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metaPR(2) : 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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Autores principales: Vaulot, Daniel, Sim, Clarence Wei Hung, Ong, Denise, Teo, Bryan, Biwer, Charlie, Jamy, Mahwash, Lopes dos Santos, Adriana
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9796713/
https://www.ncbi.nlm.nih.gov/pubmed/35762265
http://dx.doi.org/10.1111/1755-0998.13674
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author Vaulot, Daniel
Sim, Clarence Wei Hung
Ong, Denise
Teo, Bryan
Biwer, Charlie
Jamy, Mahwash
Lopes dos Santos, Adriana
author_facet Vaulot, Daniel
Sim, Clarence Wei Hung
Ong, Denise
Teo, Bryan
Biwer, Charlie
Jamy, Mahwash
Lopes dos Santos, Adriana
author_sort Vaulot, Daniel
collection PubMed
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 PR(2) reference sequence database. This database, called metaPR(2), 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.
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spelling pubmed-97967132023-01-04 metaPR(2) : 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 Mol Ecol Resour RESOURCE ARTICLES 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 PR(2) reference sequence database. This database, called metaPR(2), 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. John Wiley and Sons Inc. 2022-07-13 2022-11 /pmc/articles/PMC9796713/ /pubmed/35762265 http://dx.doi.org/10.1111/1755-0998.13674 Text en © 2022 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd. https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle RESOURCE ARTICLES
Vaulot, Daniel
Sim, Clarence Wei Hung
Ong, Denise
Teo, Bryan
Biwer, Charlie
Jamy, Mahwash
Lopes dos Santos, Adriana
metaPR(2) : A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists
title metaPR(2) : A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists
title_full metaPR(2) : A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists
title_fullStr metaPR(2) : A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists
title_full_unstemmed metaPR(2) : A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists
title_short metaPR(2) : A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists
title_sort metapr(2) : a database of eukaryotic 18s rrna metabarcodes with an emphasis on protists
topic RESOURCE ARTICLES
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9796713/
https://www.ncbi.nlm.nih.gov/pubmed/35762265
http://dx.doi.org/10.1111/1755-0998.13674
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