Improving eDNA-based protist diversity assessments using networks of amplicon sequence variants.
Journal
Environmental microbiology
ISSN: 1462-2920
Titre abrégé: Environ Microbiol
Pays: England
ID NLM: 100883692
Informations de publication
Date de publication:
11 2019
11 2019
Historique:
received:
04
03
2019
revised:
25
07
2019
accepted:
25
07
2019
pubmed:
31
7
2019
medline:
8
5
2020
entrez:
31
7
2019
Statut:
ppublish
Résumé
Effective and precise grouping of highly similar sequences remains a major bottleneck in the evaluation of high-throughput sequencing datasets. Amplicon sequence variants (ASVs) offer a promising alternative that may supersede the widely used operational taxonomic units (OTUs) in environmental sequencing studies. We compared the performance of a recently developed pipeline based on the algorithm DADA2 for obtaining ASVs against a pipeline based on the algorithm SWARM for obtaining OTUs. Illumina-sequencing of 29 individual ciliate species resulted in up to 11 ASVs per species, while SWARM produced up to 19 OTUs per species. To improve the congruency between species diversity and molecular diversity, we applied sequence similarity networks (SSNs) for second-level sequence grouping into network sequence clusters (NSCs). At 100% sequence similarity in SWARM-SSNs, NSC numbers decreased from 7.9-fold overestimation without abundance filter, to 4.5-fold overestimation when an abundance filter was applied. For the DADA2-SSN approach, NSC numbers decreased from 3.5-fold to 3-fold overestimation. Rand index cluster analyses predicted best binning results between 97% and 94% sequence similarity for both DADA2-SSNs and SWARM-SSNs. Depending on the ecological questions addressed in an environmental sequencing study with protists we recommend ASVs as replacement for OTUs, best in combination with SSNs.
Identifiants
pubmed: 31361938
doi: 10.1111/1462-2920.14764
doi:
Substances chimiques
DNA, Environmental
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
4109-4124Subventions
Organisme : Carl-Zeiss-Stiftung
Pays : International
Organisme : European Science Foundation
ID : 730984
Pays : International
Informations de copyright
© 2019 Society for Applied Microbiology and John Wiley & Sons Ltd.
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