Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Predator-driven microbial feedback loops promote plant health.

Nature communications·2026
Same author

Siderophore-producing Bacillus and free-living nematodes are associated with soil suppressiveness to banana root-knot nematodes.

Nature communications·2026
Same author

Protist size-dependent shifts of bacterial communities can reduce litter decomposition.

ISME communications·2026
Same author

A novel taxonomic database for eukaryotic mitochondrial cytochrome oxidase subunit I gene (eKOI), with a focus on protists diversity.

Database : the journal of biological databases and curation·2025
Same author

Secondary Decomposers Meet Their Predators: Decomposition Stage and Substrate Quality Jointly Structure Microbial Brown Food Webs During Fungal Necromass Decay.

Molecular ecology·2025
Same author

Biodiversity in mountain soils above the treeline.

Biological reviews of the Cambridge Philosophical Society·2025

Related Experiment Video

Updated: Oct 29, 2025

Assessment of DNA Contamination in RNA Samples Based on Ribosomal DNA
13:16

Assessment of DNA Contamination in RNA Samples Based on Ribosomal DNA

Published on: January 22, 2018

21.8K

pr2-primers: An 18S rRNA primer database for protists.

Daniel Vaulot1,2, Stefan Geisen3,4,5, Frédéric Mahé6,7

  • 1UMR 7144, ECOMAP, Station Biologique de Roscoff, CNRS, Sorbonne Université, Roscoff, France.

Molecular Ecology Resources
|July 12, 2021
PubMed
Summary

Choosing the right primers for microbial eukaryote (protist) 18S rRNA gene metabarcoding is crucial. A new database and web app help researchers select optimal primer pairs for diverse protist communities.

Keywords:
18S rRNAPCRRdatabasemetabrcodingprimersprotistsshiny

More Related Videos

mRNA Interactome Capture from Plant Protoplasts
12:29

mRNA Interactome Capture from Plant Protoplasts

Published on: July 28, 2017

9.3K
Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization
12:37

Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization

Published on: April 14, 2016

39.3K

Related Experiment Videos

Last Updated: Oct 29, 2025

Assessment of DNA Contamination in RNA Samples Based on Ribosomal DNA
13:16

Assessment of DNA Contamination in RNA Samples Based on Ribosomal DNA

Published on: January 22, 2018

21.8K
mRNA Interactome Capture from Plant Protoplasts
12:29

mRNA Interactome Capture from Plant Protoplasts

Published on: July 28, 2017

9.3K
Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization
12:37

Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization

Published on: April 14, 2016

39.3K

Area of Science:

  • Microbiology
  • Eukaryotic Genomics
  • Bioinformatics

Background:

  • 18S rRNA gene metabarcoding is a primary method for studying microbial eukaryotes (protists).
  • High protist diversity necessitates careful primer selection for accurate community profiling.
  • Existing resources for selecting 18S rRNA gene primers are limited, posing challenges for researchers.

Purpose of the Study:

  • To develop a comprehensive database of primers and primer pairs for eukaryotic 18S rRNA gene metabarcoding.
  • To create an interactive web application for evaluating primer performance and guiding primer selection.
  • To identify broadly applicable primer sets for diverse protist communities.

Main Methods:

  • Compiled a database of 285 primers and 83 primer pairs used in eukaryotic 18S rRNA gene metabarcoding.
  • Performed in silico performance testing of primer pairs against eukaryotic (PR2) and prokaryotic (SILVA) databases.
  • Developed an R-based web application for database browsing, primer performance visualization, and custom primer testing.

Main Results:

  • The database includes 285 primers and 83 primer pairs for 18S rRNA gene metabarcoding.
  • In silico analysis evaluated primer pair performance against eukaryotic and prokaryotic reference databases.
  • The web application allows users to visualize taxonomic distribution, mismatches, amplicon size, and primer specificity.

Conclusions:

  • A novel database and web application facilitate informed primer selection for microbial eukaryote metabarcoding.
  • The tool aids researchers in identifying universal and group-specific primer sets.
  • This resource aims to improve the accuracy and comprehensiveness of protist community studies.