https://researchdata.se/en/catalogue Search results en Kraken2 Arthopod Reference Database v.1Kraken2 (v2.1.2) database containing all 2,593 reference assemblies for Arthropoda available on NCBI as of March 2023. This database was built for and used in the analysis of shotgun sequencing data of bulkDNA from Malaise trap samples collected by the Insect Biome Atlas, in the context of the manuscript "Small Bugs, Big Data: Metagenomics for arthropod biodiversity monitoring" by authors: López Clinton Samantha, Iwaszkiewicz-Eggebrecht Ela, Miraldo Andreia, Goodsell Robert, Webster Mathew T, Ronquist Fredrik, van der Valk Tom (for submission to Ecology and Evolution). For custom database building, Kraken2 requires all headers in reference assembly fasta files to be annotated with "kraken:taxid|XXX" at the end of each header. Where "XXX" is the corresponding National Center for Biotechnology Information (NCBI) taxID of the species. The code used to add the taxID information to each fasta file header, and update the accession2taxid.map file required by Kraken2 for database building, is available in this GitHub repository (https://github.com/SamanthaLop/Small_Bugs_Big_Data) (also linked under "Related Materials" below). ContentBelow is a list of the files in this item (in addition to the README and MANIFEST files), and their description. The first three files (marked with a *) are required to run Kraken2 classifications using the database. - * hash.k2d.gz - A hash file with all minimiser to taxon mappings (855 GB). - * opts.k2d - A file containing all options used when building the Kraken2 database (64 B). - * taxo.k2d - A file containing the taxonomy information used to build the database (385.9 KB). - seqid2taxid.map.gz - A file containing contig accession numbers and their corresponding taxids (810.6 MB). Note that this file is needed by Kraken2 when building the database, and as it was updated during custom building, it has been included for reference, but it is not required to use the database for classification. - genome_assembly_metadata.tsv - NCBI-generated table (tsv format, gzipped) of all reference assemblies for Arthropoda as of March 2023, which were used in the database construction. This includes columns: Assembly Accession, Assembly Name, Organism Name, Organism Infraspecific Names Breed, Organism Infraspecific Names Strain, Organism Infraspecific Names Cultival, Organism Infraspecific Names Ecotype, Organism Infraspecific Names Isolate, Organism Infraspecific Names Sex, Annotation Name, Assembly Stats Total Sequence Length, Assembly Level, Assembly Submission, and WGS project accession. How to use the database- Download the hash.k2d.gz, opts.k2d, and taxo.k2d files to the same directory (e.g. /PATH/TO/DATABASE/). - Unzip the hash.k2d.gz file. - Install or load Kraken2 to run classification on sequencing data using the database. - When running Kraken2, indicate the path to the directory (not the individual files) with the --db flag (e.g. kraken2 --db /PATH/TO/DATABASE/ ...). Note that the whole database must be loaded into memory by Kraken2 to be able to classify any sequencing reads, so ensure you have access to enough memory before running (the uncompressed hash file is around 1.1 TB). We also recommend using the Kraken2 option --memory-mapping, as it ensures the database is loaded once for all samples, instead of once for each individual sample, saving considerable time and resources. For more information on using Kraken2, see the Kraken2 wiki manual (https://github.com/DerrickWood/kraken2/wiki/Manual) . This database was built by Samantha López Clinton (samantha.lopezclinton@nrm) and Tom van der Valk (tom.vandervalk@nrm.se). Mon, 18 Aug 2025 00:00:00 GMT https://researchdata.se/en/catalogue/dataset/doi-10-17044-scilifelab-29666605 https://researchdata.se/en/catalogue/dataset/doi-10-17044-scilifelab-29666605 Swedish Museum of Natural History Samantha López Clinton Tom van der Valk Phenotypic plant data and herbivory intensity data from eight Solanum dulcamara populations in four habitats, and arthropod data from five of these populations collected in pan straps and sticky traps. The phenotypic plant data include measures on growth and reproduction. Herbivory data include measures on lost leaf area. Arthropod data are divided into different taxa. Thu, 03 Sep 2026 12:19:13 GMT https://researchdata.se/en/catalogue/dataset/2026-144 https://researchdata.se/en/catalogue/dataset/2026-144 Swedish University of Agricultural Sciences Åsa Lankinen Kristin Aleklett Amplicon Sequence Variants of 418bp of CO1 from leaf litter arthropod communities collected at Malaise traps from the Insect Biome Atlas project (https://www.insectbiomeatlas.org/)  in Madagascar, as described in the IBA data paper (https://doi.org/10.1038/s41597-025-05151-0) . This dataset was published via the SBDI ASV portal (https://asv-portal.biodiversitydata.se/) , and has been updated from 'Metadata only' to 'Occurrence' type. Occurrence data were compiled from the following IBA Figshare items: Processed ASV data from the Insect Biome Atlas Project v3: (https://figshare.scilifelab.se/articles/dataset/Processed_ASV_data_from_the_Insect_Biome_Atlas_Project/27202368/3) - cleaned_noise_filtered_cluster_taxonomy_MG.tsv.gz (https://figshare.scilifelab.se/ndownloader/files/50067522) - spikeins_tax_MG.tsv.gz (https://figshare.scilifelab.se/ndownloader/files/50067525) Amplicon sequence variants from the Insect Biome Atlas project v6: (https://figshare.scilifelab.se/articles/dataset/Amplicon_sequence_variants_from_the_Insect_Biome_Atlas_project/25480681/6) - CO1_asv_counts_MG.tsv.gz (https://figshare.scilifelab.se/ndownloader/files/%2049727829) - CO1_asv_seqs_MG.fasta.gz (https://figshare.scilifelab.se/ndownloader/files/46381135) The following samples were excluded from this resource due to sequencing failure: P30904_2718, P30904_2719; or lack of non-zero counts for annotated ASVs: P30904_2599, P30904_2607, P30904_2592. Thu, 24 Apr 2025 00:00:00 GMT https://researchdata.se/en/catalogue/dataset/gbif-sweden-10-15468-pad7pc https://researchdata.se/en/catalogue/dataset/gbif-sweden-10-15468-pad7pc Swedish Museum of Natural History Andreia Miraldo John Sundh Elzbieta Iwaszkiewicz-Eggebrecht Emma Granqvist Lokeshwaran Manoharan Piotr Łukasik Ayco J. M. Tack Anders F. Andersson Tomas Roslin Fredrik Ronquist Amplicon Sequence Variants of 418bp of CO1 from homogenized arthropod community samples collected with Malaise traps from the Insect Biome Atlas project (https://www.insectbiomeatlas.org/) in Sweden, as described in the IBA data paper (https://doi.org/10.1038/s41597-025-05151-0) . This dataset was published via the SBDI ASV portal (https://asv-portal.biodiversitydata.se/) , and has been updated from 'Metadata only' to 'Occurrence' type. Occurrence data were compiled from the following IBA Figshare items: Processed ASV data from the Insect Biome Atlas Project v3: (https://figshare.scilifelab.se/articles/dataset/Processed_ASV_data_from_the_Insect_Biome_Atlas_Project/27202368/3) - cleaned_noise_filtered_cluster_taxonomy_SE.tsv.gz (https://figshare.scilifelab.se/ndownloader/files/50067528) - spikeins_tax_SE.tsv.gz (https://figshare.scilifelab.se/ndownloader/files/50067531) Amplicon sequence variants from the Insect Biome Atlas project v6: (https://figshare.scilifelab.se/articles/dataset/Amplicon_sequence_variants_from_the_Insect_Biome_Atlas_project/25480681/6) - co1_asv_counts_se.tsv.gz (https://figshare.scilifelab.se/ndownloader/files/46381132) - co1_asv_seqs_se.fasta.gz (https://figshare.scilifelab.se/ndownloader/files/46381138) The following samples were excluded from this resource due to low read counts: P28409_1377, P28409_1378, P28409_1379, P28409_1380, P28409_1382, P28409_1383, P28410_1334, P28410_1392; or lack of non-zero counts for annotated ASVs: P27361_1636, P28410_1037, P28410_1049. Thu, 07 Nov 2024 00:00:00 GMT https://researchdata.se/en/catalogue/dataset/gbif-sweden-10-15468-awjycd https://researchdata.se/en/catalogue/dataset/gbif-sweden-10-15468-awjycd Swedish Museum of Natural History Andreia Miraldo John Sundh Elzbieta Iwaszkiewicz-Eggebrecht Emma Granqvist Lokeshwaran Manoharan Piotr Łukasik Ayco J. M. Tack Anders F. Andersson Tomas Roslin Fredrik Ronquist Amplicon Sequence Variants of 418bp of CO1 from the preservative ethanol of bulk arthropod samples collected with Malaise traps from the Insect Biome Atlas project (https://www.insectbiomeatlas.org/) in Sweden, as described in the IBA data paper (https://doi.org/10.1038/s41597-025-05151-0) . This dataset was published via the SBDI ASV portal (https://asv-portal.biodiversitydata.se/) , and has been updated from 'Metadata only' to 'Occurrence' type. Occurrence data were compiled from the following IBA Figshare items: Processed ASV data from the Insect Biome Atlas Project v3: (https://figshare.scilifelab.se/articles/dataset/Processed_ASV_data_from_the_Insect_Biome_Atlas_Project/27202368/3) - cleaned_noise_filtered_cluster_taxonomy_SE.tsv.gz (https://figshare.scilifelab.se/ndownloader/files/50067528) - spikeins_tax_SE.tsv.gz (https://figshare.scilifelab.se/ndownloader/files/50067531) Amplicon sequence variants from the Insect Biome Atlas project v6: (https://figshare.scilifelab.se/articles/dataset/Amplicon_sequence_variants_from_the_Insect_Biome_Atlas_project/25480681/6) - co1_asv_counts_se.tsv.gz (https://figshare.scilifelab.se/ndownloader/files/46381132) - co1_asv_seqs_se.fasta.gz (https://figshare.scilifelab.se/ndownloader/files/46381138) Thu, 07 Nov 2024 00:00:00 GMT https://researchdata.se/en/catalogue/dataset/gbif-sweden-10-15468-af5cwp https://researchdata.se/en/catalogue/dataset/gbif-sweden-10-15468-af5cwp Swedish Museum of Natural History Andreia Miraldo John Sundh Elzbieta Iwaszkiewicz-Eggebrecht Emma Granqvist Lokeshwaran Manoharan Piotr Łukasik Ayco J. M. Tack Anders F. Andersson Tomas Roslin Fredrik Ronquist Amplicon Sequence Variants of 418bp of CO1 from mild lysed arthropod community samples collected with Malaise traps from the Insect Biome Atlas project (https://www.insectbiomeatlas.org/) in Sweden, as described in the IBA data paper (https://doi.org/10.1038/s41597-025-05151-0) . This dataset was published via the SBDI ASV portal (https://asv-portal.biodiversitydata.se/) , and has been updated from 'Metadata only' to 'Occurrence' type. Occurrence data were compiled from the following IBA Figshare items: Processed ASV data from the Insect Biome Atlas Project v3: (https://figshare.scilifelab.se/articles/dataset/Processed_ASV_data_from_the_Insect_Biome_Atlas_Project/27202368/3) - cleaned_noise_filtered_cluster_taxonomy_MG.tsv.gz (https://figshare.scilifelab.se/ndownloader/files/50067522) - spikeins_tax_MG.tsv.gz (https://figshare.scilifelab.se/ndownloader/files/50067525) Amplicon sequence variants from the Insect Biome Atlas project v6: (https://figshare.scilifelab.se/articles/dataset/Amplicon_sequence_variants_from_the_Insect_Biome_Atlas_project/25480681/6) - CO1_asv_counts_MG.tsv.gz (https://figshare.scilifelab.se/ndownloader/files/%2049727829) - CO1_asv_seqs_MG.fasta.gz (https://figshare.scilifelab.se/ndownloader/files/46381135) The following samples were excluded from this resource due to sequencing failure: P26762_1247, P26762_1333, P27359_1207, P27361_1307, P27361_1148; or lack of non-zero counts for annotated ASVs: P27359_2998, P27361_1125, P27360_1032. Thu, 24 Apr 2025 00:00:00 GMT https://researchdata.se/en/catalogue/dataset/gbif-sweden-10-15468-6u5rum https://researchdata.se/en/catalogue/dataset/gbif-sweden-10-15468-6u5rum Swedish Museum of Natural History Andreia Miraldo John Sundh Elzbieta Iwaszkiewicz-Eggebrecht Emma Granqvist Lokeshwaran Manoharan Piotr Łukasik Ayco J. M. Tack Anders F. Andersson Tomas Roslin Fredrik Ronquist Amplicon Sequence Variants of 418bp of CO1 from mild lysed arthropod community samples collected with Malaise traps from the Insect Biome Atlas project (https://www.insectbiomeatlas.org/) in Sweden, as described in the IBA data paper (https://doi.org/10.1038/s41597-025-05151-0) . This dataset was published via the SBDI ASV portal (https://asv-portal.biodiversitydata.se/) , and has been updated from 'Metadata only' to 'Occurrence' type. Occurrence data were compiled from the following IBA Figshare items: Processed ASV data from the Insect Biome Atlas Project v3: (https://figshare.scilifelab.se/articles/dataset/Processed_ASV_data_from_the_Insect_Biome_Atlas_Project/27202368/3) - cleaned_noise_filtered_cluster_taxonomy_SE.tsv.gz (https://figshare.scilifelab.se/ndownloader/files/50067528) - spikeins_tax_SE.tsv.gz (https://figshare.scilifelab.se/ndownloader/files/50067531) Amplicon sequence variants from the Insect Biome Atlas project v6: (https://figshare.scilifelab.se/articles/dataset/Amplicon_sequence_variants_from_the_Insect_Biome_Atlas_project/25480681/6) - co1_asv_counts_se.tsv.gz (https://figshare.scilifelab.se/ndownloader/files/46381132) - co1_asv_seqs_se.fasta.gz (https://figshare.scilifelab.se/ndownloader/files/46381138) The following samples were excluded from this resource due to sequencing failure: P23412_1633, P23412_1638, P23412_1641, P23412_1647; or lack of non-zero counts for annotated ASVs: P20863_1580, P23412_1318, P25061_1224, P25061_1440, P25061_1463, P25061_1711, P25061_1734, P25259_1134, P25259_1250. Thu, 07 Nov 2024 00:00:00 GMT https://researchdata.se/en/catalogue/dataset/gbif-sweden-10-15468-veahzb https://researchdata.se/en/catalogue/dataset/gbif-sweden-10-15468-veahzb Swedish Museum of Natural History Andreia Miraldo John Sundh Elzbieta Iwaszkiewicz-Eggebrecht Emma Granqvist Lokeshwaran Manoharan Piotr Łukasik Ayco J. M. Tack Anders F. Andersson Tomas Roslin Fredrik Ronquist Amplicon Sequence Variants of 418bp of CO1 from soil and leaf litter arthropod communities collected at Malaise traps from the Insect Biome Atlas project (https://www.insectbiomeatlas.org/) in Sweden, as described in the IBA data paper (https://doi.org/10.1038/s41597-025-05151-0) . This dataset was published via the SBDI ASV portal (https://asv-portal.biodiversitydata.se/) , and has been updated from 'Metadata only' to 'Occurrence' type. Occurrence data were compiled from the following IBA Figshare items: Processed ASV data from the Insect Biome Atlas Project v3: (https://figshare.scilifelab.se/articles/dataset/Processed_ASV_data_from_the_Insect_Biome_Atlas_Project/27202368/3) - cleaned_noise_filtered_cluster_taxonomy_SE.tsv.gz (https://figshare.scilifelab.se/ndownloader/files/50067528) - spikeins_tax_SE.tsv.gz (https://figshare.scilifelab.se/ndownloader/files/50067531) Amplicon sequence variants from the Insect Biome Atlas project v6: (https://figshare.scilifelab.se/articles/dataset/Amplicon_sequence_variants_from_the_Insect_Biome_Atlas_project/25480681/6) - co1_asv_counts_se.tsv.gz (https://figshare.scilifelab.se/ndownloader/files/46381132) - co1_asv_seqs_se.fasta.gz (https://figshare.scilifelab.se/ndownloader/files/46381138) The following samples were excluded from this resource due to sequencing failure: P25259_1390, P25259_1407, P25259_1411, P25259_1420, P25259_1422, P25259_1423, P25259_1428, P25259_1431, P25259_1435, P25259_1436, P25259_1439, P25259_1440, P25259_1444, P25259_1452, P25259_1460, P25259_1467, P25259_1469, P25259_1476, P25259_1591, P25259_1594, P25259_1641, P25259_1649; or lack of non-zero counts for annotated ASVs: P25259_1438, P25259_1455, P25259_1471, P25259_1475, P25259_1586, P25259_1661, P25259_1742. Thu, 07 Nov 2024 00:00:00 GMT https://researchdata.se/en/catalogue/dataset/gbif-sweden-10-15468-783jyb https://researchdata.se/en/catalogue/dataset/gbif-sweden-10-15468-783jyb Swedish Museum of Natural History Andreia Miraldo John Sundh Elzbieta Iwaszkiewicz-Eggebrecht Emma Granqvist Lokeshwaran Manoharan Piotr Łukasik Ayco J. M. Tack Anders F. Andersson Tomas Roslin Fredrik Ronquist We evaluated 27 candidate plant species for their ability to host functionally important above- and below-ground organisms — pollinators, natural enemies, herbivores, and decomposers — and assessed how the plant traits floral area, timing of peak bloom, life cycle, and plant cover affect these groups. The study was conducted during two years in two sites. Pollinators (hoverflies and wild bees - including bumblebees and solitary bees) were surveyed with visual observations for 60s twice a week while the plot was in bloom. Leaf-dwelling arthropods (predators, parasitic wasps and herbivores) were collected using vacuum sampling (30s in a 1m by 1m quadrat) of the plots with open flowers. As below-ground organisms, nematodes (predators, herbivores and decomposers) were sampled at the end of each survey season taking a composite sample consisting on three samples per plot (2cm diameter, 15cm depth). All data were summed on the plot level per site and year. For the plant traits, floral area and plant cover surveys were recorded weekly in a 1m by 1m quadrat, within 2 days of sampling pollinators and leaf-dwelling arthropods. The timing of peak bloom for each plant species was defined as the average week number between the two consecutive weeks with the highest number of open floral units. The life cycles of the plant species were classified as annual or perennial (perennial and biennial). For further information, see methods in the manuscript Rodríguez-Gasol et al. ’Plant identity determines pollinator, natural enemy, herbivore and decomposer abundances in flower plantings’. Tue, 21 Oct 2025 14:13:45 GMT https://researchdata.se/en/catalogue/dataset/2024-616 https://researchdata.se/en/catalogue/dataset/2024-616 Swedish University of Agricultural Sciences Neus Rodríguez-Gasol Fabian Boetzl Elodie Chapurlat Johan A. Stenberg Mattias Jonsson Ola Lundin Maria Viketoft We sampled pollinators, natural enemies, and herbivores, and estimated predation rates using visual observations, yellow sticky traps, pitfall traps, tiller counts and sentinel prey cards in eight pairs of pollinator attractive annual flower strips and control field margins, and their adjacent cereal fields in Skåne, Sweden in 2021. Field margins (flower strip vs spontaneous vegetation control) were characterized by estimating the percentage of plant cover and the total floral area (for each species we calculated the number of floral units x average floral area) in eight 0.6 x 0.6 m squares evenly distributed along the 100 m transect. Data was collected twice during the main period of the flower mixture. Pollinators (hoverflies, honey bees, bumblebees, solitary bees, and butterflies) visiting flowers were surveyed for 10 minutes along a 100 m long and 1 m wide transect in each field margin type. Pollinators were surveyed twice during the main period of the flower mixture on the same days as the margin characterization was done. Leaf-dwelling natural enemies and herbivores were sampled using yellow sticky traps (20 cm x 12.6 cm). Four traps of each type were placed along the 100 m transect in the field margins and another four in the adjacent crop area, at 10 m from the margins, for a total of 16 traps per site. Traps were spaced 20 m apart within each transect and remained in the field for seven days. Data was collected twice during the main period of the flower mixture. Due to a large number of samples only three traps per transect were processed and identified. Ground-dwelling natural enemies were sampled using pitfall traps made from polypropylene beakers (12 cm diameter) filled with 200 mL of soapy water. Four traps of each type were placed along the 100 m transect in the field margins and another four in the adjacent crop area, at 10 m from the margins, for a total of 16 traps per site. Traps were spaced 20 m apart within each transect and remained in the field for seven days. Data was collected twice during the main period of the flower mixture. Due to a large number of samples only three traps per transect were processed and identified. We counted and identified all arthropods found on four groups of five tillers located along each adjacent crop transect, spaced every 20 m, resulting in 80 crop tillers per site. Data was collected twice during the main period of the flower mixture. Sentinel aphid cards were set up in the field to estimate aphid predation rates. Four groups of two cards at ground level and two cards at vegetation level were set up along each adjacent crop transect, spaced every 20 m, resulting in 32 cards per site. Sentinel prey cards were set up once, exposed simultaneously during the first sampling interval of the tiller counts. After 24 hours of exposure, the sentinel prey cards were collected, and the remaining aphids were counted. This survey was conducted only in four of the eight fields. All data were aggregated across samples and survey rounds for each field margin habitat and the adjacent on-crop area. Hushållningssällskapet provided support in identifying suitable study sites, facilitating contact with farmers, and reviewing and editing the final manuscript associated with the dataset For further information, see methods in the manuscript Rodríguez-Gasol et al. "Annual flower strips under the ‘All of Sweden blooms’ initiative - how do they perform for pollinators, natural enemies and herbivores?". Thu, 29 Jan 2026 08:09:03 GMT https://researchdata.se/en/catalogue/dataset/2025-270 https://researchdata.se/en/catalogue/dataset/2025-270 Swedish University of Agricultural Sciences Neus Rodriguez-Gasol Ola Lundin Elodie Chapurlat Mattias Hammarstedt Mattias Jonsson Johan A. Stenberg Maria Viketoft