Comparing diversity levels in environmental samples: DNA sequence capture and metabarcoding approaches using 18S and COI genes.
18S and COI amplicons
ASVs
DNA sequence capture
OTUs
dada2
eDNA
eukaryotic diversity
metabarcoding
Journal
Molecular ecology resources
ISSN: 1755-0998
Titre abrégé: Mol Ecol Resour
Pays: England
ID NLM: 101465604
Informations de publication
Date de publication:
Sep 2020
Sep 2020
Historique:
received:
22
11
2019
revised:
20
04
2020
accepted:
15
05
2020
pubmed:
29
5
2020
medline:
7
8
2021
entrez:
29
5
2020
Statut:
ppublish
Résumé
Environmental DNA studies targeting multiple taxa using metabarcoding provide remarkable insights into levels of species diversity in any habitat. The main drawbacks are the presence of primer bias and difficulty in identifying rare species. We tested a DNA sequence-capture method in parallel with the metabarcoding approach to reveal possible advantages of one method over the other. Both approaches were performed using the same eDNA samples and the same 18S and COI regions, followed by high throughput sequencing. Metabarcoded eDNA libraries were PCR amplified with one primer pair from 18S and COI genes. DNA sequence-capture libraries were enriched with 3,639 baits targeting the same gene regions. We tested amplicon sequence variants (ASVs) and operational taxonomic units (OTUs) in silico approaches for both markers and methods, using for this purpose the metabarcoding data set. ASVs methods uncovered more species for the COI gene, whereas the opposite occurred for the 18S gene, suggesting that clustering reads into OTUs could bias diversity richness especially using 18S with relaxed thresholds. Additionally, metabarcoding and DNA sequence-capture recovered 80%-90% of the control sample species. DNA sequence-capture was 8x more expensive, nonetheless it identified 1.5x more species for COI and 13x more genera for 18S than metabarcoding. Both approaches offer reliable results, sharing ca. 40% species and 72% families and retrieve more taxa when nuclear and mitochondrial markers are combined. eDNA metabarcoding is quite well established and low-cost, whereas DNA-sequence capture for biodiversity assessment is still in its infancy, is more time-consuming but provides more taxonomic assignments.
Identifiants
pubmed: 32462738
doi: 10.1111/1755-0998.13201
doi:
Substances chimiques
DNA, Environmental
0
RNA, Ribosomal, 18S
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1333-1345Subventions
Organisme : Research Council of Norway
ID : 243791/E50
Organisme : German Federal Ministry of Education and Research
ID : FKZ01LI1501
Informations de copyright
© 2020 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.
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