From pathogens to partners: Temporal and biogeographical patterns in fungal associations

This dataset contains raw paired-end Illumina MiSeq reads (2 x 250 bp) targeting the fungal ITS2 region. The data originate from 14 multiplexed sequencing libraries, each representing a subset of root-associated soil samples collected across various urban and semi-natural tree habitats. Amplicons were generated using the ITS3 and ITS4 primers, and each sample was dual-barcoded with unique forward and reverse tags. No read assembly was performed prior to submission; the uploaded FASTQ files contain unassembled, demultiplexed reads with adapters and low-quality bases already removed.Note: FASTQ files represent raw, non-demultiplexed reads from 14 multiplexed sequencing libraries. Sample demultiplexing information (barcode-to-sample mapping files and primer combinations) is available via the associated Zenodo archive: https://doi.org/10.5281/zenodo.15919091.