https://researchdata.se/sv/catalogue Search results sv Soil samples were collected in mid-October 2013 from Ivantjärnsheden field station in Jädraås (60°49‘N, 16°30’E, altitude 185 m), a well-documented field site in central Sweden (Persson, 1980) with Pinus sylvestris L. overstory and an understory of ericaceous dwarf shrubs (Calluna vulgaris (L.) Hull and Vaccinium vitis-ideae L.) and mosses (Dicranum majus Turner and Pleurozium schreberi (Bridel) Mitten). To account for small-scale variability in soil fungal communities we collected 5 soil cores (5 cm diameter and 15 cm deep) in each of 12 plots in the since terminated experiment IhII (9802) (Axelsson & Bråkenhielm, 1980). After visually dividing the plot into four quadrats one core were taken from the middle of each quadrat and from the middle of the plot after peeling back the top shrub and moss layer (incl. most of the litter layer). Soil cores were separated into visually distinct podzol soil layers: organic soil (O), mineral elluvial soil (E) and mineral illuvial soil (B) before pooling the layers for each plot. From each composite soil sample two sub-samples of approximately 0.5 g wet weight were collected for DNA extraction. Approximately 1500 bp of the rDNA from all soil DNA extracts was amplified using the primer set ITS1F (Gardes & Bruns, 1993) and LR5 (Hopple Jr & Vilgalys, 1994). A total of 5, 8 and 3 samples successfully amplified for O, E and B horizons, respectively (Table S1). PCR products from the separate soil horizons were pooled to generate three amplicon libraries (SwO, SwE and SwB) for sequencing at SciLifeLab/NGI (Uppsala, Sweden) on a PacBio RS II system (Pacific Biosciences, Menlo Park, CA, USA). This dataset was published via the SBDI ASV portal. Fri, 19 Aug 2022 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/gbif-sweden-10-15468-r8gu42 https://researchdata.se/sv/catalogue/dataset/gbif-sweden-10-15468-r8gu42 Uppsala universitet Anna Rosling Since Linnaeus's time, the Kungsängen Nature Reserve has drawn frequent visitors because of its vegetation including the largest population of Fritillaria meleagris L. in Sweden. The reserve is a meadow with an abrupt moisture transition, where the wetter part has a Carex acuta dominated plant community with low species richness, visually distinct from the drier part, which has a species rich plant community including a high density of Fritillaria meleagris. To investigate the link between plant and below-ground micro-eukaryotic communities, we amplified and sequenced the ITS and LSU regions of the rDNA operon (1500 bp) from soil using PacBio SMRT sequencing, and evaluated three different methods for generation of operational taxonomic units. We found distinct communities associated with wet and mesic-dry soil conditions but estimated richness was not so different. Both soil conditions host communities dominated by protists, a large fraction of which were taxonomically assigned to Ciliphora (Alveolata), while 30-40% of all reads were assigned to kingdom Fungi. Ecological patterns were consistently recovered irrespective of the read clustering method used. However, different clustering methods affect the taxonomic and phylogenetic resolution of community characterization with implications for how well members of the micro-eukaryotic communities can be recognized in the data. This data resource contain amplicon sequence variant (ASV) sequences generated with DADA2 using the Ampliseq pipeline (https://nf-co.re/ampliseq). This dataset was published via the SBDI ASV portal (https://asv-portal.biodiversitydata.se/). Tue, 06 Sep 2022 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/gbif-sweden-10-15468-upxbwy https://researchdata.se/sv/catalogue/dataset/gbif-sweden-10-15468-upxbwy Uppsala universitet Anna Rosling Shadi Eshghi Sahraei Brendan Furneaux Kerri Kluting Mustafa Zakieh - Suppl datafile 1 MCGC_Shadi_10_21-with analysis 2023 This file contains the analysis and results presence / absence for so called Missing Core Glomeromycota Genes (MCGC). - Suppl datafile 2 CAZyme_22_10-31 This file contains the gene family counts for CAZyme families, as well as an analysis of families previously identified as Plant Cell Wall Degrading Enzymes (PCWDE) and familes selected for Figure 2 in the manuscript. Files with summary statistics from comparative genomic analysis based on Funnanotate and used for the anlaysis in the paper: busco-complete-summary-Shadis-genomes; CAZyme.all.results; CAZyme.summar.results; MEROPS.all.results; MEROPS.summary.results; pfam.results; signalp Ancestral reconstruction trees for CAZyme families and Peptideases with significant changes are available in the files Cazyme_trees and plots_peptidases_pdf. Mon, 20 May 2024 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-23553426 https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-23553426 Uppsala universitet Anna Rosling Forests and woodlands in the Guineo-Sudanian transition zone contain many tree species that form symbiotic interactions with ectomycorrhizal (ECM) fungi, which facilitate plant growth by increasing nutrient and water uptake. Despite their importance for ecosystem functioning and anthropogenic use, diversity and distribution of ECM fungi is severely under-documented in West Africa. We conducted a broad regional sampling across five West African countries using soil eDNA to characterize the ECM as well as the total soil fungal community in two vegetation types dominated by ECM host tree species. Sequencing of the entire ITS region and much of the LSU region allows us to infer a phylogeny for all detected soil fungal species. This data resource contain amplicon sequence variants (ASVs) generated from the dataset using the procedure established in Kalsoom-Khan et al. (2020) after accessing general read quality and ensuring that the majority of reads fell within the expected length (1-2 kb). In brief, raw sequence reads were filtered and trimmed, and PacBio-type chimeras were detected and removed using the tool cutadapt. Amplicons sequenced in reverse were reverse complemented. Reads were filtered using DADA2, discarding sequences with more than 3 expected errors as well as those with a length outside the range of 1200–1800 bases. Filtered sequences were then denoised using DADA2, with complete pooling and an increased alignment band size of 32. Singleton ASVs are not included in DADA2 denoising output. De novo chimera detection and removal were also performed in DADA2, with a minimum parent overabundance of 3.5 and allowing detection of chimeras with a single base difference from their parent sequence. This dataset was published via the SBDI ASV portal (https://asv-portal.biodiversitydata.se/). Mon, 22 May 2023 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/gbif-sweden-10-15468-vdavsc https://researchdata.se/sv/catalogue/dataset/gbif-sweden-10-15468-vdavsc Uppsala universitet Anna Rosling Brendan Furneaux Peter Meidl The study presents results of fungal metabarcoding community data from bark beetles and phloeme collected in burned and unburned forest sites in central Sweden and phloem chemistry data. The folder "tomicus_2021" contains data and scripts used to perform statistical analysis and generate figures presented in the paper "Fire Influence on Tomicus piniperda-Associated Fungal Communities and Phloem Nutrient Availability of Colonized Pinus sylvestris" and its supplementary material.  The folder "Corrected Tables" contains excel files with all the final tables presetned in the paper and the supplementary materail. The files pb_466_001 and 002 contain FASTQ files from the pacbio run. These can be demultiplexed with the two primer files (Primer-ITS4_Tag-setup.txt and Primer_fITS9_Tag-setup.txt) that contain info on the tag sequence for each tag used. Wed, 24 Aug 2022 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-20289000 https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-20289000 Uppsala universitet Anna Rosling Kerri Kluting Diana six Ylva Strid Project Overview The project aims to investigate species diversity and variety from a citizen science perspective (more of a random character, i.e., not a strictly scientific research character). Project Goals - Investigate species diversity and variety on a larger scale (>1,000 samples) - Give sequences a "face" = metadata such as environmental data, field images, etc. - Provide tools for species identification - Use DNA barcoding of the ITS region - Be cost-effective - Be methodologically feasible from fruiting body to analyzed sequence - Disseminate knowledge about the method Dataset Description The dataset contains DNA-barcoded samples of fungal fruiting bodies collected in Sweden. The collection has been mostly random and the selection has primarily been based on the collector's own interest. Collectors are mainly amateur mycologists. Barcoding has been performed on the ITS region and parts of the SSU and LSU regions. Additional observational metadata such as coordinates, images, and environmental descriptions are linked to the Swedish Observation System for each respective sample.This dataset was published via the SBDI ASV portal. (https://asv-portal.biodiversitydata.se/) Thu, 03 Apr 2025 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/gbif-sweden-10-15468-kscfj6 https://researchdata.se/sv/catalogue/dataset/gbif-sweden-10-15468-kscfj6 Uppsala universitet Patrick Fritzson Björn Bråvander The item contains data and figures supporting the publication with the same name. In this study we sequenced nuclei and assembled genomes for two spores from an arbuscular mycorrhizal fungi morphotypically identified as Funneliforms geosporum. The spores were collected at the Kunsgängen nature reserve just south of Uppsala, Sweden. The file "Spore nuclie scatter plots and MDA results for ..." contains information on the spores from which nuclei were sorted in this project including FACS scatterplot, well positions, MDA, PCR screening for bacteria and fungi as well as a list of which nuclei were selected for sequening.  The zipped folder "Alignments for species identification.zip" contains alignments and phylogenetic trees for there reference genes (Fox, LSU and Tor) used for species identification of the morphotyped spores agains known species. The file "Alignment of MAT contigs from all funneliformis.phy" contains one contig from each of the four Funneliformis genome assemblies with a gene homologous to one of the genes in the mating type locus identified in Rhizophagus irregulars, gene bank accession number KT946687 The file "Alignment of MAT contigs from all funneliformis extraction.fasta" contains the region from each of the four contigs that was extracted from the above alignment and used to Blast all single nuclei assemblies for potential mating type locus homologues. The two excel files "Fig 3a..." and "Fig 3b..." contains the FunAnnotate output for gene families CAZyme and MEROPS and calculations for Fig 3a and b. Mon, 12 Sep 2022 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-20120150 https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-20120150 Uppsala universitet Shadi Eshghi Sahraei Marisol Sanchez Garcia Merce Montoliu-Nerin David Manyara Claudia Bergin Søren Rosendahl Anna Rosling Data deponerade i samband med artikel som ska publiceras i tidskriften Ecography. Svamp-DNA extraherades från jordprover insamlade vid betesfria experiment på 15 platser runt Arktis för att utvärdera effekten av stora däggdjursbetare på mykorrhizasvampsamhällen. Datan inkluderar DNA-sekvensläsningar som amplifierats med primerparen ITS1m-LR5 och SSU515fngs-AML2 för långläsning, vilka riktar sig mot generella svampsekvenser respektive arbuskulära mykorrhizor. Sekvenserna har taxonomiskt tilldelats via UNITE-databasen med PlutoF samt MaarjAM-databasen och har klassificerats i svampgillen med hjälp av FUNguild. Arbetsflödet från trimmade, demultiplexerade sekvensläsningar till taxonomisk och funktionell tilldelning finns i R-skriptet "EcographySubmission_SynthesisScript.R". Jordegenskaper, datum för etablering av betesfria områden och generella metadata finns i filen "MetaData.csv", och procentuell täckning av växtfunktionella typer finns för 11 platser i filen "Cover_data.csv". Råa sekvensläsningar har deponerats i Sequence Read Archive (SRA) under titeln "Impacts of large herbivores on mycorrhizal fungal communities across the Arctic". Thu, 04 Dec 2025 14:31:06 GMT https://researchdata.se/sv/catalogue/dataset/2025-328 https://researchdata.se/sv/catalogue/dataset/2025-328 Göteborgs universitet Cole Brachmann Martin Ryberg Brendan R. Furneaux Anna Rosling Tinghai Ou Alf Ekblad Isabel C. Barrio M. Syndonia Bret-Harte Hannu Fritze Laura Gough Robert D. Hollister Ingibjörg S. Jónsdóttir Oula Kalttopää Elin Lindén Päivi Mäkiranta Johan Olofsson Rauni Partanen Kirsten A. Reid Aleksandr Sokolov Svetlana Abdulmanova Maija S. Sujala Maja Sundqvist Otso Suominen Craig E. Tweedie Amanda Young Robert G. Björk Only a small fraction of the world’s fungi is described, and a large number of fungal sequences from environmental DNA (eDNA) currently lack relevant reference sequences for taxonomic identification in metabarcoding studies. Partially because there are several deeply divergent fungal lineages, including hypothesized class- and order-level lineages, currently known only by eDNA sequences. Here, we describe the first living representative of one such lineage (previously referred to as Clade GS25). We use a phylogenomic approach to test the placement and taxonomic rank hypothesized for this lineage, and present the formally described Semicentenialea rex, as the first known species in the novel class Semicentenialomycetes (Pucciniomycotina, Basidiomycota). Additionally, we provide the first phylogenomic resolution of Pucciniomycotina, using reference genomes from all described classes with the exception of Cryptomycocolacomycetes. We propose a set of practices that could be adopted by the research community to help facilitate more connections between living fungi and eDNA sequences. The use of such practices would in turn help to alleviate some of the complications associated with fungal DNA sequences in reference databases and contribute towards a more complete understanding of fungal diversity. Wed, 28 Jan 2026 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-26894242 https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-26894242 Uppsala universitet Veera Tuovinen Nogerius Marisol Sanchez Garcia Kerri Kluting Jussi Heinonsalo Martin Ryberg Merje Toome Sajeet Haridas Stephen J. Mondo Kurt LaButti Matt Nolan Anna Lipzen Diane Bauer Igor V. Grigoriev Maxim Koriabine Mary Cathrine Aime Kerrie Barry Anna Rosling Data om biogena flyktiga organiska föreningar (BVOC) omfattar fullständig bearbetning från retentionstider, jämförelse med standarder och kvantifiering av relevanta föreningar. Ekosystemrespirationsdata är konverterade till flöde (linjär ökning av koncentrationen av koldioxid (CO2) över tid under provtagningsperioden). Plant Root Simulator (PRS), fukt- och temperaturdata är listade för varje provyta och behandling. Vegetationsdata beskrivs för varje växtsamhälle baserat på procentuell täckning av varje art. Mon, 02 Oct 2023 06:24:27 GMT https://researchdata.se/sv/catalogue/dataset/2023-177 https://researchdata.se/sv/catalogue/dataset/2023-177 Göteborgs universitet Cole Brachmann Tage Vowles Riikka Rinnan Mats Björkman Anna Ekberg Robert Björk