923, <i>Paranebria </i>Jeannel, 1937 and <i>Barbonebriola</i> Huber and Schmidt, 2017 = <i>Epinebriola</i> Daniel and Daniel, 1904; and <i>Asionebria</i> Shilenkov, 1982 = <i>Psilonebria</i> Andrewes, 1923). Six new subgenera are proposed and described for newly recognized clades: <i>Parepinebriola</i> Kavanaugh subgen. nov. (type species: <i>Nebria delicata </i>Huber and Schmidt, 2017), <i>Insulanebria</i> Kavanaugh subgen. nov. (type species: <i>Nebria carbonaria</i> Eschscholtz, 1829), <i>Erwinebria</i> Kavanaugh subgen. nov. (type species <i>Nebria sahlbergii</i> Fischer von Waldheim, 1828), <i>Nivalonebria</i> Kavanaugh subgen. nov. (type species: <i>Nebria paradisi</i> Darlington, 1931), <i>Neaptenonebria</i> Kavanaugh subgen. nov. (type species: <i>Nebria ovipennis </i>LeConte, 1878) and <i>Palaptenonebria</i> Kavanaugh subgen. nov. (type species: <i>Nebria mellyi</i> Gebler, 1847). Future efforts to better understand relationships within the supertribe should aim to expand the taxon sampling of DNA sequence data, particulary within subgenera <i>Leistus</i> and <i>Evanoleist</i>us of genus <i>Leistus</i> and the <i>Nebria</i> Complex of genus <i>Nebria</i>.</p>
ITS and nrLSU DNA sequence data from four species of Coreomyces (Laboulbeniomycetes)
<p>The genus <i>Coreomyces</i> (Laboulbeniaceae, Laboulbeniomycetes, Ascomycota) includes minute parasites on water boatmen (Corixidae, Hemiptera, Insecta). This taxonomic study is primarily based on freshly sampled corixids infected by <i>Coreomyces</i> from Sweden, although a few samples from Denmark and Turkey were also included. All records were verified using DNA sequence data from the internal transcribed spacer region and large subunit of the nuclear ribosomal DNA repeat region. We recognise four species, two of which are new to science: <i>Coreomyces confusus</i> H. Sundb. et al. sp. nov., <i>C. dextrorsus</i> H. Sundb. et al. sp. nov., <i>C. macropus</i> Thaxt., and <i>C. corixae</i> Thaxt. <i>C. corixae</i> is a new record for Denmark, Sweden, and Turkey, while <i>C. macropus</i> is a new record for Denmark and Sweden. All four species can inhabit two different yet distinct positions on the host. We observe that morphology is affected by the position on the host and that different species sharing the same position on the host tend to be difficult or impossible to separate on morphology only. We conclude that species circumscriptions in <i>Coreomyces</i> must be based on the integration of molecular and morphological data.</p>
Figure 1 in May a hybridogenetic complex regenerate the nuclear genome of both sexes of a missing ancestor? First evidence on the occurrence of a nuclear non-hybrid Squalius alburnoides (Cyprinidae) female based on DNA sequencing
Figure 1. Minimum spanning network among cytb haplotypes. The majority of the haplotypes (represented by circles) are exclusive of Squalius alburnoides (in grey) and of S. pyrenaicus (in white) individuals, except for the central one which is a haplotype shared between one S. alburnoides and two S. pyrenaicus individuals. NH indicates the haplotype of the non-hybrid female. The number of mutations between haplotypes is represented by small black dots.
Figures 6–9 in Suspended mummies in Aleiodes species (Hymenoptera: Braconidae: Rogadinae) with descriptions of six new species from western Uganda based largely on DNA sequence data
Figures 6–9. Automontage photographs of features of the Aleiodes buzurae-group. (6) A. buzurae, metasoma. (7)– (9) A. barnardae sp. n., habitus, face and metasoma, respectively.
Figure 5 in Suspended mummies in Aleiodes species (Hymenoptera: Braconidae: Rogadinae) with descriptions of six new species from western Uganda based largely on DNA sequence data
Figure 5. Two fragments of the ITS2 region aligned by eye showing marked differences between species in the Aleiodes buzurae-group. Asterisks and bold font indicate substitutions in length-conserved regions and lines show regions of length variation. Xs indicate uncertainty about number and identity of bases.
Fig. 2 in Two new Oriental species of Paramanota Tuomikoski (Diptera: Mycetophilidae), with DNA sequence data
Fig. 2. Paramanota trilobata, new species (holotype). A, Hypopygium, dorsal view; B, Hypopygium, ventral view; C, Outlines of aedeagus and associated structures, dorsal view; D, Antennal flagellomere 4, lateral view. Scale bar = 0.1 mm. cr = cercus, gs d = dorsal lobe of gonostylus, gs m = median lobe of gonostylus, gs v = ventral lobe of gonostylus, gx = gonocoxa, gx l = ventral gonocoxal lobe, hp = hypoproct, tg 9 = tergite 9, tg 10 = tergite 10.
Figure 53 in DNA sequences corroborate Soesiladeepakius as a non-salticoid genus of jumping spiders: placement with lapsiines, phylogeny, and description of six new species (Araneae, Salticidae)
Figure 53. Map of the Amazonian region showing species records.
Figure 3–4 in DNA sequences corroborate Soesiladeepakius as a non-salticoid genus of jumping spiders: placement with lapsiines, phylogeny, and description of six new species (Araneae, Salticidae)
Figure 3–4. Soesiladeepakius lyra sp. nov., male. 3, dorsal view. 4, lateral view.
Figure 1–2 in DNA sequences corroborate Soesiladeepakius as a non-salticoid genus of jumping spiders: placement with lapsiines, phylogeny, and description of six new species (Araneae, Salticidae)
Figure 1–2. Soesiladeepakius lyra sp. nov. 1, male. 2, female. Photos: G. R. S. Ruiz.
Figure 2 in Diet of the black rat (Rattus rattus) in a Canary laurel forest: species identification based on morphological markers and DNA sequences
Figure 2. Seed of Rubus bollei/palmensis found intact in rat dropping.
Supplementary material 1 from: Colgan DJ, Ahyong ST, Mardon K, Brereton IM (2021) Rare specimen identification in an un-integrated taxonomy: implications of DNA sequences from a Taiwanese Philine (Mollusca, Philinidae). ZooKeys 1060: 93-110. https://doi.org/10.3897/zookeys.1060.28809
Reconstructed micro-CT scan of C.559479
Figure 4 from: Colgan DJ, Ahyong ST, Mardon K, Brereton IM (2021) Rare specimen identification in an un-integrated taxonomy: implications of DNA sequences from a Taiwanese Philine (Mollusca, Philinidae). ZooKeys 1060: 93-110. https://doi.org/10.3897/zookeys.1060.28809
Figure 4 Phylogenetic relationships of C.559479 based on maximum likelihood analysis of the reduced 16S rRNA dataset. More distant outgroups have been removed and the topology rooted on Philine scabra + P. indistincta. Numbers near nodes refer to bootstrap percentages above 70%. The scale bar indicates 0.05 changes per site. Sequences are identified by accession number and species name or informal designation recorded in GenBank except those labelled P. quadripartita for which the species names have been changed for reasons outlined in the text. Accessions with an sp. number designation followed by a space and "TO" with a one or two digit designation refer to sequences from Oskars et al. (2015). Note that this article refers to the undescribed species in alphabetical rather than numerical order so that sp. 4 in GenBank is identified as sp. D in Oskars et al. (2015).
Supplementary material 2 from: Colgan DJ, Ahyong ST, Mardon K, Brereton IM (2021) Rare specimen identification in an un-integrated taxonomy: implications of DNA sequences from a Taiwanese Philine (Mollusca, Philinidae). ZooKeys 1060: 93-110. https://doi.org/10.3897/zookeys.1060.28809
Figure S1. Image from the reconstructed micro-CT scan of C.559479
Figure 3 from: Colgan DJ, Ahyong ST, Mardon K, Brereton IM (2021) Rare specimen identification in an un-integrated taxonomy: implications of DNA sequences from a Taiwanese Philine (Mollusca, Philinidae). ZooKeys 1060: 93-110. https://doi.org/10.3897/zookeys.1060.28809
Figure 3 C.559479, outer surface of gizzard plates from the micro-CT reconstruction A paired plate, left B unpaired plate C paired plate, right. Scale bar: 2 mm (A–C).
Figure 2 from: Colgan DJ, Ahyong ST, Mardon K, Brereton IM (2021) Rare specimen identification in an un-integrated taxonomy: implications of DNA sequences from a Taiwanese Philine (Mollusca, Philinidae). ZooKeys 1060: 93-110. https://doi.org/10.3897/zookeys.1060.28809
Figure 2 Micro-CT reconstruction images of C.559479 A ventral view of the shell B–D three perspectives from the reconstruction. Scale bar: 5 mm (A–D).
Figure 9 from: Spelda J, Reip H, Oliveira Biener U, Melzer R (2011) Barcoding Fauna Bavarica: Myriapoda – a contribution to DNA sequence-based identifications of centipedes and millipedes (Chilopoda, Diplopoda). ZooKeys 156: 123-139. https://doi.org/10.3897/zookeys.156.2176
Figure 9 - Neighbour-joining tree of COI sequence divergences (K2P model) of studied Julida. Note well-supported COI groups for each species allowing for sequence-based species identification. Numbers above and below branches show bootstrap values of NJ analysis, branch length indicates sequence divergence in %.
Figure 8 from: Spelda J, Reip H, Oliveira Biener U, Melzer R (2011) Barcoding Fauna Bavarica: Myriapoda – a contribution to DNA sequence-based identifications of centipedes and millipedes (Chilopoda, Diplopoda). ZooKeys 156: 123-139. https://doi.org/10.3897/zookeys.156.2176
Figure 8 - Neighbour-joining tree of COI sequence divergences (K2P model) of studied Polyxenida, Polydesmida and Glomerida. Solid circles: examples of excellent resolution of very close species of the genus Polydesmus. Numbers above and below branches show bootstrap values of NJ analysis, branch length indicates sequence divergence in %.
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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 is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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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.
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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.