Kantor, Rose · Shakya, Migun · Ruth, Nelson · et al.
2,095 rows · 907 KB · fasta, tsv
A virus genome database representing 21,015 near-complete virus genomes collected from untargeted ultra-deep RNA/DNA combined sequencing of wastewater. Sequence data was provided by the CASPER consortium and raw data may be found on NCBI SRA under bioprojects PRJNA1247874 and PRJNA1198001. Data underwent read trimming, rRNA and human read removal, de novo assembly, and selection of high-quality viral contigs. Contigs were clustered at 95% identity and 85% query coverage to dereplicate. Chimera-checking required at least two independent assemblies of the same viral genome or presence of the genome in another reference database. Annotation made use of RdRpCATCH, geNomad, checkV, BLASTN against NCBI core-nt, and RNAVirHost. The RdRp fasta files contain representative RdRp sequences identified through homology to major RdRp reference databases and clustered at 90% sequence identity over 75% sequence coverage. Included sequences contain all three conserved RdRp motifs (A, B, and C) arranged in either the canonical ABC configuration or the permuted CAB configuration.
Hubbard, Alfred · Solares, Edwin · Hemming-Schroeder, Elizabeth
88 rows · 18 KB · fasta
These are the files needed to run the Broad Institute's malaria amplicon pipeline for the PvGAP Plasmodium vivax panel, described in detail here . They consist of FASTA files containing the forward and reverse primers and another FASTA file containing reference sequences for each target, derived from the PvP01 reference genome.
This dataset supports the findings of the manuscript "Root anatomical traits modulate the assembly and nitrogen transformation potential of root-associated microbiomes in a temperate steppe" (NPH-MS-2026-55667). It contains root traits data, bacterial 16S rRNA gene absolute abundances, functional genes relative abundances, DNA extraction metadata, and phylogenetic marker sequences for 37 plant species from a temperate steppe ecosystem. The dataset includes the following files: 1. root traits.csv - Root traits including average diameter (AD), specific root length (SRL), specific root area (SRA), root tissue density (RTD), root nitrogen content (RNC), root carbon content (RCC), carbon‑nitrogen ratio (RCN), cortex layer number (CLN), cortex thickness (CT), and the ratio of cortex thickness to root diameter (CTRD). The first column lists plant species names. 2. Absolute abundance of 16S rRNA gene.csv - Quantitative PCR (qPCR) derived absolute abundances of bacterial 16S rRNA gene copies (copies/ng DNA) across different root compartments (rhizosphere, rhizoplane, endosphere), host species, root orders, and cotyledon classes (monocot/dicot). 3. DNA extraction sample weight.csv - Fresh weight (grams) of root material used for DNA extraction for each sample, linked by SampleID to the abundance data. 4. DNA extraction concentration.csv - Qubit‑measured DNA concentrations (ng/μL) and the sample volume (μL) used for quality control, together with sample metadata. 5. 37species.fasta - DNA sequences of two chloroplast markers (matK and rbcL) for the 37 plant species included in the study. The sequences are in FASTA format with headers formatted as ">Species". These were used for host phylogeny construction and Pagel's λ analyses. 6. Quantitative PCR results of functional gene.csv - Quantitative PCR (qPCR) derived relative abundances of bacterial 16S rRNA gene and functional genes across different root compartments (rhizosphere, rhizoplane, endosphere), host species, root orders, and cotyledon classes (monocot/dicot). 7. README.md - A detailed description of each file, column headers, abbreviations, units, and any missing value codings (NA). All data are provided to ensure transparency and reproducibility of the analyses. For methodological details, please refer to the Materials and Methods section of the associated publication. These data are under embargo until the associated research article is published. After that date, they will be freely available under a Creative Commons Attribution 4.0 International (CC BY 4.0) license. During the embargo period, the metadata (title, authors, abstract) and the DOI remain publicly visible, but the data files are not accessible. For access requests before the embargo expires, please contact the corresponding author.
Requena Rolanía, Jose María · Greif, Gonzalo · ROBELLO, CARLOS
1 files · 8.0 MB · fasta
This dataset contains the genome sequence for Trypanosoma cruzi (strain Dm28c). This genome sequence was de novo assembled using PacBio Hi-Fi and Illumina sequencing platforms by Greif et al (2026. PMID: 41501640). The genome was assembled into 32 contigs, which represent complete chromosomes. The provided Fasta file also contains an additional contig corresponding to the maxicircle (mitochondrial genome) sequence. The Fasta files included in this dataset were downloaded from GenBank (assembly GCA_044048535.1; May 22, 2026). Additional information about the Dm28cT2T genome assembly and gene annotations may be accessed through the link: https://cruzi.pasteur.uy/
Burman, Nathaniel · Buyukyoruk, Murat · Wiegand, Tanner · et al.
4 files · 8.0 MB · fasta
This folder contains a multiple sequence alignment of Cas7 homologs in .fasta format, the domain-level annotations from PFAM and CasFinder, and an associated phylogenetic tree in .newick format.
Geisler, Jan · Rakhimberdiev, Eldar · Boom, Michiel P. · et al.
29 files · 124 MB · csv, shapefiledeclared
1. Many migratory birds now reach their Arctic breeding grounds earlier in order to keep pace with advancing springs and shifting nutrient peaks, either by departing earlier from non-breeding grounds or by travelling faster. For dark-bellied brent geese, there is limited potential to travel faster, as their migration to the Siberian breeding grounds is already among the fastest of Arctic geese and swans. Earlier departure would require reaching departure body mass earlier, either through a faster accumulation of energy stores during spring staging or via adjustments earlier in the annual cycle. 2. We examined long-term shifts in spring staging phenology and changes in winter and spring body mass trajectories of brent geese at the population level, with particular emphasis on the effects of winter temperature on body mass and spring body mass on departure timing. 3. We used more than five decades of body mass measurements from individuals caught in the United Kingdom and France, and in the Dutch Wadden Sea to reconstruct changes in spring and winter mass trajectories, respectively. These data were combined with over five decades of migration counts in the Netherlands and more than two decades of counts in Denmark to quantify changes in spring staging phenology. 4. We found that brent geese have not shifted their spring arrival in the Wadden Sea but have advanced departure timing. Furthermore, brent geese were heavier during and after milder winters, and have changed mass trajectories over recent decades. They no longer lose mass during winter and the second spring staging phase, and fuelling rates in the first spring staging phase have declined. Annual variation in body mass was not related to annual departure timing. 5. These results suggest that milder winters have relaxed energetic constraints and improved body condition in brent geese throughout the non-breeding season. Our findings highlight the importance of considering the full annual cycle when assessing how animals with limited capacity to adjust migration timing or speed respond to global change.
A historical map showing a segment of the boundaries of New Spain in c. 1800. This map is fully open to fellow researchers and is available in multiple open source formats (SHP, GPKG, GeoJSON).
A historical map of the boundaries of Prussia in c. 1795. This map is fully open to fellow researchers and is available in multiple open source formats (SHP, GPKG, GeoJSON).
This dataset contains original geomorphic mapping of surface fault traces along the Dixie Valley Fault (DVF) range front and piedmont zone, central Nevada, USA. Traces were mapped directly from a 1-m bare-earth lidar digital elevation model (DEM), using hillshade and slope-raster visualizations. This dataset accompanies the manuscript: Francescone, M., et al. (in review), LiDAR-Based Fault-Scarp Analysis and Rupture Hazard Assessment: Earthquake Scenarios of the Dixie Valley Fault System (Nevada, USA). See Section 3.1 ("Fault Trace Mapping") of the manuscript for full methodological details
Meekes, Lisa · Tabaro, Francesco · Bexkens, Michiel · et al.
41 files · 8.2 GB · csv, fasta, pdfdeclared
This record contains the Python software for PEPTiGEN, a tool for generating tryptic peptides from prokaryotic gene sequences and their variants, and the associated antimicrobial resistance (AMR) peptide database. The database is provided as an SQL file and a CSV file containing all genes and predicted peptides. The README file contains explanation of the PEPTiGEN tool. The SQL database schema files contains both the database schema of the SQL database used in the PEPTiGEN analysis as the database schema of the AMR peptide datbase.
Despite the proliferation of social vulnerability assessment methodologies, selecting the most appropriate model remains a critical challenge due to inter-model variability. To explore the inter-model variability, this study systematically investigated inter-algorithmic and inter-classification variability to assess how methodological design influences outcomes.
Bir, Joyanta · Cancio, Ibon · Diaz de cerio, Oihane · et al.
3 files · 100 KB · fasta, xlsxdeclared
This data file contains the data associated with the manuscript entitled "Duplication of the Genes Coding the Proteins That Regulate RNA Polymerase III Activity and Differential Transcription in Tissues of Teleost Fish."
Mimet, Anne · Gourmemon, Damien · Amandine, Vergondy · et al.
14 files · 1.6 GB · shapefile, tiffdeclared
================================================================================ README ================================================================================ Dataset Title: Observation points, movement-proxy data, and high-resolution land cover map for the common blackbird ( Turdus merula ) in Angers, France Version: 1.0 Authors : Mimet, Anne ; Gourmelon Damien ; Oulhen, Thomas ; Vergondy, Amandine Date of biological data collection: Observation points : 15/05/2025 to 06/06/2025 Movement-proxy data : 19/04/2024 to 17/05/2024 -------------------------------------------------------------------------------- DESCRIPTION -------------------------------------------------------------------------------- This dataset contains observed presence/absence of blackbird flights across streets, as well as point observations of the common blackbird across Angers, France, during spring. The data were used to create a connectivity model for the common blackbird in Angers. The 68 point observations provided information on the land cover types used as a possible resource by the common blackbird. The presence/absence of flying blackbirds across 190 streets in Munich was used to derive the resistance of the urban landscape to the movement of common blackbirds in a landscape connectivity model. For the point observations, the presence and absence of the common blackbird was visually and acoustically confirmed after 5 minutes of observations within a radius of 25 m. Movement presence/absence was observed along 50 m street transects. Street transects were observed for 9 minutes, and the presence or absence of common blackbirds crossing this street was recorded. The observation points and movement-proxy data were selected along gradients of greenness and traffic density. -------------------------------------------------------------------------------- FILE LIST -------------------------------------------------------------------------------- 1. movement_proxy.shp Site-level data containing presence and absence of common blackbirds crossing the sampled streets, as well as covariates such as the number of pedestrians passing during the sampling period, geographic information, information on the weather, time of sampling, pseudonomized observer. Number of records: 190 Number of variables: 11 related files: movement_proxy.cpg, movement_proxy.dbf, movement_proxy.prj, movement_proxy.shp, movement_proxy.shx The related files are required because data is stored in a shapefile. For this shapefile to be correctly read by any GIS processing software, all related files need to be saved in the same folder. 2. point_observations.shp Site-level data containing presence and absence of common blackbirds at the observation points. Additionally, geographic and temporary information as well as information on the weather are provided. Number of records: 68 Number of variables: 10 related files: point_observations.cpg, point_observations.dbf, point_observations.prj, point_observations.shp, point_observations.shx The related files are required because data is stored in a shapefile. For this shapefile to be correctly read by any GIS processing software, all related files need to be saved in the same folder. 3. LULC_9Class_Angers.tif and assoociated qlm style file Land use and land cover map at 40 cm resolution for Angers. 3. README.txt This file. -------------------------------------------------------------------------------- VARIABLE DESCRIPTIONS: movement_proxy.shp -------------------------------------------------------------------------------- StreetCod Site identifier for street transect - these are the same sites as in the file Point_observations.shp (format: [text]) X Northing coordinate of the centre (latitude) (format: [degree]) Y Easting coordinate of the observation point (longitude) (format: [degree]) Obs Id of the observor (2 observors in the dataset) date Date of the observation (format [%d/%m/%y]) Daytime Starting time of observation (format: [text] hour%h%min) Windspeed Windspeed given by the mobile phone application « Accuweather » Temperatur Temperature at the time of observation in °C given by the mobile phone application « Accuweather » Pedestrian Number of pedestrians combined passing by during the time of observation CarDensity Number of cars counted on a 3-min period FlyBbird Number of common blackbirds Turdus merula that crossed the street transect during the time of observation (9 min). Every crossing event was counted. When the same individual crossed 2 times, it was counted 2 times -------------------------------------------------------------------------------- VARIABLE DESCRIPTIONS: point_observations.shp -------------------------------------------------------------------------------- StreetCod Site identifier for street transect - this are the same sites as in the file movement_proxy.shp (format: [text]) X Northing coordinate of observation point (latitude) (format: [degree]). Y Easting coordinate of the observation point (longitude) (format: [degree]) Obs Id of the observor (1 in this dataset) date Date of the observation (format [%d/%m/%y]) Daytime Starting time of observation (format: [text] hour%h%min) Windspeed Windspeed given by the mobile phone application « Accuweather » Temperatur Temperature at the time of observation in °C given by the mobile phone application « Accuweather » AbBlackb Number of common blackbirds Turdus merula that were detected by sight or sound during the 5-min observatin période, over a radius of 25 m. PABlackb Presence-Absence of observed blackbirds derived from the abundance. -------------------------------------------------------------------------------- VARIABLE DESCRIPTIONS: LULC_9Class_Angers.tif -------------------------------------------------------------------------------- 11 : Buildings < 5m 12 : Buildings 5-10m 13 : Buildings 10-18m 14 : Buildings > 18m 20 : Sealed areas 31 : vegetation < 1m 32 : Vegetation 1-3m 33 : Vegetation > 3m 40 : Farmland 50 : Bare soil 60 : Water -------------------------------------------------------------------------------- METHODS SUMMARY -------------------------------------------------------------------------------- Site Selection for Movement-Proxy Data: - 190 sites selected via stratified random sampling across vegetation cover (computed in a radius of 300m around the points) and traffic density (derived from TomTom navigation data for October 2022) - Observations along 50 m street transects - Detection of presence/absence of common blackbirds crossing the sampled streets Site Selection for Point Observations: - 68 sites selected via stratified random sampling across vegetation cover (computed in a radius of 300m around the points) and traffic density (derived from TomTom navigation data for October 2022) - Visual and acoustic detection of presence/absence of common blackbirds within a 25 m radius LULC map: Derived from land cover information from CoSIA (IGN 2023a), refined with a digital terrain model (IGN 2020) and height model (IGN 2023b) to extract building and vegetation height classes. -------------------------------------------------------------------------------- RELATED PUBLICATIONS -------------------------------------------------------------------------------- Lisa Merkens*, Meret Pundsack*, Anne Mimet*, Damien Gourmelon, Wolfgang W. Weisser. City-specific or generalisable resistances? An urban animal connectivity model performs better when parameterised from two cities. Preprint Submitted to Urban Ecosystems -------------------------------------------------------------------------------- FUNDING -------------------------------------------------------------------------------- Région Pays de la Loire through the PULSAR project VitalConnect (2024_05894 ) -------------------------------------------------------------------------------- LICENSE -------------------------------------------------------------------------------- This dataset is licensed under the Creative Commons Attribution 4.0 International License (CC-BY 4.0). You are free to: - Share: copy and redistribute the material in any medium or format - Adapt: remix, transform, and build upon the material for any purpose Under the following terms: - Attribution: You must give appropriate credit, provide a link to the license, and indicate if changes were made. Full license text: https://creativecommons.org/licenses/by/4.0/ -------------------------------------------------------------------------------- CITATION -------------------------------------------------------------------------------- If you use this dataset, please cite both the dataset and the associated publication: Dataset: Mimet, A., Gourmelon, D, Oulhen, T., Vergondy, A. (2026) Observation points, movement-proxy data, and high-resolution land cover map for the common blackbird (Turdus merula) in Angers, France [Dataset]. Zenodo. Publication: Lisa Merkens*, Meret Pundsack*, Anne Mimet*, Damien Gourmelon, Wolfgang W. Weisser. City-specific or generalisable resistances? An urban animal connectivity model performs better when parameterised from two cities. Preprint Submitted to Urban Ecosystems -------------------------------------------------------------------------------- CONTACT -------------------------------------------------------------------------------- Anne Mimet Université d'Angers Laboratoire BiodivAG, DEP ENS SCIENCES Biologie, UFR SCIENCES 2 Boulevard de Lavoisier, F-49045 Angers, France Email: anne.mimet@univ-angers.fr ORCID: 0000-0001-9498-436X ================================================================================ END OF README ================================================================================
This repository contains the complete chemosensory protein and nucleotide sequences, along with the results of evolutionary selection tests for 13 species of the genus Rhodnius . 1. Project Description This dataset supports the study of the chemosensory repertoire (ORs, GRs, IRs, OBPs, and CSPs) across 13 Rhodnius genomes. The study highlights the contrast between the conservation of Gustatory (GRs) and Ionotropic (IRs) receptors and the high dynamic evolution of Odorant Receptors (ORs), particularly in species adapted to human habitats. 2. Repository Structure 2.1 Sequence Data (FASTA) The following files contain all identified chemosensory genes in both amino acid ( .faa ) and nucleotide ( .fna ) formats: Rhodnius_OR_proteins.faa / Rhodnius_OR_CDS.fna : Odorant Receptors. Rhodnius_GR_proteins.faa / Rhodnius_GR_CDS.fna : Gustatory Receptors Rhodnius_IR_proteins.faa / Rhodnius_IR_CDS.fna : Ionotropic Receptors. Rhodnius_OBP_proteins.faa / Rhodnius_OBP_CDS.fna : Odorant-Binding Proteins. Rhodnius_CSP_proteins.faa / Rhodnius_CSP_CDS.fna : Chemosensory Proteins. 2.2 Phylogenetic Trees Archives containing the multiple sequence alignments and the resulting phylogenetic trees (Newick/Treefile format): OR_trees.zip : Alignment ( OR.ali.fasta ) and tree file ( OR.ali.treefile ) for Odorant Receptors. GR_trees.zip : Alignment ( GR.ali.fasta ) and tree file ( GR.ali.treefile ) for Gustatory Receptors. IR_trees.zip : Alignment ( IR.ali.fasta ) and tree file ( IR.ali.treefile ) for Ionotropic Receptors. OBP_trees.zip : Alignment ( OBP.ali.fasta ) and tree file ( OBP.ali.treefile ) for Odorant-Binding Proteins. CSP_trees.zip : Alignment ( CSP.ali.fasta ) and tree file ( CSP.ali.treefile ) for Chemosensory Proteins. 2.3 Evolutionary Selection Tests These archives contain the results of selection pressure analyses (e.g., dN/dS ratios, Likelihood Ratio Tests). Each gene family folder is subdivided by orthologous groups (e.g., GR1, GR2). OR_selection.zip GR_selection.zip IR_selection.zip Inside each selection archive, you will find: *_ali.fasta : Codon-based multiple sequence alignment. *_ali.pml : Codon-based multiple sequence alignment in PAML-friendly format. tree : The phylogenetic tree used for the selection model. LRT_BM.xls / BM_LRT.xls : Results for the Branch Model tests (domiciliary species vs. sylvatic species, see the associated paper). LRT_SM.xls / SM_LRT.xls : Results for the Site Model tests. 3. Methods Brief Genomes: Genomic data were sourced from NCBI (see paper for specific assembly accessions) . Annotation : Initial identification was performed using insectOR and Exonerate , followed by manual curation of gene models. Trees : Alignements was performed using MAFFT and ML trees using IQ-TREE . Selection Tests : Positive selection was assessed using PAML (codeml, EasyCodeML) on codon-aligned sequences. 4. Species Included Rhodnius bretesi Rhodnius colombiensis Rhodnius (=Psammolestes) coreodes Rhodnius domesticus Rhodnius milesi Rhodnius montenegrensis Rhodnius nastutus Rhodnius neglectus Rhodnius neivai Rhodnius pallescens Rhodnius pictipes Rhodnius prolixus Rhodnius robustus 5. Usage and Citation If you use these data, please cite the original publication: Merle, M. et al. (2026). Evolutionary Dynamics of the Complete Chemosensory Repertoire in Kissing Bugs of the Genus Rhodnius: Divergent Odorant Receptors Contrast with Conserved Gene Families. ( in prep ) For the specific dataset version, you can also cite this Zenodo DOI: DOI: 10.5281/zenodo.19064793
A historical map of the boundaries of the Kazakh Steppe in c. 1848. This map is fully open to fellow researchers and is available in multiple open source formats (SHP, GPKG, GeoJSON).
Akandil, Cengiz · Plekhanova, Elena · Rietze, Nils · et al.
33 files · 1.2 GB · csv, shapefile, tiffdeclared
This repository contains the processed datasets used to analyse the spatial relationship between artificial light at night (ALAN) and Arctic fire occurrence. The dataset includes cumulative ALAN layers, binary masked ALAN layers, fire polygon shapefiles, and a final analysis table. The cumulative ALAN layers provide aggregate digital number (DN) values representing light intensity. The masked ALAN layers are binary rasters, where values of 1 indicate lit areas and values of 0 indicate unlit areas. Fire scar centroids were generated from the fire polygons and used to calculate the distance from each fire scar to the nearest lit area. The final analysis table contains the distance to the nearest lit area for each fire scar and control points. The fire polygon shapefile includes fire scars for the period 2001-2013.
This deliverable presents the Phase 2 results of the BioProWRAP project, developed under the CLIMAAX framework, and focuses on enriching the initial wildfire‑risk assessment of Phase 1 through the integration of drought risk-an interconnected hazard with potential cascading effects-alongside diverse local datasets and live biodiversity inputs (crowdsourcing observations and eDNA). Phase 2 also enhances public engagement and inclusion through educational workshops and guided excursions in the three high‑risk, high‑value areas identified in Phase 1. The work was carried out by the REMTH team with continued scientific support from UTH, Greece.
Genome assembly of Cardita leana (Bivalvia: Archiheterodonta) and the associated gene models predicted with AUGUSTUS. The 'Tree' folder contains species trees inferred using different tree reconstruction programs. The MCMC_analysis folder contains inputs and ouputs for every MCMCTree analysis