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68 results for “environmental sequencing”
IBP-database and environmental IBP sequences for functional analysis of microalgae
<p>Database for analysis of ice binding protein (IBP) sequences (Uhlig et al. (2015)):</p> <p>(1) DUF3494_seqs_Uniprot.fasta: full length sequences with DUF3494 domain used for the calculation of the backbone tree in the phylogenetic placement</p> <p>(2) env_IBPs.fasta: potential IBP sequences from one Arctic and five Antarctic sea ice metatranscriptomes (Sanger or 454)</p> <p>(3) DUF3494_substree_fig2a_UniprotIDs.txt: UniProtIDs for subtree in Fig 2a</p> <p>(4) DUF3494_confirmed_IBPactivity_UniprotIDs.txt: UniProtIDs for sequences with confirmed IBP function of the protein</p> <p>If using this dataset please cite the following publication: Uhlig, C., Kilpert, F., Frickenhaus, S., Kegel, J.U., Krell, A., Mock, T., Valentin, K., Beszteri, B., (2015) The significance of antifreeze proteins for eukaryotic microbial communities of Arctic and Antarctic sea ice, The ISME Journal, 9, 2537–2540, doi:10.1038/ismej.2015.43</p>
Raw sequencing data PhD Mixoplankton spatio-temporal diversity and its environmental drivers in the North Sea
<p>Raw sequencing data PhD Mixoplankton spatio-temporal diversity and its environmental drivers in the North Sea</p>
A Comprehensive Assessment of Demographic, Environmental and Host Genetic Associations with Gut Microbiome Diversity in Healthy Individuals (16S rRNA gene sequencing data)
<p>Microbiome data accompanying manuscript "A Comprehensive Assessment of Demographic, Environmental and Host Genetic Associations with Gut Microbiome Diversity in Healthy Individuals". Data is available for alpha- and beta- diversity, as well as for individual taxa both in binary and quantitative phenotypic representation. Data is available for 827 individuals that gave consent for their data to be shared outside of the Milieu intérieur consortium. </p>
Distribution System Environmental and Sequencing Datasets for Assessing the Impacts of Lead Corrosion Control on the Microbial Ecology and Abundance of Drinking Water Associated Pathogens in a Full-Scale Drinking Water Distribution System
<p>The dataset of environmental parameters and sequence fastqs used to create figures and do analysis in the paper <strong>Assessing the Impacts of Lead Corrosion Control on the Microbial Ecology and Abundance of Drinking Water Associated Pathogens in a Full-Scale Drinking Water Distribution System </strong>submitted to Environmental Science & Technology</p>
Data from: Accumulation curves of environmental DNA sequences predict coastal fish diversity in the Coral Triangle
Environmental DNA (eDNA) has the potential to provide more comprehensive biodiversity assessments particularly for vertebrates in species-rich regions. Yet, this method requires the completeness of a reference database, i.e. a list of DNA sequences attached to each species, which is never met. As an alternative, a diversity of Operational Taxonomic Units (OTUs) can be extracted from eDNA metabarcoding. However, the extent to which the diversity of OTUs provided by a limited eDNA sampling effort can predict regional species diversity is unknown. Here, by modelling OTU accumulation curves of eDNA seawater samples across the Coral Triangle, we obtained an asymptote reaching 1,531 fish OTUs while 1,611 fish species are recorded in the region. Besides, we also accurately predict (R² = 0.92) the distribution of species richness among fish families from OTU-based asymptotes. Thus, the multi-model framework of OTU accumulation curves extends the use of eDNA metabarcoding in ecology, biogeography and conservation.
Influence of Quaternary environmental changes on mole populations inferred from mitochondrial sequences and evolutionary rate estimation
<p><span><span><span><span><span><span><span><span><span><span><span>Quaternary environmental changes fundamentally influenced genetic diversity of the temperate-zone terrestrial animals, including those on the Japanese Archipelago. The genetic diversity of present-day populations are taxon and region specific, but its determinants are poorly understood. Here, we analyzed cytochrome <i>b</i> gene (<i>Cytb</i>) sequences (1,140 bp) of mitochondrial DNA (mtDNA) to elucidate factors determining the genetic variation in three species of large moles: <i>Mogera imaizumii</i> and <i>Mogera wogura</i> occur in Northern and Southern mainland Japan (Honshu, Shikoku, and Kyushu), and <i>Mogera robusta </i>occurs on the nearby Asian continent<i>.</i> Network construction with the <i>Cytb</i> sequences revealed 10 star-shaped clusters with apparent geographic affinity. Mismatch distribution analysis showed that modes of pairwise nucleotide differences (t values) were grouped into five classes in terms of the level, implying the occurrence of five stages for the rapid expansion. It is conceivable that a severe cold periods and a subsequent warm periods during the late Quaternary are responsible for the population expansion events. The first and third oldest events include island-derived haplotypes, indicative of involvement of land bridge formation between remote islands, hence suggesting association of the ends of the penultimate (PGM, ca. 130,000 years ago) and last (LGM, ca. 15,000 years ago) glacial maxima, respectively. Since the third one is followed by the fourth one, it is plausible that the termination of Younger Dryas and subsequent abrupt warming at ca. 11,500 years ago facilitated the fourth expansion event. The second is most likely corresponding to the early marine isotope stage (MIS) 3 (ca. 53,000 years ago) when the glaciation and subsequent warming period are predicted to have influenced biodiversity. Utilization of the critical times of 130,000, 53,000, 15,000, and 11,500, years ago as calibration points yielded evolutionary rates of 0.03, 0.045, 0.10 and 0.10 substitutions/site/million years, respectively, showing the time-dependent manner whose pattern is similar to that seen in small rodents reported in our previous studies. The age of the fifth expansion event was calculated to be 5,800 years ago with the rate of 0.10 substitutions/site/million years ago, during the mid-Holocene, suggestive of influence of humans or other unspecified reason, such as the Jomon marine transgression. </span></span></span></span></span></span></span></span></span></span></span></p>
Single-Cell RNA-Sequencing Reveals Placental Response under Environmental Stress
<p>This repository provides scRNA-seq data corresponding to the manuscript "Single-Cell RNA-Sequencing Reveals Placental Response under Environmental Stress" by Van Buren, Azzara, Rangel-Moreno, de la Luz Garcia-Hernandez, Murphy, Cohen, Lin, and Park. The repository includes both count by gene matrices output from CellRanger version 6.0.1 (file names *_filtered_feature_matrix.h5 for each of the eight samples Control_1_M, Control_1_F, Control_2_M, Control_2_F, As_1_M, As_1_F, As_2_M, As_2_F), and a finalized Seurat object including cell type assignments as used for analyses in the manuscript (file name final_Seurat_obj.RData). Accompanying code used in analysis can be found at https://github.com/edvanburen/placenta_code.</p>
Comprehensive, targeted eukaryotic metagenomics analysis of environmental DNA biodiversity using Oxford Nanopore sequencing
<p><span>Metagenomics has become a prominent technology for studying the functional potential of all organisms in a microbial and eukaryotic community. The study of symbiotic organisms from different classes or kingdoms, including those previously unknown, is possible with simultaneous and equally efficient metagenomic analysis of these species. A variety of targeted primer sets are used for eukaryotic metagenomic biodiversity, including those that are universal for specific families, classes</span><span>,<span> or kingdoms. The most universal for all existing cellular organisms is the presence of ribosomal RNA encoding gene sequences. For eukaryotic sequences, these are 16S and 23s rDNA, </span>and <span>for eukaryotic sequences of nuclear (18S and 28S) and mitochondrial (12S and 16S) ribosomal RNA. Here we present the application of the eukaryotic metagenomics approach to the simultaneous, quantitative</span>,<span> and unbiased identification of most eukaryotic species. To achieve this, we have developed a universal PCR assay that targets the most conservative nuclear regions of the ribosomal gene for all cellular organisms, including plants, algae, fungi, protists, insects</span>,<span> and animals. The amplification product contains polymorphic regions of both ribosomal genes and the intergenic spacer. The size of the PCR products varies by class, kingdom</span>,<span> or domain, ranging from 2 kb for fungi to 7 kb for birds. This assay is also adapted for use with the Oxford Nanopore Rapid Barcoding Library Kit, which enables metagenomic biodiversity analysis. Our approach provides a rapid, sensitive</span>,<span> and equally efficient way to study the composition of eDNA from mixed species in the environment. This protocol reduces the time and cost of metagenomic biodiversity analysis using Oxford Nanopore sequencing. We can efficiently analyze the biodiversity of mixed species present in environmental samples.</span></span></p>
Oxford Nanopore sequencing for comprehensive, targeted eukaryotic metagenomics analysis of environmental DNA biodiversity
<p><span>The study of symbiotic organisms from different classes or kingdoms, including those previously unknown, is possible with simultaneous and equally efficient metagenomic analysis of these species. A variety of targeted primer sets are used for eukaryotic metagenomic biodiversity, including those that are universal for specific families, classes</span><span>,<span> or kingdoms. The most universal for all existing cellular organisms is the presence of ribosomal RNA encoding gene sequences. For eukaryotic sequences, these are 16S and 23s rDNA, </span>and <span>for eukaryotic sequences of nuclear (18S and 28S) and mitochondrial (12S and 16S) ribosomal RNA. Here, we present the application of the eukaryotic metagenomics approach to the simultaneous, quantitative</span>,<span> and unbiased identification of most eukaryotic species. </span></span></p>
Environmental effects of the December 2020 earthquake sequence near Petrinja, Croatia
<p>Those files (Spreadsheet of observations of coseismic deformation features, Surface rupture shapefile) are in support of the paper submitted to Geophysical Journal International. The data have been collected by the coauthors of this paper, implemented in the files by them, and the database has been processed and verified by SB, AT, SP.</p> <p>The complete of authors of the paper is as follows:</p> <p>S. Baize<sup>1</sup>, S. Amoroso<sup>2,3</sup>, N. Belić<sup>4</sup>, L. Benedetti<sup>5</sup>, P. Boncio<sup>2</sup>, M. Budić<sup>4</sup>, F.R. Cinti<sup>3</sup>, M. Henriquet<sup>5</sup>, P. Jamšek Rupnik<sup>6</sup>, B. Kordić<sup>4</sup>, S. Markušić<sup>7</sup>, L. Minarelli<sup>3</sup>, D. Pantosti<sup>3</sup>, S. Pucci<sup>3</sup>, M. Špelić<sup>4</sup>, A. Testa<sup>2</sup>, S. Valkaniotis<sup>8</sup>, M. Vukovski<sup>4</sup>, J. Atanackov<sup>6</sup>, J. Barbača<sup>4</sup>, M. Bavec<sup>6</sup>, R. Brajkovič<sup>6</sup>, V. Brčić<sup>4</sup>, M. Caciagli<sup>3</sup>, B. Celarc<sup>6</sup>, R. Civico<sup>3</sup>, P.M. De Martini<sup>3</sup>, R. Filjak<sup>4</sup>, F. Iezzi<sup>2</sup>, A. Moulin<sup>5</sup>, T. Kurečić<sup>4</sup>, M. Métois<sup>9</sup>, R. Nappi<sup>3</sup>, A. Novak<sup>6,10</sup>, M. Novak<sup>6</sup>, B. Pace<sup>2</sup>, D. Palenik<sup>4</sup>, T. Ricci<sup>3</sup></p> <p><sup>1</sup> Institut de Radioprotection et de Sûreté Nucléaire, IRSN/PRP-ENV/SCAN/BERSSIN, 92262 Fontenay-Aux-Roses, France</p> <p><sup>2</sup> Università “G. d'Annunzio” Chieti - Pescara, Via dei Vestini 31, 66100, Chieti, Italy</p> <p><sup>3</sup> Istituto Nazionale di Geofisica e Vulcanologia, Via di Vigna Murata 605, 00143 Rome, Italy</p> <p><sup>4</sup> Croatian Geological Survey, Department of Geology, Sachsova 2, Zagreb, 10000, Croatia</p> <p><sup>5</sup> Aix Marseille Univ, CNRS, IRD, INRAE, CEREGE, Aix-en-Provence, France</p> <p><sup>6</sup> Geological Survey of Slovenia, GeoZS, Dimičeva ulica 14, 1000 Ljubljana, Slovenia</p> <p><sup>7</sup> University of Zagreb, Faculty of Science, Department of Geophysics, Zagreb, Croatia</p> <p><sup>8</sup> Department of Civil Engineering, Polytechnic School, Democritus University of Thrace, 67100 Xanthi, Greece</p> <p><sup>9 </sup>Laboratoire de Géologie de Lyon (LGLTPE), Université Claude Bernard Lyon 1, campus de La Doua, 69100 Villeurbane, France</p> <p><sup>10 </sup>University of Ljubljana, Faculty of Natural Sciences and Engineering, Department of Geology, Croatia</p>
Urban Stream Environmental and Sequencing Datasets for Exploring the Impacts of Full-Scale Distribution System Orthophosphate Corrosion Control Implementation on the Microbial Ecology of Hydrologically Connected Urban Streams
<p>The dataset of environmental parameters and sequence fastqs used to create figures and do analysis in the paper <strong>Exploring the Impacts of Full-Scale Distribution System Orthophosphate Corrosion Control Implementation on the Microbial Ecology of Hydrologically Connected Urban Streams </strong>submitted to Applied and Environmental Microbiology. </p>
DNA sequences of transgenes detected via environmental DNA (raw ABI files, processed FASTA files, and reference alignments)
We demonstrate that simple, non-invasive environmental DNA (eDNA) methods can detect transgenes of genetically modified (GM) animals from terrestrial and aquatic sources in invertebrate and vertebrate systems. We detected transgenic fragments between 82-234 bp through targeted PCR amplification of environmental DNA extracted from food media of GM fruit flies (<i>Drosophila melanogaster</i>), feces, urine, and saliva of GM laboratory mice (<i>Mus musculus</i>), and aquarium water of GM tetra fish (<i>Gymnocorymbus ternetzi</i>). With rapidly growing accessibility of genome-editing technologies such as CRISPR, the prevalence and diversity of GM animals will increase dramatically. GM animals have already been released into the wild with more releases planned in the future. eDNA methods have the potential to address the critical need for sensitive, accurate, and cost-effective detection and monitoring of GM animals and their transgenes in nature.
The topological nature of tag jumping in environmental DNA metabarcoding studies (sequencing raw data)
<p>Metabarcoding of environmental DNA constitutes a state-of-the-art tool for environmental studies. One fundamental principle implicit in most metabarcoding studies is that individual sample amplicons can still be identified after being pooled with others – based on their unique combinations of tags – during the so-called demultiplexing step that follows sequencing. Nevertheless, it has been recognized that tags can sometimes be changed (i.e. tag jumping), which ultimately leads to sample crosstalk. Here, using four DNA metabarcoding datasets derived from the analysis of soils and sediments, we show that tag jumping follows very specific and systematic patterns. Specifically, we find a strong correlation between the number of reads in blank samples and their topological position in the tag matrix (described by vertical and horizontal vectors). This observed spatial pattern of artefactual sequences could be explained by polymerase activity, which leads to the exchange of the 3' tag of single stranded tagged sequences through the formation of heteroduplexes with mixed barcodes. Importantly, tag jumping substantially distorted our datasets – despite our use of methods suggested to minimize this error. We developed a topologic model to estimate the noise based on the counts in our blanks, which suggested that 40-80% of the taxa in our soil and sedimentary samples were likely false positives introduced through tag jumping. We highlight that the amount of false positive detections caused by tag jumping strongly biased our community analyses. </p>
Metadata for: Environmental adaptations by the intertidal Antarctic cyanobacterium Halotia branconii CENA392 as revealed using long-read genome sequencing
<p>Antarctica poses numerous challenges to life such as cold shock, low nutrient concentrations and periodic desiccation over a wide range of extreme temperatures. Cyanobacteria survive this harsh environment having evolved adaptive metabolic plasticity to become the dominant primary producers. The type strain cyanobacterium <em>Halotia branconii</em> CENA392 was isolated from an Antarctic intertidal seashore. The complete circular genome of this strain is presented herein, which was assembled using long sequence reads. The genome encoded some stress-related genes associated with low-temperature adaptation and biosynthesis of mycosporine-like amino acid (MAA) photoprotective compounds. Empirical experimentation demonstrated constitutive production of the MAA porphyra-334 and total carotenoids without exposure to low temperatures or ultraviolet radiation stress. Phylogenetic analysis provided insights on the taxonomic placement and the evolutionary history of some annotated genes. These data exemplify the importance of generating complete quality genome sequences of microorganisms isolated from extreme intertidal environments, facilitating in-depth evaluation of ecological and taxonomic inferences.</p>
Fastq sequence files supporting: Assessing the degradation of environmental DNA and RNA based on genomic origin in a metabarcoding context
<p>Molecular tools of species identification based on eNAs (environmental nucleic acids; eDNA and eRNA) have the potential to greatly transform biodiversity science. However, the ability of eNAs to obtain "real-time" biodiversity estimates may be complicated by the differential persistence and degradation dynamics of the molecular template (eDNA or eRNA) and the barcode marker used. Here, we collected water samples over a 28-day period to comparatively assess species detection using eDNA and eRNA metabarcoding of two distinct barcode markers—a mitochondrial mRNA marker (COI) and a nuclear rRNA marker (18S)—following complete removal of <em>Arthropoda </em>taxa in a semi-natural freshwater system. Our findings demonstrate that <em>Arthropoda </em>community composition was largely influenced by marker choice, rather than molecular template, individual microcosm, or sampling time point. Further, although eRNA may capture similar species diversity as the established eDNA method, this finding may be marker dependent. Although we found little to no difference in decay rates observed among sample groups (COI eDNA, COI eRNA, 18S eDNA, 18S eRNA), this result is likely due to limitations in the ability of eNA-based metabarcoding to provide a strong correlation between true eNA copy numbers present in the environment and final read counts obtained (following the metabarcoding workflow). Collectively, our findings provide further support for the use of multi-marker assessments in metabarcoding surveys to unravel the broadest taxonomic diversity possible, highlight the limitations of eNA metabarcoding methods in providing accurate decay rate estimates, as well as establish the need for further comparative studies using both metabarcoding and single-species detection methods to assess the persistence and degradation dynamics of eNAs for a diverse range of taxa.</p>
Data from: Detecting aquatic invasive species in bait and pond stores with targeted environmental (e) DNA high-throughput sequencing metabarcode assays: angler, retailer, and manager implications
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DNA sequences of transgenes detected via environmental DNA (raw ABI files, processed FASTA files, and reference alignments)
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Fastq sequence files supporting: Assessing the degradation of environmental DNA and RNA based on genomic origin in a metabarcoding context
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Influence of Quaternary environmental changes on mole populations inferred from mitochondrial sequences and evolutionary rate estimation
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Habitats and environmental variables investigated in a diversity survey on Polynucleobacter bacteria revealed by amplicon sequencing of priB genes
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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OpenNeuro
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