PR2-Based Curated Reference Database and Trimmed Sub-databases

README Overview This directory contains data and intermediate results used for evaluating primer performance in algal metabarcoding analyses based on the PR2 database (version 5.1.0). File description 1. pr2_version_5.1.0_cleaned_SSU_dada2_all_withsp.fasta Reference sequence file derived from the PR2 database (version 5.1.0, Guillou et al., 2016), including cleaned 18S SSU sequences. Taxonomic classification of algal lineages was curated based on Moestrup (2006) and Adl et al. (2019), assigning taxa to corresponding phyla. For sequences with incomplete taxonomic information, annotations were supplemented using the Catalogue of Life (COL) and AlgaeBase databases. 2. pr2_algal_taxonomy_table.csv A taxonomy table containing algal taxa extracted from the PR2 database. This file was used to define algal lineages for downstream filtering and analysis. 3. trimmed_sequences_by_primer/ Raw in silico PCR outputs obtained by primer-based trimming of reference sequences, without any downstream filtering or processing. File name prefixes represent primer ID, which can be cross-referenced with Table S1 for detailed information.These datasets can be used as primer-specific reference databases for taxonomic assignment of corresponding amplicon sequences; however, this approach may not be optimal, as it may lead to an underestimation of diversity due to the exclusion of incomplete or mismatched reference sequences. Notes Only primers targeting the 18S rRNA gene region were retained for analysis to ensure compatibility with the PR2 database. In silico PCR was performed using approximate matching with mismatch allowance and reverse-complement detection, followed by extraction of simulated amplicons. These data were used for downstream evaluation of primer performance in terms of diversity recovery and taxonomic coverage. References Adl, S. M., et al. (2019). Revisions to the classification, nomenclature, and diversity of eukaryotes. Journal of Eukaryotic Microbiology. https://doi.org/10.1111/jeu.12691 Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L., ... & Christen, R. (2012). The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucleic acids research, 41(D1), D597-D604. https://doi.org/10.1093/nar/gks1160 Moestrup, Ø. (2006). Algal taxonomy: Historical overview. In Encyclopedia of Life Sciences. John Wiley & Sons. https://doi.org/10.1002/9780470015902.a0000328.pub2