One‐locus‐several‐primers: A strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies
In diet metabarcoding analyses, insufficient taxonomic coverage of PCR primer sets generates false negatives that may dramatically distort biodiversity estimates. In this paper, we investigated the taxonomic coverage and complementarity of three cytochrome c oxidase subunit I gene (COI) primer sets...
Main Authors: | , , , , , , , , , , , |
---|---|
Format: | Dataset |
Language: | unknown |
Published: |
2022
|
Subjects: | |
Online Access: | https://zenodo.org/record/5034805 https://doi.org/10.5061/dryad.2ck7120 |
id |
ftzenodo:oai:zenodo.org:5034805 |
---|---|
record_format |
openpolar |
spelling |
ftzenodo:oai:zenodo.org:5034805 2023-06-06T11:52:16+02:00 One‐locus‐several‐primers: A strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies Corse, Emmanuel Tougard, Christelle Archambaud-Suard, Gaït Agnèse, Jean-François Messu Mandeng, Françoise D. Bilong Bilong, Charles F. Duneau, David Zinger, Lucie Chappaz, Rémi Xu, Charles C. Y. Meglécz, Emese Dubut, Vincent 2022-08-24 https://zenodo.org/record/5034805 https://doi.org/10.5061/dryad.2ck7120 unknown doi:10.1002/ece3.5063 https://zenodo.org/communities/dryad https://zenodo.org/record/5034805 https://doi.org/10.5061/dryad.2ck7120 oai:zenodo.org:5034805 info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/legalcode Araneomorphae PCR primers Zingel asper Diet Analysis Myotis emarginatus Micrathena schreibersi Pomatoschistus microps Rhinolophus ferrumequinum Epiplatys infrafasciatus False negatives Pholcidae Barbastella barbastellus Miniopterus schreibersii Rhinolophus euryale Pipistrellus pipistrellus Eptesicus serotinus Chiroptera Myotis nattereri info:eu-repo/semantics/other dataset 2022 ftzenodo https://doi.org/10.5061/dryad.2ck712010.1002/ece3.5063 2023-04-13T20:45:20Z In diet metabarcoding analyses, insufficient taxonomic coverage of PCR primer sets generates false negatives that may dramatically distort biodiversity estimates. In this paper, we investigated the taxonomic coverage and complementarity of three cytochrome c oxidase subunit I gene (COI) primer sets based on in silico analyses and we conducted an in vivo evaluation using fecal and spider web samples from different invertivores, environments, and geographic locations. Our results underline the lack of predictability of both the coverage and complementarity of individual primer sets: (a) sharp discrepancies exist observed between in silico and in vivo analyses (to the detriment of in silico analyses); (b) both coverage and complementarity depend greatly on the predator and on the taxonomic level at which preys are considered; (c) primer sets' complementarity is the greatest at fine taxonomic levels (molecular operational taxonomic units [MOTUs] and variants). We then formalized the "one‐locus‐several‐primer‐sets" (OLSP) strategy, that is, the use of several primer sets that target the same locus (here the first part of the COI gene) and the same group of taxa (here invertebrates). The proximal aim of the OLSP strategy is to minimize false negatives by increasing total coverage through multiple primer sets. We illustrate that the OLSP strategy is especially relevant from this perspective since distinct variants within the same MOTUs were not equally detected across all primer sets. Furthermore, the OLSP strategy produces largely overlapping and comparable sequences, which cannot be achieved when targeting different loci. This facilitates the use of haplotypic diversity information contained within metabarcoding datasets, for example, for phylogeography and finer analyses of prey–predator interactions. Villsen2022_sample_fastq_correspondence.csv CSV file with tag combinations to identify the samples and technical replicates from each fastq file Villsen2022_Metabarcoding_Filtered_Data_040822.xlsx CSV file reporting ... Dataset Barbastella barbastellus Myotis nattereri Pipistrellus pipistrellus Zenodo |
institution |
Open Polar |
collection |
Zenodo |
op_collection_id |
ftzenodo |
language |
unknown |
topic |
Araneomorphae PCR primers Zingel asper Diet Analysis Myotis emarginatus Micrathena schreibersi Pomatoschistus microps Rhinolophus ferrumequinum Epiplatys infrafasciatus False negatives Pholcidae Barbastella barbastellus Miniopterus schreibersii Rhinolophus euryale Pipistrellus pipistrellus Eptesicus serotinus Chiroptera Myotis nattereri |
spellingShingle |
Araneomorphae PCR primers Zingel asper Diet Analysis Myotis emarginatus Micrathena schreibersi Pomatoschistus microps Rhinolophus ferrumequinum Epiplatys infrafasciatus False negatives Pholcidae Barbastella barbastellus Miniopterus schreibersii Rhinolophus euryale Pipistrellus pipistrellus Eptesicus serotinus Chiroptera Myotis nattereri Corse, Emmanuel Tougard, Christelle Archambaud-Suard, Gaït Agnèse, Jean-François Messu Mandeng, Françoise D. Bilong Bilong, Charles F. Duneau, David Zinger, Lucie Chappaz, Rémi Xu, Charles C. Y. Meglécz, Emese Dubut, Vincent One‐locus‐several‐primers: A strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies |
topic_facet |
Araneomorphae PCR primers Zingel asper Diet Analysis Myotis emarginatus Micrathena schreibersi Pomatoschistus microps Rhinolophus ferrumequinum Epiplatys infrafasciatus False negatives Pholcidae Barbastella barbastellus Miniopterus schreibersii Rhinolophus euryale Pipistrellus pipistrellus Eptesicus serotinus Chiroptera Myotis nattereri |
description |
In diet metabarcoding analyses, insufficient taxonomic coverage of PCR primer sets generates false negatives that may dramatically distort biodiversity estimates. In this paper, we investigated the taxonomic coverage and complementarity of three cytochrome c oxidase subunit I gene (COI) primer sets based on in silico analyses and we conducted an in vivo evaluation using fecal and spider web samples from different invertivores, environments, and geographic locations. Our results underline the lack of predictability of both the coverage and complementarity of individual primer sets: (a) sharp discrepancies exist observed between in silico and in vivo analyses (to the detriment of in silico analyses); (b) both coverage and complementarity depend greatly on the predator and on the taxonomic level at which preys are considered; (c) primer sets' complementarity is the greatest at fine taxonomic levels (molecular operational taxonomic units [MOTUs] and variants). We then formalized the "one‐locus‐several‐primer‐sets" (OLSP) strategy, that is, the use of several primer sets that target the same locus (here the first part of the COI gene) and the same group of taxa (here invertebrates). The proximal aim of the OLSP strategy is to minimize false negatives by increasing total coverage through multiple primer sets. We illustrate that the OLSP strategy is especially relevant from this perspective since distinct variants within the same MOTUs were not equally detected across all primer sets. Furthermore, the OLSP strategy produces largely overlapping and comparable sequences, which cannot be achieved when targeting different loci. This facilitates the use of haplotypic diversity information contained within metabarcoding datasets, for example, for phylogeography and finer analyses of prey–predator interactions. Villsen2022_sample_fastq_correspondence.csv CSV file with tag combinations to identify the samples and technical replicates from each fastq file Villsen2022_Metabarcoding_Filtered_Data_040822.xlsx CSV file reporting ... |
format |
Dataset |
author |
Corse, Emmanuel Tougard, Christelle Archambaud-Suard, Gaït Agnèse, Jean-François Messu Mandeng, Françoise D. Bilong Bilong, Charles F. Duneau, David Zinger, Lucie Chappaz, Rémi Xu, Charles C. Y. Meglécz, Emese Dubut, Vincent |
author_facet |
Corse, Emmanuel Tougard, Christelle Archambaud-Suard, Gaït Agnèse, Jean-François Messu Mandeng, Françoise D. Bilong Bilong, Charles F. Duneau, David Zinger, Lucie Chappaz, Rémi Xu, Charles C. Y. Meglécz, Emese Dubut, Vincent |
author_sort |
Corse, Emmanuel |
title |
One‐locus‐several‐primers: A strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies |
title_short |
One‐locus‐several‐primers: A strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies |
title_full |
One‐locus‐several‐primers: A strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies |
title_fullStr |
One‐locus‐several‐primers: A strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies |
title_full_unstemmed |
One‐locus‐several‐primers: A strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies |
title_sort |
one‐locus‐several‐primers: a strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies |
publishDate |
2022 |
url |
https://zenodo.org/record/5034805 https://doi.org/10.5061/dryad.2ck7120 |
genre |
Barbastella barbastellus Myotis nattereri Pipistrellus pipistrellus |
genre_facet |
Barbastella barbastellus Myotis nattereri Pipistrellus pipistrellus |
op_relation |
doi:10.1002/ece3.5063 https://zenodo.org/communities/dryad https://zenodo.org/record/5034805 https://doi.org/10.5061/dryad.2ck7120 oai:zenodo.org:5034805 |
op_rights |
info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/legalcode |
op_doi |
https://doi.org/10.5061/dryad.2ck712010.1002/ece3.5063 |
_version_ |
1767958117115494400 |