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19,342 results for “sequence”
Multi-Domain Translation between Single-Cell Imaging and Sequencing Data using Autoencoders
<p>This record contains raw data related to the article "Multi-Domain Translation between Single-Cell Imaging and Sequencing Data using Autoencoders".</p>
Immigration of Sogatella furcifera from the Greater Mekong Subregion into northern China revealed by 2b-RAD sequencing
Background The white-backed planthopper (WBPH), Sogatella furcifera (Horváth) (Hemiptera, Delphacidae), is a migratory pest of rice in Asia. Shandong Province, in northern China, is located on the migration pathway of WBPH between southern and northeast China. The potential sources of WBPH in northern China are poorly understood. We studied the sources of WBPH in Shandong Province by determining the population genetic structure of WBPH in 18 sites distributed in Shandong and in six regions of the Greater Mekong Subregion (GMS). We used mitochondrial gene and single-nucleotide polymorphism (SNP) markers (2b-RAD sequencing) for analysis. Results All of the WBPH populations studied in the seven regions had low genetic diversity. Pairwise F ST values ranged from -0.061 to 0.285, while F ST based on SNP data ranged from -0.007 to 0.009. These two molecular markers revealed that 4.40% (mtDNA) and 0.19% (SNP) genetic variation could be explained by the interpopulation variation, while the rest came from intrapopulation variation. The populations in the seven geographic regions comprised four hypothetical genetic clusters (K = 4) not associated with geographic location. Eighty-four of 129 individuals distributed across the given area were designated as recent migrants or of admixed ancestry. Although the substantial migration presented, a weak but significant correlation between genetic and geographic distances was found (r = 0.083, P = 0.004). Conclusion GMS was the main source of WBPH in Shandong, while other source populations may also exist. The genetic structure of WBPH is shaped by both migration and geographic barriers. These results help clarify the migration route and the source of WBPH in northern China.
Utilizing next-generation sequencing to identify prey DNA in western North Atlantic grey seal (Halichoerus grypus) diet
<p>Increasing grey seal (<i>Halichoerus grypus</i>) abundance in coastal New England is leading to social, political, economic, and ecological controversies. We studied grey seal feeding habits through next-generation sequencing of prey DNA using 16S amplicons from seal scat (N = 74) collected from a breeding colony on Monomoy Island in Massachusetts, U.S. and report frequency of occurrence and relative read abundance. We also assigned seal sex to scat samples using a revised PCR assay. In contrast to current understanding of grey seal diet from hard parts and fatty acid analysis, we found no significant difference between male and female diet measured by alpha and beta diversity. Overall, we detected 24 prey groups, 18 of which resolved to species. Sand lance (<i>Ammodytes</i> spp.) was the most frequently consumed prey group, with a frequency of occurrence (FO) of 97.3%, consistent with previous studies, but Atlantic menhaden (<i>Brevoortia tyrannus</i>), the second most frequently consumed species (FO = 60.8%), has not been documented in U.S. grey seal diet previously. Our results suggest that a metabarcoding approach to seal food habits can yield important new ecological insights, but that traditional hard parts analysis does not underestimate consumption of Atlantic cod (<i>Gadus morhua; </i>FO =<i> </i>6.7% Gadidae spp.) and salmon (<i>Salmo salar; </i>FO = 0%), two particularly valuable species of concern.</p>
Next-generation sequencing of DNA from resting eggs: signatures of eutrophication in a lake's sediment
<p>Supplementary data</p>
Near-complete sequence of a novel reovirus genome identified from Callinectes sapidus
<p>The Atlantic blue crab, <i>Callinectes sapidus</i>,<i> </i>is an estuarine keystone species that functions as both predator and prey in food webs and supports a multi-million dollar fishery along the western Atlantic coast from the US mid-Atlantic to southern Brazil. Throughout their range, blue crabs are host to viral, bacterial, fungal, protozoan, and metazoan pathogens. <span class="fontstyle01"><span>Reoviruses are non-enveloped icosahedral viruses with genomes comprised of 9 to 12 segments of linear double-stranded RNA (dsRNA). They have been found in diverse host species including brachyuran crustaceans. </span></span>This work describes the sequence of a novel reovirus genome, discovered in <i>Callinectes sapidus</i>. The <span class="fontstyle01"><span>double-stranded RNA</span></span> genome of CsRV2 consists of 12 segments that encode 13 putative proteins. High nucleotide sequence identity with <span class="fontstyle01"><span><i>Eriocheir sinensis</i></span></span><span class="fontstyle01"><span> Reovirus 905 </span></span>revealed this virus belongs to <i>Cardoreovirus </i>within the <i>Reoviridae </i>family.</p>
Data for bioinformatics practical course (TP) 1 - Whole Genome Sequencing (WGS)
<p>This data are fastq (.fq) files for the Whole Genome Sequencing (WGS) TP1 (09/12/2020) of the Master Infectiologie-Vaccinologie (University of Tours)</p>
Shards, sequences, and shorelines: two new species of Bembidion from North America (Coleoptera: Carabidae)
<p>Two new species of <i>Bembidion</i> are described from river shores in North America. One, <b><i>Bembidion mimbres </i>sp. nov.</b>, from the Gila River watershed in the lands of the Mimbres culture in New Mexico and Arizona, is closely related to the widespread <i>Bembidion levigatum</i>. DNA sequences from several linkage groups provide evidence of the distinctiveness of <i>B. mimbres</i>. The second, <b><i>Bembidion corgenoma </i>sp. nov</b>., has been the subject of recent genomic and transcriptomic studies. It belongs in the <i>Bembidion transversale</i> subgroup, and occurs from California north to British Columbia, east to Montana and Nevada. The <i>B. transversale</i> subgroup as a whole is reviewed, and characters that distinguish <i>B. corgenoma</i> from the similar and sympatric <i>B. transversale</i> and <i>B. erosum</i> are described and illustrated. DNA sequences of these three species show no consistent differences in 28S, COI, CAD, and Topoisomerase, and a coalescent species delimitation analysis reveals no notable structure within the complex. This is the first known trio of species within <i>Bembidion</i> for which those genes provide no clear signal of species boundaries. A neotype is designated for the one name in the group that lacks a primary type, <i>Bembidium haplogonum</i> Chaudoir. Chromosomes of the new species and their relatives are as is typical for <i>Bembidion</i>, with 11 pairs of autosomes and an XY/XX sex chromosome system.</p>
Decentralized Runtime Enforcement of Message Sequences in Message-Based Systems (video)
<p>Full video presentation of the paper: Decentralized Runtime Enforcement of Message Sequences in Message-Based Systems.<br> <br> Appears in Session 6 of the 24th International Conference on Principles of Distributed Systems OPODIS 2020<br> <a href="https://opodis2020.unistra.fr">https://opodis2020.unistra.fr</a></p>
Coregonus spp. opsin amplicon sequence alignments
<p>Local adaptation can drive diversification of closely related species across environmental gradients and promote convergence of distantly related taxa that experience similar conditions. We examined a potential case of adaptation to novel visual environments in a species flock (Great Lakes salmonids, genus <i>Coregonus</i>) using a new amplicon genotyping protocol on the Oxford Nanopore Flongle. Five visual opsin genes were sequenced for individuals of <i>C. artedi</i>,<i> C. hoyi</i>,<i> C. kiyi</i>, and <i>C. zenithicus.</i> Comparisons revealed species-specific differences in a key spectral tuning amino acid in <i>rhodopsin</i> (Tyr261Phe substitution), suggesting local adaptation of <i>C. kiyi </i>to the blue-shifted depths of Lake Superior. Ancestral state reconstruction demonstrates that parallel evolution and "toggling" at this amino acid residue has occurred several times across the fish tree of life, resulting in identical changes to the visual systems of distantly related taxa across replicated environmental gradients. Our results suggest that ecological differences and local adaptation to distinct visual environments are strong drivers of both evolutionary parallelism and diversification.</p>
Quantifying transmission dynamics of acute hepatitis C virus infections in a heterogeneous population using sequence data
<p>This upload contains data and all the scripts required to reproduce the results of the artice entitled "Quantifying transmission dynamics of acute hepatitis C virus infections in a heterogeneous population using sequence data".</p> <p><strong>Code is located within Code.zip</strong> . It contains scripts in R and Bash and launchers. Some of the scripts require data files contained within Data.zip.</p> <p><strong>Data is located within Data.zip</strong> , such as the sequences, the inferred phylogeny and the Beast XML file.</p>
The influence of intraspecific sequence variation during DNA metabarcoding: A case study of eleven fungal species
<p><span><span><span><span><span><span><span><span><span><span><span>DNA metabarcoding has become a powerful approach for analyzing complex communities from environmental samples, but there are still methodological challenges limiting its full potential. While conserved DNA markers, like 16S and 18S, often are not able to discriminate among closely related species, other more variable markers – like the fungal ITS region, may include considerable intraspecific variation, which can lead to over-splitting of species during DNA metabarcoding analyses. Here we assess the effects of intraspecific sequence variation in DNA metabarcoding, by analyzing local populations of eleven fungal species. We investigated the allelic diversity of ITS2 haplotypes using both Sanger sequencing and high throughput sequencing (HTS) coupled with error correction with the software <span><span><span><span><span><span>dada2</span></span></span></span></span></span>. All focal species, except one, included some level of intraspecific variation in the ITS2 region. Overall, we observed a high correspondence between haplotypes generated by Sanger sequencing and HTS, with the exception of a few additional haplotypes detected using either approach. These extra haplotypes, often occurring in low frequencies, were likely due to PCR and sequencing errors or intragenomic variation in the rDNA region. The presence of intraspecific (and possibly intragenomic) variation in ITS2 suggest that haplotypes (or ASVs) should not be used as basic units in ITS-based fungal community analyses, but an extra clustering step is needed to reach species-level resolution. </span></span></span></span></span></span></span></span></span></span></span> </p> <p> </p>
Helicos direct RNA sequencing of FPA mutants and overexpressors
<p>Genes involved in disease resistance are some of the fastest evolving and most diverse components of genomes. Large numbers of nucleotide-binding, leucine-rich repeat receptor (NLR) genes are found in plant genomes and are required for disease resistance. However, NLRs can trigger autoimmunity, disrupt beneficial microbiota or reduce fitness. It is therefore crucial to understand how NLRs are controlled. Here we show that the RNA-binding protein FPA mediates widespread premature cleavage and polyadenylation of NLR transcripts, controlling their functional expression and impacting immunity. Using long-read nanopore direct RNA sequencing we resolve the complexity of NLR transcript processing and gene annotation. Our results uncover a co-transcriptional layer of NLR control with implications for understanding the regulatory and evolutionary dynamics of NLRs in the immune responses of plants.</p>
Kraken analysis from shotgun sequenced museum specimens via krona plot visualization
<p>This dataset contains html files with krona plots from Kraken analysis on shotgun sequenced museum specimens.</p>
FIGURE 19 in Three new species and DNA sequence data of the rare South American water beetle genus Adelphydraena Perkins, 1989 (Coleoptera: Hydraenidae)
FIGURE 19. Phylogenetic tree obtained with IQ-TREE. Numbers in nodes, ultrafast bootstrap / SH-like aLRT support.
FIGURES 14–15. 14 in Three new species and DNA sequence data of the rare South American water beetle genus Adelphydraena Perkins, 1989 (Coleoptera: Hydraenidae)
FIGURES 14–15. 14. Geographical distribution of Adelphydraena species. 15. Type locality of Adelphydraena spinosa, in Guyana. Photo. by A. Short.
FIGURES 16–18 in Three new species and DNA sequence data of the rare South American water beetle genus Adelphydraena Perkins, 1989 (Coleoptera: Hydraenidae)
FIGURES 16–18. Habitats of Adelphydraena species. 16–17. Collecting locality of Adelphydraena orchymonti, in Venezuela, Amazonas prov., Cerro Cuau env. 18. Collecting locality of Adelphydraena spangleri, in Venezuela, Bolívar prov., La Gran Sabana, Yaro Parú. Photos. by F. Čiampor.
FIGURES 11–12. 11. Adelphydraena spinosa n in Three new species and DNA sequence data of the rare South American water beetle genus Adelphydraena Perkins, 1989 (Coleoptera: Hydraenidae)
FIGURES 11–12. 11. Adelphydraena spinosa n. sp., spermatheca and terminal abdominal segments. 12. Adelphydraena surinamensis n. sp., spermatheca and terminal abdominal segments.
FIGURES 5–6. 5 in Three new species and DNA sequence data of the rare South American water beetle genus Adelphydraena Perkins, 1989 (Coleoptera: Hydraenidae)
FIGURES 5–6. 5. Adelphydraena spangleri Perkins, non-type aedeagus and last tergites. 6. Adelphydraena surinamensis n. sp., holotype aedeagus and last tergite.
FIGURES 9–10. 9. Adelphydraenaspinosa n in Three new species and DNA sequence data of the rare South American water beetle genus Adelphydraena Perkins, 1989 (Coleoptera: Hydraenidae)
FIGURES 9–10. 9. Adelphydraenaspinosa n. sp., holotypeaedeagus. 10. Adelphydraenaorchymonti Perkins, non-type, aedeagus.
A multi-tiered sequence capture strategy spanning broad evolutionary scales: application for phylogenetic and phylogeographic studies of orchids
<p><span><span><span><span><span><span><span><span><span><span><span>With over 25,000 species, the drivers of diversity in the Orchidaceae remain to be fully understood. Here we outline a multi-tiered sequence capture strategy aimed at capturing 100's of loci to enable phylogenetic resolution from subtribe to subspecific levels in orchids of the tribe Diurideae. For the probe design, we mined subsets of 18 transcriptomes, to give five target sequence sets aimed at the tribe (Sets 1 & 2), subtribe (Set 3), and within subtribe levels (Sets 4 & 5). Analysis included alternative <i>de novo </i>and reference-guided assembly, before target sequence extraction, annotation and alignment, and application of a homology-aware <i>k-mer</i> block phylogenomic approach, prior to phylogenetic inference using maximum-likelihood. Our evaluation considered 87 taxa in two test datasets: 67 samples spanning the tribe, and 72samples involving 24 closely related <i>Caladenia</i> species. The tiered design achieved high target loci recovery (>89%), with the median number of recovered loci in Sets 1–5 as follows: 212, 219, 816, 1024, and 1009, respectively. Interestingly, as a first test of the homologous <i>k</i>-mer approach for targeted sequence capture data, our study revealed its potential for enabling robust phylogenetic species tree inferences. Specifically, we found matching, and in one case improved phylogenetic resolution within species complexes, compared to conventional phylogenetic analysis involving target gene extraction. Our findings indicate that a customised multi-tiered sequence capture strategy, in combination with promising yet under-utilized phylogenomic approaches, will be effective for groups where interspecific divergence is recent, but information on deeper phylogenetic relationships is also required.</span></span></span></span></span></span></span></span></span></span></span></p>
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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.