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pr2-primers: an 18S rRNA primer database for protists

View ORCID ProfileDaniel Vaulot, View ORCID ProfileStefan Geisen, View ORCID ProfileFrédéric Mahé, View ORCID ProfileDavid Bass
doi: https://doi.org/10.1101/2021.01.04.425170
Daniel Vaulot
1UMR 7144, ECOMAP, CNRS, Sorbonne Université, CNRS, Station Biologique de Roscoff, 29680 Roscoff, France
2Asian School of the Environment, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798
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  • For correspondence: vaulot@gmail.com
Stefan Geisen
3Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6700 AB Wageningen, The Netherlands
4Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
5Nanjing Agricultural University, Nanjing, 210095, P.R. China
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Frédéric Mahé
6CIRAD, UMR BGPI, F-34398, Montpellier, France
7BGPI, Univ Montpellier, CIRAD, IRD, Montpellier SupAgro, Montpellier, France
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David Bass
8Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, UK
9Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
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Abstract

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 Statement

The authors have declared no competing interest.

Footnotes

  • https://app.pr2-primers.org

  • https://github.com/pr2database/pr2-primers

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted January 04, 2021.
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pr2-primers: an 18S rRNA primer database for protists
Daniel Vaulot, Stefan Geisen, Frédéric Mahé, David Bass
bioRxiv 2021.01.04.425170; doi: https://doi.org/10.1101/2021.01.04.425170
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pr2-primers: an 18S rRNA primer database for protists
Daniel Vaulot, Stefan Geisen, Frédéric Mahé, David Bass
bioRxiv 2021.01.04.425170; doi: https://doi.org/10.1101/2021.01.04.425170

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