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

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 d...

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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
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Online Access:https://hdl.handle.net/10356/163812
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Institution: Nanyang Technological University
Language: English
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spelling sg-ntu-dr.10356-1638122023-02-28T16:40:26Z metaPR² : a database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists Vaulot, Daniel Sim, Clarence Wei Hung Ong, Denise Teo, Bryan Biwer, Charlie Jamy, Mahwash Lopes Dos Santos, Adriana Asian School of the Environment Engineering::Environmental engineering Science::Biological sciences Metabarcodes Protist 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. Ministry of Education (MOE) Published version Daniel Vaulot was partially supported by the ANR Phenomap (ANR-20- CE02-0025). Adriana Lopes dos Santos and Clarence Wei Hung Sim were supported by grants RG26/19 and RG91/21 from the Singapore Ministry of Education, Academic Research Fund Tier 1. The work of Mahwash Jamy and Charlie Biwer was supported by a grant from Science for Life Laboratory available to F. Burki. 2022-12-19T02:45:27Z 2022-12-19T02:45:27Z 2022 Journal Article Vaulot, D., Sim, C. W. H., Ong, D., Teo, B., Biwer, C., Jamy, M. & Lopes Dos Santos, A. (2022). metaPR² : a database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists. Molecular Ecology Resources, 22(8), 3188-3201. https://dx.doi.org/10.1111/1755-0998.13674 1755-098X https://hdl.handle.net/10356/163812 10.1111/1755-0998.13674 35762265 2-s2.0-85133959275 8 22 3188 3201 en RG26/19 RG91/21 Molecular Ecology Resources © 2022 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited application/pdf
institution Nanyang Technological University
building NTU Library
continent Asia
country Singapore
Singapore
content_provider NTU Library
collection DR-NTU
language English
topic Engineering::Environmental engineering
Science::Biological sciences
Metabarcodes
Protist
spellingShingle Engineering::Environmental engineering
Science::Biological sciences
Metabarcodes
Protist
Vaulot, Daniel
Sim, Clarence Wei Hung
Ong, Denise
Teo, Bryan
Biwer, Charlie
Jamy, Mahwash
Lopes Dos Santos, Adriana
metaPR² : a database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists
description 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.
author2 Asian School of the Environment
author_facet Asian School of the Environment
Vaulot, Daniel
Sim, Clarence Wei Hung
Ong, Denise
Teo, Bryan
Biwer, Charlie
Jamy, Mahwash
Lopes Dos Santos, Adriana
format Article
author Vaulot, Daniel
Sim, Clarence Wei Hung
Ong, Denise
Teo, Bryan
Biwer, Charlie
Jamy, Mahwash
Lopes Dos Santos, Adriana
author_sort Vaulot, Daniel
title metaPR² : a database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists
title_short metaPR² : a database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists
title_full metaPR² : a database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists
title_fullStr metaPR² : a database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists
title_full_unstemmed metaPR² : a database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists
title_sort metapr² : a database of eukaryotic 18s rrna metabarcodes with an emphasis on protists
publishDate 2022
url https://hdl.handle.net/10356/163812
_version_ 1759854565493047296