metaPR² : a database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists

• Main Authors: Vaulot, Daniel, Sim, Clarence Wei Hung, Ong, Denise, Teo, Bryan, Biwer, Charlie, Jamy, Mahwash, Lopes Dos Santos, Adriana
• Other Authors: Asian School of the Environment
• Format: Article
• Language: English
• Published: 2022
• Subjects: Engineering::Environmental engineering; Science::Biological sciences; Metabarcodes; Protist
• Online Access: https://hdl.handle.net/10356/163812
• Institution: Nanyang Technological University

In recent years, metabarcoding has become the method of choice for investigating the composition and assembly of microbial eukaryotic communities. The number of environmental data sets published has increased very rapidly. Although unprocessed sequence files are often publicly available, processed data, in particular clustered sequences, are rarely available in a usable format. Clustered sequences are reported as operational taxonomic units (OTUs) with different similarity levels or more recently as amplicon sequence variants (ASVs). This hampers comparative studies between different environments and data sets, for example examining the biogeographical patterns of specific groups/species, as well analysing the genetic microdiversity within these groups. Here, we present a newly-assembled database of processed 18S rRNA metabarcodes that are annotated with the PR2 reference sequence database. This database, called metaPR2 , contains 41 data sets corresponding to more than 4000 samples and 90,000 ASVs. The database, which is accessible through both a web-based interface (https://shiny.metapr2.org) and an R package, should prove very useful to all researchers working on protist diversity in a variety of systems.