pr2-Wormifier: A Bioinformatics Pipeline to Create Custom Reference Databases for Improved Metabarcoding of Marine...

Area of Science:

• Marine biology
• Bioinformatics
• Genomics

Background:

• Metabarcoding of environmental DNA (eDNA) and sedimentary ancient DNA (sedaDNA) is crucial for marine community assessment.
• Existing reference databases for 18S rRNA gene metabarcoding, especially for protists, lack comprehensiveness and taxonomic resolution.
• This limits the accuracy of biodiversity monitoring and paleoenvironmental reconstructions.

Purpose of the Study:

• To introduce pr2-wormifier, a bioinformatics pipeline for generating customized and improved 18S rRNA-based reference databases.
• To enhance taxonomic assignments for marine protists, including ciliates and dinoflagellates, at genus and species levels.
• To address limitations of current databases, such as low resolution and missing taxa.

Main Methods:

• The pr2-wormifier pipeline integrates sequences from PR2 and NCBI databases.
• It incorporates taxonomic information from the World Register of Marine Species (WoRMS) and AlgaeBase.
• The pipeline was benchmarked using a Baltic Sea sedimentary ancient DNA dataset.

Main Results:

• pr2-wormifier successfully generated customized reference databases for marine protists.
• The customized database improved taxonomic assignments at genus and species levels compared to using PR2 alone.
• The pipeline maintained taxonomic consistency and quality in sequence identification.

Conclusions:

• pr2-wormifier provides a flexible and scalable solution for creating tailored reference databases.
• It enhances the accuracy and resolution of protist identification in metabarcoding studies.
• This tool facilitates more reliable biodiversity assessments in marine and paleoenvironmental research.