GloSED - Global standardised soil eukaryome dataset

Global Standardised Soil Eukaryome Dataset (GloSED) Dataset description The GloSED dataset is a metabarcoding-based dataset encompassing the entire spectrum of soil eukaryotes collected and analysed using standardized protocols. Key characteristics - Sampling sites: 4,147 globally distributed locations across 121 countries - Taxonomic scope: Complete soil eukaryome including fungi, protists, animals, and plants - Operational taxonomic units: 988,824 curated OTUs - Sequencing technology: PacBio long-read sequencing of full-length ITS Data collection and processing - Standardized sampling design: 50x50 m plots - Soil cores: 40 cores per plot (5 cm diameter x 5 cm depth), pooled by volume - DNA extraction: PowerMax Soil DNA Isolation kit (Qiagen) with FavorPrep cleanup - Primers: universal eukaryotic primers ITS9mun/ITS4ngsUni - Processing: NextITS v.1.0.0 workflow (DOI: 10.5281/zenodo.15074882) - Taxonomic annotation: EUKARYOME v.1.9.4 database (DOI: 10.1093/database/baae043) Data files and formats Core data - `GloSED__OTU_sequences.fasta.gz`: Quality-filtered representative sequences for all OTUs, FASTA format - `GloSED__OTU_table.tsv.zip`: Sample-by-OTU abundance matrix (TSV format) - `GloSED__Taxonomy.tsv.zip`: Complete taxonomic annotations with UNITE-based species hypotheses (TSV format) - `GloSED__OTU_table.parquet`: Columnar format of abundance data for efficient querying (Parquet format) - `GloSED__Taxonomy.parquet`: Columnar format of taxonomic data (Parquet format) - `GloSED__phyloseq.RData`: phyloseq object for R-based analyses - `GloSED__BIOM.biom`: BIOM v.2.1 format compatible with QIIME2 Metadata files - `GloSED__Sample_metadata.xlsx`: Sample metadata - `DRI.json`: Data Reuse Information tag with ORCID identifiers - `DRI.csv`: Tabular format mapping accession IDs - `Contributors.xlsx`: List of contributors Usage notes To load the phyloseq object in R, use the following command: library(phyloseq)physeq <- readRDS("GloSED__phyloseq.RData")physeq Related resources Raw sequence data: European Nucleotide Archive (ENA) project: PRJEB103811 Sample accessions: ERS27941879 - ERS27946063 Sequence accessions: ERR15957609 - ERR15964175 Bioinformatics pipeline: NextITS Reference databases: EUKARYOME, UNITE