RT Journal Article SR Electronic T1 pr2-primers: an 18S rRNA primer database for protists JF bioRxiv FD Cold Spring Harbor Laboratory SP 2021.01.04.425170 DO 10.1101/2021.01.04.425170 A1 Daniel Vaulot A1 Stefan Geisen A1 Frédéric Mahé A1 David Bass YR 2021 UL http://biorxiv.org/content/early/2021/01/04/2021.01.04.425170.abstract AB Metabarcoding of microbial eukaryotes (collectively known as protists) has developed tremendously in the last decade, almost uniquely relying on the 18S rRNA gene. As microbial eukaryotes are extremely diverse, many primers and primer pairs have been developed. To cover a relevant and representative fraction of the protist community in a given study system, a wise primer choice is needed as no primer pair can target all protists equally well. As such, a smart primer choice is very difficult even for experts and there are very few on-line resources available to list existing primers. We built a database listing 179 primers and 76 primer pairs that have been used for eukaryotic 18S rRNA metabarcoding. In silico performance of primer pairs was tested against two sequence databases: PR2 for eukaryotes and a subset of Silva for prokaryotes. This allowed to determine the taxonomic specificity of primer pairs, the location of mismatches as well as amplicon size. We developed a R-based web application that allows to browse the database, visualize the taxonomic distribution of the amplified sequences with the number of mismatches, and to test any user-defined primer set (https://app.pr2-primers.org). This tool will provide the basis for guided primer choices that will help a wide range of ecologists to implement protists as part of their investigations.Competing Interest StatementThe authors have declared no competing interest.